Merge pull request #2214 from gitbucket/gitbucket-4.30.0-release

Updates for GitBucket 4.30.0 release

.travis.yml

@@ -2,6 +2,9 @@ language: scala
 sudo: true
 jdk: 
   - oraclejdk8
+  - oraclejdk11
+  - openjdk8
+  - openjdk11
 script:
   - sbt scalafmtSbtCheck scalafmtCheck test:scalafmtCheck test
 before_script:

CHANGELOG.md

@@ -1,12 +1,64 @@
 # Changelog
 All changes to the project will be documented in this file.
 
-### 4.23.1 - 10 Apr 2018
+## 4.30.0 - xx Dec 2018
+- Automatic ChangeLog Summary generation for new Releases
+- A lot of GitBucket Web API updates to increase compatibility with the GitHub API.
+- Display of checkboxes in Markdown files in Git repositories
+- A new extension point for plugins: anonymousAccessiblePaths
+- Group support in the Gist Plugin
+- Allow redirection to the Release Page from the Activity Timeline Page
+
+## 4.29.0 - 29 Sep 2018
+- Official Docker image has been available
+- Enhance file edit and delete buttons of the repository viewer
+- Fix Patch button to generate patches for all files in the commit
+- Display confirmation dialog for Transfer Ownership and Garbage collection
+- Fix wrong url encoding in "Compare & pull request"
+
+## 4.28.0 - 1 Sep 2018
+- Proxy support for plugin installation
+- Fix some bugs around pull requests
+
+## 4.27.0 - 29 Jul 2018
+- Create new tag on the browser
+- EditorConfig support
+- Improve issues / pull requests search
+- Some improvements and bug fixes for plugin installation via internet and pull request commenting
+
+## 4.26.0 - 30 Jun 2018
+- Installing plugins from the central registry
+- Repositories tab in the dashboard
+- Fork dialog enhancement
+- Adjust pull request creation suggestor
+- Keep showing incompleted task list
+- New notification hooks
+
+## 4.25.0 - 29 May 2018
+- Security improvements
+- Show mail address at the profile page
+- Task list on commit comments
+- More detailed editing history of issues and pull requests
+- Expose user public keys
+- Download repository improvements
+
+## 4.24.1 - 1 May 2018
+- Fix bug in Web API authentication
+
+## 4.24.0 - 30 Apr 2018
+- Diff for each review comment on pull requests
+- Extra mail addresses support
+- Show tags at the commit list
+- Keep wrap mode of the online editor
+- Renew layout of gitbucket-gist-plugin
+- Web API of gitbucket-ci-plugin
+
+## 4.23.1 - 10 Apr 2018
 - Fix bug that the contents API doesn't work for the repository root
 - Fix shutdown problem in Tomcat deployment
 - Render by plugins at the blob view even if it's a binary file
 
-### 4.23.0 - 31 Mar 2018
+## 4.23.0 - 31 Mar 2018
 - Allow tail slash in URL
 - Display commit message of tags at the releases page
 - Add labels property to issues and pull requests API response
@@ -14,26 +66,26 @@ All changes to the project will be documented in this file.
 - Git authentication with personal access token
 - Max parallel builds and max stored history in CI plugin became configurable
 
-### 4.22.0 - 3 Mar 2018
+## 4.22.0 - 3 Mar 2018
 - Pull request merge strategy settings
 - Create repository with an empty commit
 - Improve database viewer
 - Update maven-repository-plugin
 
-### 4.21.2 - 27 Jan 2018
+## 4.21.2 - 27 Jan 2018
 - Bugfix
 
-### 4.21.1 - 27 Jan 2018
+## 4.21.1 - 27 Jan 2018
 - Bugfix
 
-### 4.21.0 - 27 Jan 2018
+## 4.21.0 - 27 Jan 2018
 - Release page
 - OpenID Connect support
 - New database viewer
 - Submodule links to web page
 - Clarify close/reopen button
 
-## 4.20.0 - 23 Dec 2017
+# 4.20.0 - 23 Dec 2017
 - Squash and rebase merge strategy for pull requests
 - Quick pull request creation
 - Download patch from the diff view

README.md

@@ -1,4 +1,4 @@
-GitBucket [![Gitter chat](https://badges.gitter.im/gitbucket/gitbucket.svg)](https://gitter.im/gitbucket/gitbucket) [![Build Status](https://travis-ci.org/gitbucket/gitbucket.svg?branch=master)](https://travis-ci.org/gitbucket/gitbucket)
+GitBucket [![Gitter chat](https://badges.gitter.im/gitbucket/gitbucket.svg)](https://gitter.im/gitbucket/gitbucket) [![Build Status](https://travis-ci.org/gitbucket/gitbucket.svg?branch=master)](https://travis-ci.org/gitbucket/gitbucket) [![Maven Central](https://maven-badges.herokuapp.com/maven-central/io.github.gitbucket/gitbucket_2.12/badge.svg)](https://maven-badges.herokuapp.com/maven-central/io.github.gitbucket/gitbucket_2.12) [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/gitbucket/gitbucket/blob/master/LICENSE)
 =========
 
 GitBucket is a Git web platform powered by Scala offering:
@@ -68,19 +68,14 @@ Support
 - If you can't find same question and report, send it to [gitter room](https://gitter.im/gitbucket/gitbucket) before raising an issue.
 - The highest priority of GitBucket is the ease of installation and API compatibility with GitHub, so your feature request might be rejected if they go against those principles.
 
-What's New in 4.23.x
+What's New in 4.30.x
 -------------
-### 4.23.1 - 10 Apr 2018
-- Fix bug that the contents API doesn't work for the repository root
-- Fix shutdown problem in Tomcat deployment
-- Render by plugins at the blob view even if it's a binary file
-
-### 4.23.0 - 31 Mar 2018
-- Allow tail slash in URL
-- Display commit message of tags at the releases page
-- Add labels property to issues and pull requests API response
-- Plugins list API
-- Git authentication with personal access token
-- Max parallel builds and max stored history in CI plugin became configurable
+### 4.30.0 - xx Dec 2018
+- Automatic ChangeLog Summary generation for new Releases
+- A lot of GitBucket Web API updates to increase compatibility with the GitHub API.
+- Display of checkboxes in Markdown files in Git repositories
+- A new extension point for plugins: anonymousAccessiblePaths
+- Group support in the Gist Plugin
+- Allow redirection to the Release Page from the Activity Timeline Page
 
 See the [change log](CHANGELOG.md) for all of the updates.

build.sbt

@@ -3,12 +3,13 @@ import com.typesafe.sbt.pgp.PgpKeys._
 
 val Organization = "io.github.gitbucket"
 val Name = "gitbucket"
-val GitBucketVersion = "4.23.1"
-val ScalatraVersion = "2.6.1"
-val JettyVersion = "9.4.7.v20170914"
+val GitBucketVersion = "4.30.0"
+val ScalatraVersion = "2.6.3"
+val JettyVersion = "9.4.14.v20181114"
+val JgitVersion = "5.1.3.201810200350-r"
 
 lazy val root = (project in file("."))
-  .enablePlugins(SbtTwirl, ScalatraPlugin, JRebelPlugin)
+  .enablePlugins(SbtTwirl, ScalatraPlugin)
   .settings(
     )
 
@@ -16,7 +17,7 @@ sourcesInBase := false
 organization := Organization
 name := Name
 version := GitBucketVersion
-scalaVersion := "2.12.5"
+scalaVersion := "2.12.8"
 
 scalafmtOnCompile := true
 
@@ -30,45 +31,46 @@ resolvers ++= Seq(
 )
 
 libraryDependencies ++= Seq(
-  "org.eclipse.jgit"                % "org.eclipse.jgit.http.server" % "4.11.0.201803080745-r",
-  "org.eclipse.jgit"                % "org.eclipse.jgit.archive"     % "4.11.0.201803080745-r",
+  "org.eclipse.jgit"                % "org.eclipse.jgit.http.server" % JgitVersion,
+  "org.eclipse.jgit"                % "org.eclipse.jgit.archive"     % JgitVersion,
   "org.scalatra"                    %% "scalatra"                    % ScalatraVersion,
   "org.scalatra"                    %% "scalatra-json"               % ScalatraVersion,
   "org.scalatra"                    %% "scalatra-forms"              % ScalatraVersion,
-  "org.json4s"                      %% "json4s-jackson"              % "3.5.3",
+  "org.json4s"                      %% "json4s-jackson"              % "3.6.2",
   "commons-io"                      % "commons-io"                   % "2.6",
-  "io.github.gitbucket"             % "solidbase"                    % "1.0.2",
+  "io.github.gitbucket"             % "solidbase"                    % "1.0.3",
   "io.github.gitbucket"             % "markedj"                      % "1.0.15",
-  "org.apache.commons"              % "commons-compress"             % "1.15",
+  "org.apache.commons"              % "commons-compress"             % "1.18",
   "org.apache.commons"              % "commons-email"                % "1.5",
-  "org.apache.httpcomponents"       % "httpclient"                   % "4.5.4",
-  "org.apache.sshd"                 % "apache-sshd"                  % "1.6.0" exclude ("org.slf4j", "slf4j-jdk14"),
-  "org.apache.tika"                 % "tika-core"                    % "1.17",
-  "com.github.takezoe"              %% "blocking-slick-32"           % "0.0.10",
+  "org.apache.httpcomponents"       % "httpclient"                   % "4.5.6",
+  "org.apache.sshd"                 % "apache-sshd"                  % "2.1.0" exclude ("org.slf4j", "slf4j-jdk14") exclude ("org.apache.sshd", "sshd-mina") exclude ("org.apache.sshd", "sshd-netty"),
+  "org.apache.tika"                 % "tika-core"                    % "1.19.1",
+  "com.github.takezoe"              %% "blocking-slick-32"           % "0.0.11",
   "com.novell.ldap"                 % "jldap"                        % "2009-10-07",
-  "com.h2database"                  % "h2"                           % "1.4.196",
-  "org.mariadb.jdbc"                % "mariadb-java-client"          % "2.2.3",
-  "org.postgresql"                  % "postgresql"                   % "42.1.4",
+  "com.h2database"                  % "h2"                           % "1.4.197",
+  "org.mariadb.jdbc"                % "mariadb-java-client"          % "2.3.0",
+  "org.postgresql"                  % "postgresql"                   % "42.2.5",
   "ch.qos.logback"                  % "logback-classic"              % "1.2.3",
-  "com.zaxxer"                      % "HikariCP"                     % "2.7.4",
-  "com.typesafe"                    % "config"                       % "1.3.2",
-  "com.typesafe.akka"               %% "akka-actor"                  % "2.5.8",
+  "com.zaxxer"                      % "HikariCP"                     % "3.2.0",
+  "com.typesafe"                    % "config"                       % "1.3.3",
+  "com.typesafe.akka"               %% "akka-actor"                  % "2.5.18",
   "fr.brouillard.oss.security.xhub" % "xhub4j-core"                  % "1.0.0",
   "com.github.bkromhout"            % "java-diff-utils"              % "2.1.1",
-  "org.cache2k"                     % "cache2k-all"                  % "1.0.1.Final",
-  "com.enragedginger"               %% "akka-quartz-scheduler"       % "1.6.1-akka-2.5.x" exclude ("c3p0", "c3p0"),
+  "org.cache2k"                     % "cache2k-all"                  % "1.2.0.Final",
+  "com.enragedginger"               %% "akka-quartz-scheduler"       % "1.7.0-akka-2.5.x" exclude ("c3p0", "c3p0") exclude ("com.zaxxer", "HikariCP-java6"),
   "net.coobird"                     % "thumbnailator"                % "0.4.8",
   "com.github.zafarkhaja"           % "java-semver"                  % "0.9.0",
-  "com.nimbusds"                    % "oauth2-oidc-sdk"              % "5.45",
+  "com.nimbusds"                    % "oauth2-oidc-sdk"              % "5.64.4",
   "org.eclipse.jetty"               % "jetty-webapp"                 % JettyVersion % "provided",
   "javax.servlet"                   % "javax.servlet-api"            % "3.1.0" % "provided",
   "junit"                           % "junit"                        % "4.12" % "test",
   "org.scalatra"                    %% "scalatra-scalatest"          % ScalatraVersion % "test",
-  "org.mockito"                     % "mockito-core"                 % "2.13.0" % "test",
-  "com.wix"                         % "wix-embedded-mysql"           % "3.0.0" % "test",
-  "ru.yandex.qatools.embed"         % "postgresql-embedded"          % "2.6" % "test",
-  "net.i2p.crypto"                  % "eddsa"                        % "0.2.0",
-  "is.tagomor.woothee"              % "woothee-java"                 % "1.7.0"
+  "org.mockito"                     % "mockito-core"                 % "2.23.4" % "test",
+  "com.wix"                         % "wix-embedded-mysql"           % "4.2.0" % "test",
+  "ru.yandex.qatools.embed"         % "postgresql-embedded"          % "2.10" % "test",
+  "net.i2p.crypto"                  % "eddsa"                        % "0.3.0",
+  "is.tagomor.woothee"              % "woothee-java"                 % "1.8.0",
+  "org.ec4j.core"                   % "ec4j-core"                    % "0.0.3"
 )
 
 // Compiler settings
@@ -96,21 +98,6 @@ assemblyMergeStrategy in assembly := {
   case x => MergeStrategy.first
 }
 
-// JRebel
-//Seq(jrebelSettings: _*)
-
-//jrebel.webLinks += (target in webappPrepare).value
-//jrebel.enabled := System.getenv().get("JREBEL") != null
-javaOptions in Jetty ++= Option(System.getenv().get("JREBEL")).toSeq.flatMap { path =>
-  if (path.endsWith(".jar")) {
-    // Legacy JRebel agent
-    Seq("-noverify", "-XX:+UseConcMarkSweepGC", "-XX:+CMSClassUnloadingEnabled", s"-javaagent:${path}")
-  } else {
-    // New JRebel agent
-    Seq(s"-agentpath:${path}")
-  }
-}
-
 // Exclude a war file from published artifacts
 signedArtifacts := {
   signedArtifacts.value.filterNot {
@@ -170,12 +157,17 @@ executableKey := {
   // include plugins
   val pluginsDir = temp / "WEB-INF" / "classes" / "plugins"
   IO createDirectory (pluginsDir)
-  IO copyFile (Keys.baseDirectory.value / "plugins.json", pluginsDir / "plugins.json")
 
-  val json = IO read (Keys.baseDirectory.value / "plugins.json")
-  PluginsJson.getUrls(json).foreach { url =>
-    log info s"Download: ${url}"
-    IO transfer (new java.net.URL(url).openStream, pluginsDir / url.substring(url.lastIndexOf("/") + 1))
+  val plugins = IO readLines (Keys.baseDirectory.value / "src" / "main" / "resources" / "bundle-plugins.txt")
+  plugins.foreach { plugin =>
+    plugin.trim.split(":") match {
+      case Array(pluginId, pluginVersion) =>
+        val url = "https://plugins.gitbucket-community.org/releases/" +
+          s"gitbucket-${pluginId}-plugin/gitbucket-${pluginId}-plugin-gitbucket_${version.value}-${pluginVersion}.jar"
+        log info s"Download: ${url}"
+        IO transfer (new java.net.URL(url).openStream, pluginsDir / url.substring(url.lastIndexOf("/") + 1))
+      case _ => ()
+    }
   }
 
   // zip it up

doc/comment_action.md

@@ -6,22 +6,26 @@ The details are saved at `ISSUE_COMMENT` table.
 To determine if it was any operation, you see the `ACTION` column.
 And in the case of some actions, `CONTENT` column value contains additional information.
 
-|ACTION          |CONTENT               |
-|----------------|----------------------|
-|comment         |comment               |
-|close_comment   |comment               |
-|reopen_comment  |comment               |
-|close           |"Close"               |
-|reopen          |"Reopen"              |
-|commit          |comment commitId      |
-|merge           |comment               |
-|delete_branch   |branchName            |
-|refer           |issueId:title         |
-|add_label       |labelName             |
-|delete_label    |labelName             |
-|change_priority |oldPriority:priority  |
-|change_milestone|oldMilestone:milestone|
-|assign          |oldAssigned:assigned  |
+|ACTION          |CONTENT                   |
+|----------------|--------------------------|
+|comment         |comment                   |
+|close_comment   |comment                   |
+|reopen_comment  |comment                   |
+|close           |"Close"                   |
+|reopen          |"Reopen"                  |
+|commit          |comment commitId          |
+|merge           |comment                   |
+|delete_branch   |branchName                |
+|refer           |issueId:title             |
+|add_label       |labelName                 |
+|delete_label    |labelName                 |
+|change_priority |oldPriority:priority      |
+|change_milestone|oldMilestone:milestone    |
+|assign          |oldAssigned:assigned      |
+|change_title    |oldTitle(CRLF)title \[1\] |
+
+\[1\]: (CRLF) is "\r\n"
+
 
 ### comment
 
@@ -79,3 +83,7 @@ This value is saved when users have changed the milestone.
 ### assign
 
 This value is saved when users have assign issue/PR to user or remove the assign.
+
+### change_title
+
+This value is saved when users have changed the title.

doc/jrebel.md

@@ -1,119 +0,0 @@
-JRebel integration (optional)
-=============================
-
-[JRebel](https://zeroturnaround.com/software/jrebel/) is a JVM plugin that makes developing web apps much faster.
-JRebel is generally able to eliminate the need for the slow "app restart" per modification of codes. Alsp it's only used during development, and doesn't change your deployed app in any way.
-
-JRebel is not open source, but we can use it free for non-commercial use.
-
-----
-
-## 1. Get a JRebel license
-
-Sign up for a [myJRebel](https://my.jrebel.com/register). You will need to create an account.
-
-## 2. Download JRebel
-
-Download the most recent ["nosetup" JRebel zip](https://zeroturnaround.com/software/jrebel/download/prev-releases/).
-Next, unzip the downloaded file.
-
-## 3. Activate
-
-Follow `readme.txt` in the extracted directory to activate your downloaded JRebel.
-
-You don't need to integrate with your IDE, since we're using sbt to do the servlet deployment.
-
-## 4. Tell jvm where JRebel is
-
-Fortunately, the gitbucket project is already set up to use JRebel.
-You only need to tell jvm where to find the jrebel jar.
-
-To do so, edit your shell resource file (usually `~/.bash_profile` on Mac, and `~/.bashrc` on Linux) and set the environment variable `JREBEL`.
-For example, if you unzipped your JRebel download in your home directory, you would use:
-
-```bash
-export JREBEL=~/jrebel/legacy/jrebel.jar      # legacy agent
-export JREBEL=~/jrebel/lib/libjrebel64.dylib  # new agent
-```
-
-You can choose the legacy JRebel agent or the new one.
-See [the document](https://zeroturnaround.com/software/jrebel/jrebel7-agent-upgrade-cli/) for details.
-
-Now reload your shell:
-
-```
-$ source ~/.bash_profile # on Mac
-$ source ~/.bashrc       # on Linux
-```
-
-## 5. See it in action!
-
-Now you're ready to use JRebel with the gitbucket.
-When you run sbt as normal, you will see a long message from JRebel, indicating it has loaded.
-Here's an abbreviated version of what you will see:
-
-```
-$ ./sbt
-[info] Loading project definition from /git/gitbucket/project
-[info] Set current project to gitbucket (in build file:/git/gitbucket/)
->
-```
-
-You will start the servlet container slightly differently now that you're using sbt.
-
-```
-> jetty:quickstart
-:
-2017-09-21 15:46:35 JRebel:
-2017-09-21 15:46:35 JRebel:  #############################################################
-2017-09-21 15:46:35 JRebel:
-2017-09-21 15:46:35 JRebel:  Legacy Agent 7.0.15 (201709080836)
-2017-09-21 15:46:35 JRebel:  (c) Copyright ZeroTurnaround AS, Estonia, Tartu.
-2017-09-21 15:46:35 JRebel:
-2017-09-21 15:46:35 JRebel:  Over the last 2 days JRebel prevented
-2017-09-21 15:46:35 JRebel:  at least 8 redeploys/restarts saving you about 0.3 hours.
-2017-09-21 15:46:35 JRebel:
-2017-09-21 15:46:35 JRebel:  Licensed to Naoki Takezoe (using myJRebel).
-2017-09-21 15:46:35 JRebel:
-2017-09-21 15:46:35 JRebel:
-2017-09-21 15:46:35 JRebel:  #############################################################
-2017-09-21 15:46:35 JRebel:
-:
-
-> ~compile
-[success] Total time: 2 s, completed 2017/09/21 15:50:06
-1. Waiting for source changes... (press enter to interrupt)
-```
-
-Finally, change your code.
-For example, you can change the title on `src/main/twirl/gitbucket/core/main.scala.html` like this:
-
-```html
-:
-  <a href="@context.path/" class="logo">
-    <img src="@helpers.assets("/common/images/gitbucket.svg")" style="width: 24px; height: 24px; display: inline;"/>
-    GitBucket
-    change code !!!!!!!!!!!!!!!!
-    <span class="header-version">@gitbucket.core.GitBucketCoreModule.getVersions.last.getVersion</span>
-  </a>
-:
-```
-
-If JRebel is doing is correctly installed you will see a notice for you:
-
-```
-1. Waiting for source changes... (press enter to interrupt)
-[info] Compiling 1 Scala source to /Users/naoki.takezoe/gitbucket/target/scala-2.12/classes...
-[success] Total time: 1 s, completed 2017/09/21 15:55:40
-```
-
-And you reload browser, JRebel give notice of that it has reloaded classes:
-
-```
-2. Waiting for source changes... (press enter to interrupt)
-2017-09-21 15:55:40 JRebel: Reloading class 'gitbucket.core.html.main$'.
-```
-
-## 6. Limitations
-
-JRebel is nearly always able to eliminate the need to explicitly reload your container after a code change. However, if you change any of your routing patterns, there is nothing JRebel can do, you will have to restart by `jetty:quickstart`.

doc/readme.md

@@ -8,5 +8,4 @@ Developer's Guide
  * [Activity Types](activity.md)
  * [Automatic Schema Updating](auto_update.md)
  * [Release Operation](release.md)
- * [JRebel integration (optional)](jrebel.md)
  * [Licenses](licenses.md)

doc/release.md

@@ -47,7 +47,7 @@ $ sbt executable
 For plug-in development, we have to publish the GitBucket jar file to the Maven central repository as well. At first, hit following command to publish artifacts to the sonatype OSS repository:
 
 ```bash
-$ sbt publish-signed
+$ sbt publishSigned
 ```
 
 Then logged-in https://oss.sonatype.org/ and delete following files from the staging repository:

plugins.json

@@ -1,54 +0,0 @@
-[
-  {
-    "id": "notifications",
-    "name": "Notifications Plugin",
-    "description": "Provides notifications feature on GitBucket.",
-    "versions": [
-      {
-        "version": "1.5.0",
-        "range": ">=4.23.0",
-        "url": "https://github.com/gitbucket/gitbucket-notifications-plugin/releases/download/1.5.0/gitbucket-notifications-plugin-assembly-1.5.0.jar"
-      }
-    ],
-    "default": true
-  },
-  {
-    "id": "emoji",
-    "name": "Emoji Plugin",
-    "description": "Provides Emoji support for GitBucket.",
-    "versions": [
-      {
-        "version": "4.5.0",
-        "range": ">=4.18.0",
-        "url": "https://github.com/gitbucket/gitbucket-emoji-plugin/releases/download/4.5.0/gitbucket-emoji-plugin_2.12-4.5.0.jar"
-      }
-    ],
-    "default": false
-  },
-  {
-    "id": "gist",
-    "name": "Gist Plugin",
-    "description": "Provides Gist feature on GitBucket.",
-    "versions": [
-      {
-        "version": "4.13.0",
-        "range": ">=4.23.0",
-        "url": "https://github.com/gitbucket/gitbucket-gist-plugin/releases/download/4.13.0/gitbucket-gist-plugin-assembly-4.13.0.jar"
-      }
-    ],
-    "default": false
-  },
-  {
-    "id": "pages",
-    "name": "Pages Plugin",
-    "description": "Project pages for gitbucket",
-    "versions": [
-      {
-        "version": "1.7.0",
-        "range": ">=4.23.0",
-        "url": "https://github.com/gitbucket/gitbucket-pages-plugin/releases/download/v1.7.0/gitbucket-pages-plugin_2.12-1.7.0.jar"
-      }
-    ],
-    "default": false
-  }
-]

project/build.properties

@@ -1 +1 @@
-sbt.version=1.1.3
+sbt.version=1.2.6

project/build.sbt

@@ -1 +1 @@
-libraryDependencies += "com.eclipsesource.minimal-json" % "minimal-json" % "0.9.4"
+libraryDependencies += "com.eclipsesource.minimal-json" % "minimal-json" % "0.9.5"

project/plugins.sbt

@@ -1,11 +1,10 @@
 scalacOptions ++= Seq("-unchecked", "-deprecation", "-feature")
 
-addSbtPlugin("com.geirsson"     % "sbt-scalafmt" % "1.4.0")
-addSbtPlugin("com.typesafe.sbt" % "sbt-twirl"    % "1.3.13")
-addSbtPlugin("com.eed3si9n"     % "sbt-assembly" % "0.14.5")
-//addSbtPlugin("com.earldouglas"      % "xsbt-web-plugin"   % "4.0.0")
-//addSbtPlugin("fi.gekkio.sbtplugins" % "sbt-jrebel-plugin" % "0.10.0")
-addSbtPlugin("org.scalatra.sbt" % "sbt-scalatra" % "1.0.1")
-addSbtPlugin("com.jsuereth"     % "sbt-pgp"      % "1.1.0")
+addSbtPlugin("com.geirsson"     % "sbt-scalafmt" % "1.5.0")
+addSbtPlugin("com.typesafe.sbt" % "sbt-twirl"    % "1.3.15")
+addSbtPlugin("com.eed3si9n"     % "sbt-assembly" % "0.14.9")
+addSbtPlugin("org.scalatra.sbt" % "sbt-scalatra" % "1.0.3")
+addSbtPlugin("com.jsuereth"     % "sbt-pgp"      % "1.1.2")
 addSbtCoursier
-addSbtPlugin("com.typesafe.sbt" % "sbt-license-report" % "1.2.0")
+addSbtPlugin("com.typesafe.sbt" % "sbt-license-report"   % "1.2.0")
+addSbtPlugin("net.virtual-void" % "sbt-dependency-graph" % "0.9.2")

src/main/resources/bundle-plugins.txt

@@ -0,0 +1 @@
+notifications:1.6.0

src/main/resources/update/gitbucket-core_4.24.xml

@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<changeSet>
+  <createTable tableName="ACCOUNT_EXTRA_MAIL_ADDRESS">
+    <column name="USER_NAME" type="varchar(100)" nullable="false"/>
+    <column name="EXTRA_MAIL_ADDRESS" type="varchar(100)" nullable="false"/>
+  </createTable>
+
+  <addPrimaryKey constraintName="IDX_ACCOUNT_EXTRA_MAIL_ADDRESS_PK" tableName="ACCOUNT_EXTRA_MAIL_ADDRESS" columnNames="USER_NAME, EXTRA_MAIL_ADDRESS"/>
+  <addUniqueConstraint constraintName="IDX_ACCOUNT_EXTRA_MAIL_ADDRESS_1" tableName="ACCOUNT_EXTRA_MAIL_ADDRESS" columnNames="EXTRA_MAIL_ADDRESS"/>
+</changeSet>

src/main/resources/update/gitbucket-core_4.25.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<changeSet>
+  <modifyDataType columnName="PASSWORD" newDataType="varchar(200)" tableName="ACCOUNT"/>
+
+  <delete tableName="ACCOUNT_EXTRA_MAIL_ADDRESS">
+    <where>EXTRA_MAIL_ADDRESS = ''</where>
+  </delete>
+</changeSet>

src/main/resources/update/gitbucket-core_4.27.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<changeSet>
+  <addColumn tableName="COMMIT_COMMENT">
+    <column name="ORIGINAL_COMMIT_ID" type="varchar(100)" nullable="true"/>
+    <column name="ORIGINAL_OLD_LINE" type="int" nullable="true"/>
+    <column name="ORIGINAL_NEW_LINE" type="int" nullable="true"/>
+  </addColumn>
+  <update tableName="COMMIT_COMMENT">
+    <column name="ORIGINAL_COMMIT_ID" valueComputed="COMMIT_ID"/>
+    <column name="ORIGINAL_OLD_LINE" valueComputed="OLD_LINE_NUMBER"/>
+    <column name="ORIGINAL_NEW_LINE" valueComputed="NEW_LINE_NUMBER"/>
+  </update>
+  <addNotNullConstraint columnName="ORIGINAL_COMMIT_ID" tableName="COMMIT_COMMENT" columnDataType="varchar(100)"/>
+</changeSet>

src/main/scala/ScalatraBootstrap.scala

@@ -28,7 +28,7 @@ class ScalatraBootstrap extends LifeCycle with SystemSettingsService {
     context.addFilter("apiAuthenticationFilter", new ApiAuthenticationFilter)
     context
       .getFilterRegistration("apiAuthenticationFilter")
-      .addMappingForUrlPatterns(EnumSet.allOf(classOf[DispatcherType]), true, "/api/v3/*")
+      .addMappingForUrlPatterns(EnumSet.allOf(classOf[DispatcherType]), true, "/api/*")
 
     // Register controllers
     context.mount(new PreProcessController, "/*")

src/main/scala/gitbucket/core/GitBucketCoreModule.scala

@@ -51,5 +51,13 @@ object GitBucketCoreModule
       new Version("4.21.2"),
       new Version("4.22.0", new LiquibaseMigration("update/gitbucket-core_4.22.xml")),
       new Version("4.23.0", new LiquibaseMigration("update/gitbucket-core_4.23.xml")),
-      new Version("4.23.1")
+      new Version("4.23.1"),
+      new Version("4.24.0", new LiquibaseMigration("update/gitbucket-core_4.24.xml")),
+      new Version("4.24.1"),
+      new Version("4.25.0", new LiquibaseMigration("update/gitbucket-core_4.25.xml")),
+      new Version("4.26.0"),
+      new Version("4.27.0", new LiquibaseMigration("update/gitbucket-core_4.27.xml")),
+      new Version("4.28.0"),
+      new Version("4.29.0"),
+      new Version("4.30.0")
     )

src/main/scala/gitbucket/core/api/AddACollaborator.scala

@@ -0,0 +1,9 @@
+package gitbucket.core.api
+
+case class AddACollaborator(permission: String) {
+  val role: String = permission match {
+    case "admin" => "ADMIN"
+    case "push"  => "DEVELOPER"
+    case "pull"  => "GUEST"
+  }
+}

src/main/scala/gitbucket/core/api/ApiGroup.scala

@@ -0,0 +1,20 @@
+package gitbucket.core.api
+
+import java.util.Date
+
+import gitbucket.core.model.Account
+
+case class ApiGroup(login: String, description: Option[String], created_at: Date) {
+  val id = 0 // dummy id
+  val url = ApiPath(s"/api/v3/orgs/${login}")
+  val html_url = ApiPath(s"/${login}")
+  val avatar_url = ApiPath(s"/${login}/_avatar")
+}
+
+object ApiGroup {
+  def apply(group: Account): ApiGroup = ApiGroup(
+    login = group.userName,
+    description = group.description,
+    created_at = group.registeredDate
+  )
+}

src/main/scala/gitbucket/core/api/ApiIssue.scala

@@ -18,6 +18,7 @@ case class ApiIssue(
   updated_at: Date,
   body: String
 )(repositoryName: RepositoryName, isPullRequest: Boolean) {
+  val id = 0 // dummy id
   val comments_url = ApiPath(s"/api/v3/repos/${repositoryName.fullName}/issues/${number}/comments")
   val html_url = ApiPath(s"/${repositoryName.fullName}/${if (isPullRequest) { "pull" } else { "issues" }}/${number}")
   val pull_request = if (isPullRequest) {

src/main/scala/gitbucket/core/api/ApiPullRequest.scala

@@ -23,6 +23,7 @@ case class ApiPullRequest(
   labels: List[ApiLabel],
   assignee: Option[ApiUser]
 ) {
+  val id = 0 // dummy id
   val html_url = ApiPath(s"${base.repo.html_url.path}/pull/${number}")
   //val diff_url            = ApiPath(s"${base.repo.html_url.path}/pull/${number}.diff")
   //val patch_url           = ApiPath(s"${base.repo.html_url.path}/pull/${number}.patch")

src/main/scala/gitbucket/core/api/ApiPullRequestReviewComment.scala

@@ -17,7 +17,7 @@ case class ApiPullRequestReviewComment(
   commit_id: String, // "0d1a26e67d8f5eaf1f6ba5c57fc3c7d91ac0fd1c",
   // "original_commit_id": "0d1a26e67d8f5eaf1f6ba5c57fc3c7d91ac0fd1c",
   user: ApiUser,
-  body: String, // "Maybe you should use more emojji on this line.",
+  body: String, // "Maybe you should use more emoji on this line.",
   created_at: Date, // "2015-05-05T23:40:27Z",
   updated_at: Date // "2015-05-05T23:40:27Z",
 )(repositoryName: RepositoryName, issueId: Int)

src/main/scala/gitbucket/core/api/ApiRepository.scala

@@ -14,6 +14,7 @@ case class ApiRepository(
   default_branch: String,
   owner: ApiUser
 )(urlIsHtmlUrl: Boolean) {
+  val id = 0 // dummy id
   val forks_count = forks
   val watchers_count = watchers
   val url = if (urlIsHtmlUrl) {

src/main/scala/gitbucket/core/api/ApiUser.scala

@@ -5,6 +5,7 @@ import gitbucket.core.model.Account
 import java.util.Date
 
 case class ApiUser(login: String, email: String, `type`: String, site_admin: Boolean, created_at: Date) {
+  val id = 0 // dummy id
   val url = ApiPath(s"/api/v3/users/${login}")
   val html_url = ApiPath(s"/${login}")
   val avatar_url = ApiPath(s"/${login}/_avatar")

src/main/scala/gitbucket/core/api/CreateAPullRequest.scala

@@ -0,0 +1,16 @@
+package gitbucket.core.api
+
+case class CreateAPullRequest(
+  title: String,
+  head: String,
+  base: String,
+  body: Option[String],
+  maintainer_can_modify: Option[Boolean]
+)
+
+case class CreateAPullRequestAlt(
+  issue: Integer,
+  head: String,
+  base: String,
+  maintainer_can_modify: Option[Boolean]
+)

src/main/scala/gitbucket/core/api/CreateAUser.scala

@@ -0,0 +1,11 @@
+package gitbucket.core.api
+
+case class CreateAUser(
+  login: String,
+  password: String,
+  email: String,
+  fullName: Option[String],
+  isAdmin: Option[Boolean],
+  description: Option[String],
+  url: Option[String]
+)

src/main/scala/gitbucket/core/api/JsonFormat.scala

@@ -24,6 +24,7 @@ object JsonFormat {
         }, { case x: Date => JString(OffsetDateTime.ofInstant(x.toInstant, ZoneId.of("UTC")).format(parserISO)) }
     )
   ) + FieldSerializer[ApiUser]() +
+    FieldSerializer[ApiGroup]() +
     FieldSerializer[ApiPullRequest]() +
     FieldSerializer[ApiRepository]() +
     FieldSerializer[ApiCommitListItem.Parent]() +

src/main/scala/gitbucket/core/api/UpdateAUser.scala

@@ -0,0 +1,11 @@
+package gitbucket.core.api
+
+case class UpdateAUser(
+  name: Option[String],
+  email: Option[String],
+  blog: Option[String],
+  company: Option[String],
+  location: Option[String],
+  hireable: Option[Boolean],
+  bio: Option[String]
+)

src/main/scala/gitbucket/core/controller/AccountController.scala

@@ -1,8 +1,10 @@
 package gitbucket.core.controller
 
+import java.io.File
+
 import gitbucket.core.account.html
 import gitbucket.core.helper
-import gitbucket.core.model.{AccountWebHook, GroupMember, RepositoryWebHook, Role, WebHook, WebHookContentType}
+import gitbucket.core.model._
 import gitbucket.core.plugin.PluginRegistry
 import gitbucket.core.service._
 import gitbucket.core.service.WebHookService._
@@ -54,6 +56,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
     password: String,
     fullName: String,
     mailAddress: String,
+    extraMailAddresses: List[String],
     description: Option[String],
     url: Option[String],
     fileId: Option[String]
@@ -63,6 +66,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
     password: Option[String],
     fullName: String,
     mailAddress: String,
+    extraMailAddresses: List[String],
     description: Option[String],
     url: Option[String],
     fileId: Option[String],
@@ -78,6 +82,9 @@ trait AccountControllerBase extends AccountManagementControllerBase {
     "password" -> trim(label("Password", text(required, maxlength(20), password))),
     "fullName" -> trim(label("Full Name", text(required, maxlength(100)))),
     "mailAddress" -> trim(label("Mail Address", text(required, maxlength(100), uniqueMailAddress()))),
+    "extraMailAddresses" -> list(
+      trim(label("Additional Mail Address", text(maxlength(100), uniqueExtraMailAddress())))
+    ),
     "description" -> trim(label("bio", optional(text()))),
     "url" -> trim(label("URL", optional(text(maxlength(200))))),
     "fileId" -> trim(label("File ID", optional(text())))
@@ -87,6 +94,9 @@ trait AccountControllerBase extends AccountManagementControllerBase {
     "password" -> trim(label("Password", optional(text(maxlength(20), password)))),
     "fullName" -> trim(label("Full Name", text(required, maxlength(100)))),
     "mailAddress" -> trim(label("Mail Address", text(required, maxlength(100), uniqueMailAddress("userName")))),
+    "extraMailAddresses" -> list(
+      trim(label("Additional Mail Address", text(maxlength(100), uniqueExtraMailAddress("userName"))))
+    ),
     "description" -> trim(label("bio", optional(text()))),
     "url" -> trim(label("URL", optional(text(maxlength(200))))),
     "fileId" -> trim(label("File ID", optional(text()))),
@@ -219,13 +229,15 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   get("/:userName") {
     val userName = params("userName")
     getAccountByUserName(userName).map { account =>
+      val extraMailAddresses = getAccountExtraMailAddresses(userName)
       params.getOrElse("tab", "repositories") match {
         // Public Activity
         case "activity" =>
           gitbucket.core.account.html.activity(
             account,
             if (account.isGroupAccount) Nil else getGroupsByUserName(userName),
-            getActivitiesByUser(userName, true)
+            getActivitiesByUser(userName, true),
+            extraMailAddresses
           )
 
         // Members
@@ -234,6 +246,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
           gitbucket.core.account.html.members(
             account,
             members,
+            extraMailAddresses,
             context.loginAccount.exists(
               x =>
                 members.exists { member =>
@@ -250,6 +263,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
             account,
             if (account.isGroupAccount) Nil else getGroupsByUserName(userName),
             getVisibleRepositories(context.loginAccount, Some(userName)),
+            extraMailAddresses,
             context.loginAccount.exists(
               x =>
                 members.exists { member =>
@@ -268,6 +282,12 @@ trait AccountControllerBase extends AccountManagementControllerBase {
     helper.xml.feed(getActivitiesByUser(userName, true))
   }
 
+  get("/:userName.keys") {
+    val keys = getPublicKeys(params("userName"))
+    contentType = "text/plain; charset=utf-8"
+    keys.map(_.publicKey).mkString("", "\n", "\n")
+  }
+
   get("/:userName/_avatar") {
     val userName = params("userName")
     contentType = "image/png"
@@ -276,7 +296,9 @@ trait AccountControllerBase extends AccountManagementControllerBase {
         response.setDateHeader("Last-Modified", account.updatedDate.getTime)
         account.image
           .map { image =>
-            Some(RawData(FileUtil.getMimeType(image), new java.io.File(getUserUploadDir(userName), image)))
+            Some(
+              RawData(FileUtil.getMimeType(image), new File(getUserUploadDir(userName), FileUtil.checkFilename(image)))
+            )
           }
           .getOrElse {
             if (account.isGroupAccount) {
@@ -295,26 +317,29 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   get("/:userName/_edit")(oneselfOnly {
     val userName = params("userName")
     getAccountByUserName(userName).map { x =>
-      html.edit(x, flash.get("info"), flash.get("error"))
+      val extraMails = getAccountExtraMailAddresses(userName)
+      html.edit(x, extraMails, flash.get("info"), flash.get("error"))
     } getOrElse NotFound()
   })
 
   post("/:userName/_edit", editForm)(oneselfOnly { form =>
     val userName = params("userName")
-    getAccountByUserName(userName).map { account =>
-      updateAccount(
-        account.copy(
-          password = form.password.map(sha1).getOrElse(account.password),
-          fullName = form.fullName,
-          mailAddress = form.mailAddress,
-          description = form.description,
-          url = form.url
+    getAccountByUserName(userName).map {
+      account =>
+        updateAccount(
+          account.copy(
+            password = form.password.map(pbkdf2_sha256).getOrElse(account.password),
+            fullName = form.fullName,
+            mailAddress = form.mailAddress,
+            description = form.description,
+            url = form.url
+          )
         )
-      )
 
-      updateImage(userName, form.fileId, form.clearImage)
-      flash += "info" -> "Account information has been updated."
-      redirect(s"/${userName}/_edit")
+        updateImage(userName, form.fileId, form.clearImage)
+        updateAccountExtraMailAddresses(userName, form.extraMailAddresses.filter(_ != ""))
+        flash += "info" -> "Account information has been updated."
+        redirect(s"/${userName}/_edit")
 
     } getOrElse NotFound()
   })
@@ -335,13 +360,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
 //        FileUtils.deleteDirectory(getWikiRepositoryDir(userName, repositoryName))
 //        FileUtils.deleteDirectory(getTemporaryDir(userName, repositoryName))
 //      }
-          // Remove from GROUP_MEMBER and COLLABORATOR
-          removeUserRelatedData(userName)
-          updateAccount(account.copy(isRemoved = true))
-
-          // call hooks
-          PluginRegistry().getAccountHooks.foreach(_.deleted(userName))
-
+          suspendAccount(account)
           session.invalidate
           redirect("/")
         }
@@ -402,7 +421,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
     redirect(s"/${userName}/_application")
   })
 
-  get("/:userName/_hooks")(oneselfOnly {
+  get("/:userName/_hooks")(managersOnly {
     val userName = params("userName")
     getAccountByUserName(userName).map { account =>
       gitbucket.core.account.html.hooks(account, getAccountWebHooks(account.userName), flash.get("info"))
@@ -412,7 +431,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   /**
    * Display the account web hook edit page.
    */
-  get("/:userName/_hooks/new")(oneselfOnly {
+  get("/:userName/_hooks/new")(managersOnly {
     val userName = params("userName")
     getAccountByUserName(userName).map { account =>
       val webhook = AccountWebHook(userName, "", WebHookContentType.FORM, None)
@@ -423,7 +442,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   /**
    * Add the account web hook URL.
    */
-  post("/:userName/_hooks/new", accountWebHookForm(false))(oneselfOnly { form =>
+  post("/:userName/_hooks/new", accountWebHookForm(false))(managersOnly { form =>
     val userName = params("userName")
     addAccountWebHook(userName, form.url, form.events, form.ctype, form.token)
     flash += "info" -> s"Webhook ${form.url} created"
@@ -433,7 +452,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   /**
    * Delete the account web hook URL.
    */
-  get("/:userName/_hooks/delete")(oneselfOnly {
+  get("/:userName/_hooks/delete")(managersOnly {
     val userName = params("userName")
     deleteAccountWebHook(userName, params("url"))
     flash += "info" -> s"Webhook ${params("url")} deleted"
@@ -443,7 +462,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   /**
    * Display the account web hook edit page.
    */
-  get("/:userName/_hooks/edit")(oneselfOnly {
+  get("/:userName/_hooks/edit")(managersOnly {
     val userName = params("userName")
     getAccountByUserName(userName).flatMap { account =>
       getAccountWebHook(userName, params("url")).map {
@@ -456,7 +475,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   /**
    * Update account web hook settings.
    */
-  post("/:userName/_hooks/edit", accountWebHookForm(true))(oneselfOnly { form =>
+  post("/:userName/_hooks/edit", accountWebHookForm(true))(managersOnly { form =>
     val userName = params("userName")
     updateAccountWebHook(userName, form.url, form.events, form.ctype, form.token)
     flash += "info" -> s"webhook ${form.url} updated"
@@ -466,7 +485,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   /**
    * Send the test request to registered account web hook URLs.
    */
-  ajaxPost("/:userName/_hooks/test")(oneselfOnly {
+  ajaxPost("/:userName/_hooks/test")(managersOnly {
     // TODO Is it possible to merge with [[RepositorySettingsController.ajaxPost]]?
     import scala.concurrent.duration._
     import scala.concurrent._
@@ -544,7 +563,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
     if (context.settings.allowAccountRegistration) {
       createAccount(
         form.userName,
-        sha1(form.password),
+        pbkdf2_sha256(form.password),
         form.fullName,
         form.mailAddress,
         false,
@@ -552,6 +571,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
         form.url
       )
       updateImage(form.userName, form.fileId, false)
+      updateAccountExtraMailAddresses(form.userName, form.extraMailAddresses.filter(_ != ""))
       redirect("/signin")
     } else NotFound()
   }
@@ -687,7 +707,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
           }
           helper.html.forkrepository(
             repository,
-            (groups zip managerPermissions).toMap
+            (groups zip managerPermissions).sortBy(_._1)
           )
         case _ => redirect(s"/${loginUserName}")
       }
@@ -715,7 +735,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
 
   private def existsAccount: Constraint = new Constraint() {
     override def validate(name: String, value: String, messages: Messages): Option[String] =
-      if (getAccountByUserName(value).isEmpty) Some("User or group does not exist.") else None
+      if (getAccountByUserNameIgnoreCase(value).isEmpty) Some("User or group does not exist.") else None
   }
 
   private def uniqueRepository: Constraint = new Constraint() {
@@ -727,7 +747,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
     ): Option[String] = {
       for {
         userName <- params.optionValue("owner")
-        _ <- getRepositoryNamesOfUser(userName).find(_ == value)
+        _ <- getRepositoryNamesOfUser(userName).find(_.equalsIgnoreCase(value))
       } yield {
         "Repository already exists."
       }

src/main/scala/gitbucket/core/controller/ApiController.scala

@@ -1,27 +1,26 @@
 package gitbucket.core.controller
 
 import gitbucket.core.api._
-import gitbucket.core.model._
-import gitbucket.core.service.IssuesService.IssueSearchCondition
-import gitbucket.core.service.PullRequestService._
+import gitbucket.core.controller.api._
 import gitbucket.core.service._
-import gitbucket.core.util.Directory._
 import gitbucket.core.util.Implicits._
-import gitbucket.core.util.JGitUtil._
-import gitbucket.core.util.SyntaxSugars._
 import gitbucket.core.util._
 import gitbucket.core.plugin.PluginRegistry
-import gitbucket.core.view.helpers.{isRenderable, renderMarkup}
-import org.eclipse.jgit.api.Git
-import org.eclipse.jgit.revwalk.RevWalk
-import org.scalatra.{Created, NoContent, UnprocessableEntity}
-
-import scala.collection.JavaConverters._
-import scala.concurrent.Await
-import scala.concurrent.duration.Duration
 
 class ApiController
     extends ApiControllerBase
+    with ApiGitReferenceControllerBase
+    with ApiIssueCommentControllerBase
+    with ApiIssueControllerBase
+    with ApiIssueLabelControllerBase
+    with ApiOrganizationControllerBase
+    with ApiPullRequestControllerBase
+    with ApiRepositoryBranchControllerBase
+    with ApiRepositoryCollaboratorControllerBase
+    with ApiRepositoryCommitControllerBase
+    with ApiRepositoryControllerBase
+    with ApiRepositoryStatusControllerBase
+    with ApiUserControllerBase
     with RepositoryService
     with AccountService
     with ProtectedBranchService
@@ -34,12 +33,15 @@ class ApiController
     with RepositoryCreationService
     with IssueCreationService
     with HandleCommentService
+    with MergeService
     with WebHookService
     with WebHookPullRequestService
     with WebHookIssueCommentService
+    with WebHookPullRequestReviewCommentService
     with WikiService
     with ActivityService
     with PrioritiesService
+    with AdminAuthenticator
     with OwnerAuthenticator
     with UsersAuthenticator
     with GroupManagerAuthenticator
@@ -48,25 +50,6 @@ class ApiController
     with WritableUsersAuthenticator
 
 trait ApiControllerBase extends ControllerBase {
-  self: RepositoryService
-    with AccountService
-    with ProtectedBranchService
-    with IssuesService
-    with LabelsService
-    with MilestonesService
-    with PullRequestService
-    with CommitsService
-    with CommitStatusService
-    with RepositoryCreationService
-    with IssueCreationService
-    with HandleCommentService
-    with PrioritiesService
-    with OwnerAuthenticator
-    with UsersAuthenticator
-    with GroupManagerAuthenticator
-    with ReferrerAuthenticator
-    with ReadableUsersAuthenticator
-    with WritableUsersAuthenticator =>
 
   /**
    * 404 for non-implemented api
@@ -74,6 +57,18 @@ trait ApiControllerBase extends ControllerBase {
   get("/api/v3/*") {
     NotFound()
   }
+  post("/api/v3/*") {
+    NotFound()
+  }
+  put("/api/v3/*") {
+    NotFound()
+  }
+  delete("/api/v3/*") {
+    NotFound()
+  }
+  patch("/api/v3/*") {
+    NotFound()
+  }
 
   /**
    * https://developer.github.com/v3/#root-endpoint
@@ -82,311 +77,6 @@ trait ApiControllerBase extends ControllerBase {
     JsonFormat(ApiEndPoint())
   }
 
-  /**
-   * https://developer.github.com/v3/orgs/#get-an-organization
-   */
-  get("/api/v3/orgs/:groupName") {
-    getAccountByUserName(params("groupName")).filter(account => account.isGroupAccount).map { account =>
-      JsonFormat(ApiUser(account))
-    } getOrElse NotFound()
-  }
-
-  /**
-   * https://developer.github.com/v3/users/#get-a-single-user
-   * This API also returns group information (as GitHub).
-   */
-  get("/api/v3/users/:userName") {
-    getAccountByUserName(params("userName")).map { account =>
-      JsonFormat(ApiUser(account))
-    } getOrElse NotFound()
-  }
-
-  /**
-   * https://developer.github.com/v3/repos/#list-organization-repositories
-   */
-  get("/api/v3/orgs/:orgName/repos") {
-    JsonFormat(getVisibleRepositories(context.loginAccount, Some(params("orgName"))).map { r =>
-      ApiRepository(r, getAccountByUserName(r.owner).get)
-    })
-  }
-
-  /**
-   * https://developer.github.com/v3/repos/#list-user-repositories
-   */
-  get("/api/v3/users/:userName/repos") {
-    JsonFormat(getVisibleRepositories(context.loginAccount, Some(params("userName"))).map { r =>
-      ApiRepository(r, getAccountByUserName(r.owner).get)
-    })
-  }
-
-  /*
-   * https://developer.github.com/v3/repos/branches/#list-branches
-   */
-  get("/api/v3/repos/:owner/:repo/branches")(referrersOnly { repository =>
-    JsonFormat(
-      JGitUtil
-        .getBranches(
-          owner = repository.owner,
-          name = repository.name,
-          defaultBranch = repository.repository.defaultBranch,
-          origin = repository.repository.originUserName.isEmpty
-        )
-        .map { br =>
-          ApiBranchForList(br.name, ApiBranchCommit(br.commitId))
-        }
-    )
-  })
-
-  /**
-   * https://developer.github.com/v3/repos/branches/#get-branch
-   */
-  get("/api/v3/repos/:owner/:repo/branches/*")(referrersOnly { repository =>
-    //import gitbucket.core.api._
-    (for {
-      branch <- params.get("splat") if repository.branchList.contains(branch)
-      br <- getBranches(
-        repository.owner,
-        repository.name,
-        repository.repository.defaultBranch,
-        repository.repository.originUserName.isEmpty
-      ).find(_.name == branch)
-    } yield {
-      val protection = getProtectedBranchInfo(repository.owner, repository.name, branch)
-      JsonFormat(
-        ApiBranch(branch, ApiBranchCommit(br.commitId), ApiBranchProtection(protection))(RepositoryName(repository))
-      )
-    }) getOrElse NotFound()
-  })
-
-  /*
-   * https://developer.github.com/v3/repos/contents/#get-contents
-   */
-  get("/api/v3/repos/:owner/:repo/contents")(referrersOnly { repository =>
-    getContents(repository, ".", params.getOrElse("ref", repository.repository.defaultBranch))
-  })
-
-  /*
-   * https://developer.github.com/v3/repos/contents/#get-contents
-   */
-  get("/api/v3/repos/:owner/:repo/contents/*")(referrersOnly { repository =>
-    getContents(repository, multiParams("splat").head, params.getOrElse("ref", repository.repository.defaultBranch))
-  })
-
-  private def getContents(repository: RepositoryService.RepositoryInfo, path: String, refStr: String) = {
-    def getFileInfo(git: Git, revision: String, pathStr: String): Option[FileInfo] = {
-      val (dirName, fileName) = pathStr.lastIndexOf('/') match {
-        case -1 =>
-          (".", pathStr)
-        case n =>
-          (pathStr.take(n), pathStr.drop(n + 1))
-      }
-      getFileList(git, revision, dirName).find(f => f.name.equals(fileName))
-    }
-
-    using(Git.open(getRepositoryDir(params("owner"), params("repo")))) { git =>
-      val fileList = getFileList(git, refStr, path)
-      if (fileList.isEmpty) { // file or NotFound
-        getFileInfo(git, refStr, path)
-          .flatMap { f =>
-            val largeFile = params.get("large_file").exists(s => s.equals("true"))
-            val content = getContentFromId(git, f.id, largeFile)
-            request.getHeader("Accept") match {
-              case "application/vnd.github.v3.raw" => {
-                contentType = "application/vnd.github.v3.raw"
-                content
-              }
-              case "application/vnd.github.v3.html" if isRenderable(f.name) => {
-                contentType = "application/vnd.github.v3.html"
-                content.map { c =>
-                  List(
-                    "<div data-path=\"",
-                    path,
-                    "\" id=\"file\">",
-                    "<article>",
-                    renderMarkup(path.split("/").toList, new String(c), refStr, repository, false, false, true).body,
-                    "</article>",
-                    "</div>"
-                  ).mkString
-                }
-              }
-              case "application/vnd.github.v3.html" => {
-                contentType = "application/vnd.github.v3.html"
-                content.map { c =>
-                  List(
-                    "<div data-path=\"",
-                    path,
-                    "\" id=\"file\">",
-                    "<div class=\"plain\">",
-                    "<pre>",
-                    play.twirl.api.HtmlFormat.escape(new String(c)).body,
-                    "</pre>",
-                    "</div>",
-                    "</div>"
-                  ).mkString
-                }
-              }
-              case _ =>
-                Some(JsonFormat(ApiContents(f, RepositoryName(repository), content)))
-            }
-          }
-          .getOrElse(NotFound())
-
-      } else { // directory
-        JsonFormat(fileList.map { f =>
-          ApiContents(f, RepositoryName(repository), None)
-        })
-      }
-    }
-  }
-
-  /*
-   * https://developer.github.com/v3/git/refs/#get-a-reference
-   */
-  get("/api/v3/repos/:owner/:repo/git/refs/*")(referrersOnly { repository =>
-    val revstr = multiParams("splat").head
-    using(Git.open(getRepositoryDir(params("owner"), params("repo")))) { git =>
-      val ref = git.getRepository().findRef(revstr)
-
-      if (ref != null) {
-        val sha = ref.getObjectId().name()
-        JsonFormat(ApiRef(revstr, ApiObject(sha)))
-
-      } else {
-        val refs = git
-          .getRepository()
-          .getAllRefs()
-          .asScala
-          .collect { case (str, ref) if str.startsWith("refs/" + revstr) => ref }
-
-        JsonFormat(refs.map { ref =>
-          val sha = ref.getObjectId().name()
-          ApiRef(revstr, ApiObject(sha))
-        })
-      }
-    }
-  })
-
-  /**
-   * https://developer.github.com/v3/repos/collaborators/#list-collaborators
-   */
-  get("/api/v3/repos/:owner/:repo/collaborators")(referrersOnly { repository =>
-    // TODO Should ApiUser take permission? getCollaboratorUserNames does not return owner group members.
-    JsonFormat(getCollaboratorUserNames(params("owner"), params("repo")).map(u => ApiUser(getAccountByUserName(u).get)))
-  })
-
-  /**
-   * https://developer.github.com/v3/users/#get-the-authenticated-user
-   */
-  get("/api/v3/user") {
-    context.loginAccount.map { account =>
-      JsonFormat(ApiUser(account))
-    } getOrElse Unauthorized()
-  }
-
-  /**
-   * List user's own repository
-   * https://developer.github.com/v3/repos/#list-your-repositories
-   */
-  get("/api/v3/user/repos")(usersOnly {
-    JsonFormat(getVisibleRepositories(context.loginAccount, Option(context.loginAccount.get.userName)).map { r =>
-      ApiRepository(r, getAccountByUserName(r.owner).get)
-    })
-  })
-
-  /**
-   * Create user repository
-   * https://developer.github.com/v3/repos/#create
-   */
-  post("/api/v3/user/repos")(usersOnly {
-    val owner = context.loginAccount.get.userName
-    (for {
-      data <- extractFromJsonBody[CreateARepository] if data.isValid
-    } yield {
-      LockUtil.lock(s"${owner}/${data.name}") {
-        if (getRepository(owner, data.name).isEmpty) {
-          val f = createRepository(
-            context.loginAccount.get,
-            owner,
-            data.name,
-            data.description,
-            data.`private`,
-            data.auto_init
-          )
-          Await.result(f, Duration.Inf)
-          val repository = getRepository(owner, data.name).get
-          JsonFormat(ApiRepository(repository, ApiUser(getAccountByUserName(owner).get)))
-        } else {
-          ApiError(
-            "A repository with this name already exists on this account",
-            Some("https://developer.github.com/v3/repos/#create")
-          )
-        }
-      }
-    }) getOrElse NotFound()
-  })
-
-  /**
-   * Create group repository
-   * https://developer.github.com/v3/repos/#create
-   */
-  post("/api/v3/orgs/:org/repos")(managersOnly {
-    val groupName = params("org")
-    (for {
-      data <- extractFromJsonBody[CreateARepository] if data.isValid
-    } yield {
-      LockUtil.lock(s"${groupName}/${data.name}") {
-        if (getRepository(groupName, data.name).isEmpty) {
-          val f = createRepository(
-            context.loginAccount.get,
-            groupName,
-            data.name,
-            data.description,
-            data.`private`,
-            data.auto_init
-          )
-          Await.result(f, Duration.Inf)
-          val repository = getRepository(groupName, data.name).get
-          JsonFormat(ApiRepository(repository, ApiUser(getAccountByUserName(groupName).get)))
-        } else {
-          ApiError(
-            "A repository with this name already exists for this group",
-            Some("https://developer.github.com/v3/repos/#create")
-          )
-        }
-      }
-    }) getOrElse NotFound()
-  })
-
-  /**
-   * https://developer.github.com/v3/repos/#enabling-and-disabling-branch-protection
-   */
-  patch("/api/v3/repos/:owner/:repo/branches/*")(ownerOnly { repository =>
-    import gitbucket.core.api._
-    (for {
-      branch <- params.get("splat") if repository.branchList.contains(branch)
-      protection <- extractFromJsonBody[ApiBranchProtection.EnablingAndDisabling].map(_.protection)
-      br <- getBranches(
-        repository.owner,
-        repository.name,
-        repository.repository.defaultBranch,
-        repository.repository.originUserName.isEmpty
-      ).find(_.name == branch)
-    } yield {
-      if (protection.enabled) {
-        enableBranchProtection(
-          repository.owner,
-          repository.name,
-          branch,
-          protection.status.enforcement_level == ApiBranchProtection.Everyone,
-          protection.status.contexts
-        )
-      } else {
-        disableBranchProtection(repository.owner, repository.name, branch)
-      }
-      JsonFormat(ApiBranch(branch, ApiBranchCommit(br.commitId), protection)(RepositoryName(repository)))
-    }) getOrElse NotFound()
-  })
-
   /**
    * @see https://developer.github.com/v3/rate_limit/#get-your-current-rate-limit-status
    * but not enabled.
@@ -397,459 +87,6 @@ trait ApiControllerBase extends ControllerBase {
     org.scalatra.NotFound(ApiError("Rate limiting is not enabled."))
   }
 
-  /**
-   * https://developer.github.com/v3/issues/#list-issues-for-a-repository
-   */
-  get("/api/v3/repos/:owner/:repository/issues")(referrersOnly { repository =>
-    val page = IssueSearchCondition.page(request)
-    // TODO: more api spec condition
-    val condition = IssueSearchCondition(request)
-    val baseOwner = getAccountByUserName(repository.owner).get
-
-    val issues: List[(Issue, Account)] =
-      searchIssueByApi(
-        condition = condition,
-        offset = (page - 1) * PullRequestLimit,
-        limit = PullRequestLimit,
-        repos = repository.owner -> repository.name
-      )
-
-    JsonFormat(issues.map {
-      case (issue, issueUser) =>
-        ApiIssue(
-          issue = issue,
-          repositoryName = RepositoryName(repository),
-          user = ApiUser(issueUser),
-          labels = getIssueLabels(repository.owner, repository.name, issue.issueId)
-            .map(ApiLabel(_, RepositoryName(repository)))
-        )
-    })
-  })
-
-  /**
-   * https://developer.github.com/v3/issues/#get-a-single-issue
-   */
-  get("/api/v3/repos/:owner/:repository/issues/:id")(referrersOnly { repository =>
-    (for {
-      issueId <- params("id").toIntOpt
-      issue <- getIssue(repository.owner, repository.name, issueId.toString)
-      openedUser <- getAccountByUserName(issue.openedUserName)
-    } yield {
-      JsonFormat(
-        ApiIssue(
-          issue,
-          RepositoryName(repository),
-          ApiUser(openedUser),
-          getIssueLabels(repository.owner, repository.name, issue.issueId).map(ApiLabel(_, RepositoryName(repository)))
-        )
-      )
-    }) getOrElse NotFound()
-  })
-
-  /**
-   * https://developer.github.com/v3/issues/#create-an-issue
-   */
-  post("/api/v3/repos/:owner/:repository/issues")(readableUsersOnly { repository =>
-    if (isIssueEditable(repository)) { // TODO Should this check is provided by authenticator?
-      (for {
-        data <- extractFromJsonBody[CreateAnIssue]
-        loginAccount <- context.loginAccount
-      } yield {
-        val milestone = data.milestone.flatMap(getMilestone(repository.owner, repository.name, _))
-        val issue = createIssue(
-          repository,
-          data.title,
-          data.body,
-          data.assignees.headOption,
-          milestone.map(_.milestoneId),
-          None,
-          data.labels,
-          loginAccount
-        )
-        JsonFormat(
-          ApiIssue(
-            issue,
-            RepositoryName(repository),
-            ApiUser(loginAccount),
-            getIssueLabels(repository.owner, repository.name, issue.issueId)
-              .map(ApiLabel(_, RepositoryName(repository)))
-          )
-        )
-      }) getOrElse NotFound()
-    } else Unauthorized()
-  })
-
-  /**
-   * https://developer.github.com/v3/issues/comments/#list-comments-on-an-issue
-   */
-  get("/api/v3/repos/:owner/:repository/issues/:id/comments")(referrersOnly { repository =>
-    (for {
-      issueId <- params("id").toIntOpt
-      comments = getCommentsForApi(repository.owner, repository.name, issueId)
-    } yield {
-      JsonFormat(comments.map {
-        case (issueComment, user, issue) =>
-          ApiComment(issueComment, RepositoryName(repository), issueId, ApiUser(user), issue.isPullRequest)
-      })
-    }) getOrElse NotFound()
-  })
-
-  /**
-   * https://developer.github.com/v3/issues/comments/#create-a-comment
-   */
-  post("/api/v3/repos/:owner/:repository/issues/:id/comments")(readableUsersOnly { repository =>
-    (for {
-      issueId <- params("id").toIntOpt
-      issue <- getIssue(repository.owner, repository.name, issueId.toString)
-      body <- extractFromJsonBody[CreateAComment].map(_.body) if !body.isEmpty
-      action = params.get("action").filter(_ => isEditable(issue.userName, issue.repositoryName, issue.openedUserName))
-      (issue, id) <- handleComment(issue, Some(body), repository, action)
-      issueComment <- getComment(repository.owner, repository.name, id.toString())
-    } yield {
-      JsonFormat(
-        ApiComment(
-          issueComment,
-          RepositoryName(repository),
-          issueId,
-          ApiUser(context.loginAccount.get),
-          issue.isPullRequest
-        )
-      )
-    }) getOrElse NotFound()
-  })
-
-  /**
-   * List all labels for this repository
-   * https://developer.github.com/v3/issues/labels/#list-all-labels-for-this-repository
-   */
-  get("/api/v3/repos/:owner/:repository/labels")(referrersOnly { repository =>
-    JsonFormat(getLabels(repository.owner, repository.name).map { label =>
-      ApiLabel(label, RepositoryName(repository))
-    })
-  })
-
-  /**
-   * Get a single label
-   * https://developer.github.com/v3/issues/labels/#get-a-single-label
-   */
-  get("/api/v3/repos/:owner/:repository/labels/:labelName")(referrersOnly { repository =>
-    getLabel(repository.owner, repository.name, params("labelName")).map { label =>
-      JsonFormat(ApiLabel(label, RepositoryName(repository)))
-    } getOrElse NotFound()
-  })
-
-  /**
-   * Create a label
-   * https://developer.github.com/v3/issues/labels/#create-a-label
-   */
-  post("/api/v3/repos/:owner/:repository/labels")(writableUsersOnly { repository =>
-    (for {
-      data <- extractFromJsonBody[CreateALabel] if data.isValid
-    } yield {
-      LockUtil.lock(RepositoryName(repository).fullName) {
-        if (getLabel(repository.owner, repository.name, data.name).isEmpty) {
-          val labelId = createLabel(repository.owner, repository.name, data.name, data.color)
-          getLabel(repository.owner, repository.name, labelId).map { label =>
-            Created(JsonFormat(ApiLabel(label, RepositoryName(repository))))
-          } getOrElse NotFound()
-        } else {
-          // TODO ApiError should support errors field to enhance compatibility of GitHub API
-          UnprocessableEntity(
-            ApiError(
-              "Validation Failed",
-              Some("https://developer.github.com/v3/issues/labels/#create-a-label")
-            )
-          )
-        }
-      }
-    }) getOrElse NotFound()
-  })
-
-  /**
-   * Update a label
-   * https://developer.github.com/v3/issues/labels/#update-a-label
-   */
-  patch("/api/v3/repos/:owner/:repository/labels/:labelName")(writableUsersOnly { repository =>
-    (for {
-      data <- extractFromJsonBody[CreateALabel] if data.isValid
-    } yield {
-      LockUtil.lock(RepositoryName(repository).fullName) {
-        getLabel(repository.owner, repository.name, params("labelName")).map {
-          label =>
-            if (getLabel(repository.owner, repository.name, data.name).isEmpty) {
-              updateLabel(repository.owner, repository.name, label.labelId, data.name, data.color)
-              JsonFormat(
-                ApiLabel(
-                  getLabel(repository.owner, repository.name, label.labelId).get,
-                  RepositoryName(repository)
-                )
-              )
-            } else {
-              // TODO ApiError should support errors field to enhance compatibility of GitHub API
-              UnprocessableEntity(
-                ApiError(
-                  "Validation Failed",
-                  Some("https://developer.github.com/v3/issues/labels/#create-a-label")
-                )
-              )
-            }
-        } getOrElse NotFound()
-      }
-    }) getOrElse NotFound()
-  })
-
-  /**
-   * Delete a label
-   * https://developer.github.com/v3/issues/labels/#delete-a-label
-   */
-  delete("/api/v3/repos/:owner/:repository/labels/:labelName")(writableUsersOnly { repository =>
-    LockUtil.lock(RepositoryName(repository).fullName) {
-      getLabel(repository.owner, repository.name, params("labelName")).map { label =>
-        deleteLabel(repository.owner, repository.name, label.labelId)
-        NoContent()
-      } getOrElse NotFound()
-    }
-  })
-
-  /**
-   * https://developer.github.com/v3/pulls/#list-pull-requests
-   */
-  get("/api/v3/repos/:owner/:repository/pulls")(referrersOnly { repository =>
-    val page = IssueSearchCondition.page(request)
-    // TODO: more api spec condition
-    val condition = IssueSearchCondition(request)
-    val baseOwner = getAccountByUserName(repository.owner).get
-
-    val issues: List[(Issue, Account, Int, PullRequest, Repository, Account, Option[Account])] =
-      searchPullRequestByApi(
-        condition = condition,
-        offset = (page - 1) * PullRequestLimit,
-        limit = PullRequestLimit,
-        repos = repository.owner -> repository.name
-      )
-
-    JsonFormat(issues.map {
-      case (issue, issueUser, commentCount, pullRequest, headRepo, headOwner, assignee) =>
-        ApiPullRequest(
-          issue = issue,
-          pullRequest = pullRequest,
-          headRepo = ApiRepository(headRepo, ApiUser(headOwner)),
-          baseRepo = ApiRepository(repository, ApiUser(baseOwner)),
-          user = ApiUser(issueUser),
-          labels = getIssueLabels(repository.owner, repository.name, issue.issueId)
-            .map(ApiLabel(_, RepositoryName(repository))),
-          assignee = assignee.map(ApiUser.apply),
-          mergedComment = getMergedComment(repository.owner, repository.name, issue.issueId)
-        )
-    })
-  })
-
-  /**
-   * https://developer.github.com/v3/pulls/#get-a-single-pull-request
-   */
-  get("/api/v3/repos/:owner/:repository/pulls/:id")(referrersOnly { repository =>
-    (for {
-      issueId <- params("id").toIntOpt
-      (issue, pullRequest) <- getPullRequest(repository.owner, repository.name, issueId)
-      users = getAccountsByUserNames(
-        Set(repository.owner, pullRequest.requestUserName, issue.openedUserName),
-        Set.empty
-      )
-      baseOwner <- users.get(repository.owner)
-      headOwner <- users.get(pullRequest.requestUserName)
-      issueUser <- users.get(issue.openedUserName)
-      assignee = issue.assignedUserName.flatMap { userName =>
-        getAccountByUserName(userName, false)
-      }
-      headRepo <- getRepository(pullRequest.requestUserName, pullRequest.requestRepositoryName)
-    } yield {
-      JsonFormat(
-        ApiPullRequest(
-          issue = issue,
-          pullRequest = pullRequest,
-          headRepo = ApiRepository(headRepo, ApiUser(headOwner)),
-          baseRepo = ApiRepository(repository, ApiUser(baseOwner)),
-          user = ApiUser(issueUser),
-          labels = getIssueLabels(repository.owner, repository.name, issue.issueId)
-            .map(ApiLabel(_, RepositoryName(repository))),
-          assignee = assignee.map(ApiUser.apply),
-          mergedComment = getMergedComment(repository.owner, repository.name, issue.issueId)
-        )
-      )
-    }) getOrElse NotFound()
-  })
-
-  /**
-   * https://developer.github.com/v3/pulls/#list-commits-on-a-pull-request
-   */
-  get("/api/v3/repos/:owner/:repository/pulls/:id/commits")(referrersOnly { repository =>
-    val owner = repository.owner
-    val name = repository.name
-    params("id").toIntOpt.flatMap {
-      issueId =>
-        getPullRequest(owner, name, issueId) map {
-          case (issue, pullreq) =>
-            using(Git.open(getRepositoryDir(owner, name))) { git =>
-              val oldId = git.getRepository.resolve(pullreq.commitIdFrom)
-              val newId = git.getRepository.resolve(pullreq.commitIdTo)
-              val repoFullName = RepositoryName(repository)
-              val commits = git.log
-                .addRange(oldId, newId)
-                .call
-                .iterator
-                .asScala
-                .map { c =>
-                  ApiCommitListItem(new CommitInfo(c), repoFullName)
-                }
-                .toList
-              JsonFormat(commits)
-            }
-        }
-    } getOrElse NotFound()
-  })
-
-  /**
-   * https://developer.github.com/v3/repos/#get
-   */
-  get("/api/v3/repos/:owner/:repository")(referrersOnly { repository =>
-    JsonFormat(ApiRepository(repository, ApiUser(getAccountByUserName(repository.owner).get)))
-  })
-
-  /**
-   * https://developer.github.com/v3/repos/statuses/#create-a-status
-   */
-  post("/api/v3/repos/:owner/:repo/statuses/:sha")(writableUsersOnly { repository =>
-    (for {
-      ref <- params.get("sha")
-      sha <- JGitUtil.getShaByRef(repository.owner, repository.name, ref)
-      data <- extractFromJsonBody[CreateAStatus] if data.isValid
-      creator <- context.loginAccount
-      state <- CommitState.valueOf(data.state)
-      statusId = createCommitStatus(
-        repository.owner,
-        repository.name,
-        sha,
-        data.context.getOrElse("default"),
-        state,
-        data.target_url,
-        data.description,
-        new java.util.Date(),
-        creator
-      )
-      status <- getCommitStatus(repository.owner, repository.name, statusId)
-    } yield {
-      JsonFormat(ApiCommitStatus(status, ApiUser(creator)))
-    }) getOrElse NotFound()
-  })
-
-  /**
-   * https://developer.github.com/v3/repos/statuses/#list-statuses-for-a-specific-ref
-   *
-   * ref is Ref to list the statuses from. It can be a SHA, a branch name, or a tag name.
-   */
-  val listStatusesRoute = get("/api/v3/repos/:owner/:repo/commits/:ref/statuses")(referrersOnly { repository =>
-    (for {
-      ref <- params.get("ref")
-      sha <- JGitUtil.getShaByRef(repository.owner, repository.name, ref)
-    } yield {
-      JsonFormat(getCommitStatuesWithCreator(repository.owner, repository.name, sha).map {
-        case (status, creator) =>
-          ApiCommitStatus(status, ApiUser(creator))
-      })
-    }) getOrElse NotFound()
-  })
-
-  /**
-   * https://developer.github.com/v3/repos/statuses/#list-statuses-for-a-specific-ref
-   *
-   * legacy route
-   */
-  get("/api/v3/repos/:owner/:repo/statuses/:ref") {
-    listStatusesRoute.action()
-  }
-
-  /**
-   * https://developer.github.com/v3/repos/statuses/#get-the-combined-status-for-a-specific-ref
-   *
-   * ref is Ref to list the statuses from. It can be a SHA, a branch name, or a tag name.
-   */
-  get("/api/v3/repos/:owner/:repo/commits/:ref/status")(referrersOnly { repository =>
-    (for {
-      ref <- params.get("ref")
-      owner <- getAccountByUserName(repository.owner)
-      sha <- JGitUtil.getShaByRef(repository.owner, repository.name, ref)
-    } yield {
-      val statuses = getCommitStatuesWithCreator(repository.owner, repository.name, sha)
-      JsonFormat(ApiCombinedCommitStatus(sha, statuses, ApiRepository(repository, owner)))
-    }) getOrElse NotFound()
-  })
-
-  /**
-   * https://developer.github.com/v3/repos/commits/#get-a-single-commit
-   */
-  get("/api/v3/repos/:owner/:repo/commits/:sha")(referrersOnly { repository =>
-    val owner = repository.owner
-    val name = repository.name
-    val sha = params("sha")
-
-    using(Git.open(getRepositoryDir(owner, name))) {
-      git =>
-        val repo = git.getRepository
-        val objectId = repo.resolve(sha)
-        val commitInfo = using(new RevWalk(repo)) { revWalk =>
-          new CommitInfo(revWalk.parseCommit(objectId))
-        }
-
-        JsonFormat(
-          ApiCommits(
-            repositoryName = RepositoryName(repository),
-            commitInfo = commitInfo,
-            diffs = JGitUtil.getDiffs(git, Some(commitInfo.parents.head), commitInfo.id, false, true),
-            author = getAccount(commitInfo.authorName, commitInfo.authorEmailAddress),
-            committer = getAccount(commitInfo.committerName, commitInfo.committerEmailAddress),
-            commentCount = getCommitComment(repository.owner, repository.name, sha).size
-          )
-        )
-    }
-  })
-
-  private def getAccount(userName: String, email: String): Account = {
-    getAccountByMailAddress(email).getOrElse {
-      Account(
-        userName = userName,
-        fullName = userName,
-        mailAddress = email,
-        password = "xxx",
-        isAdmin = false,
-        url = None,
-        registeredDate = new java.util.Date(),
-        updatedDate = new java.util.Date(),
-        lastLoginDate = None,
-        image = None,
-        isGroupAccount = false,
-        isRemoved = true,
-        description = None
-      )
-    }
-  }
-
-  private def isEditable(owner: String, repository: String, author: String)(implicit context: Context): Boolean =
-    hasDeveloperRole(owner, repository, context.loginAccount) || author == context.loginAccount.get.userName
-
-  /**
-   * non-GitHub compatible API for Jenkins-Plugin
-   */
-  get("/api/v3/repos/:owner/:repo/raw/*")(referrersOnly { repository =>
-    val (id, path) = repository.splitPath(multiParams("splat").head)
-    using(Git.open(getRepositoryDir(repository.owner, repository.name))) { git =>
-      val revCommit = JGitUtil.getRevCommitFromId(git, git.getRepository.resolve(id))
-
-      getPathObjectId(git, path, revCommit).map { objectId =>
-        responseRawFile(git, objectId, path, repository)
-      } getOrElse NotFound()
-    }
-  })
-
   /**
    * non-GitHub compatible API for listing plugins
    */

src/main/scala/gitbucket/core/controller/ControllerBase.scala

@@ -1,8 +1,8 @@
 package gitbucket.core.controller
 
-import java.io.FileInputStream
+import java.io.{File, FileInputStream}
 
-import gitbucket.core.api.ApiError
+import gitbucket.core.api.{ApiError, JsonFormat}
 import gitbucket.core.model.Account
 import gitbucket.core.service.{AccountService, RepositoryService, SystemSettingsService}
 import gitbucket.core.util.SyntaxSugars._
@@ -46,6 +46,7 @@ abstract class ControllerBase
 
   before("/api/v3/*") {
     contentType = formats("json")
+    request.setAttribute(Keys.Request.APIv3, true)
   }
 
   override def requestPath(uri: String, idx: Int): String = {
@@ -67,14 +68,11 @@ abstract class ControllerBase
         // Git repository
         chain.doFilter(request, response)
       } else {
-        if (path.startsWith("/api/v3/")) {
-          httpRequest.setAttribute(Keys.Request.APIv3, true)
-        }
         // Scalatra actions
         super.doFilter(request, response, chain)
       }
     } finally {
-      contextCache.remove();
+      contextCache.remove()
     }
 
   private val contextCache = new java.lang.ThreadLocal[Context]()
@@ -125,7 +123,7 @@ abstract class ControllerBase
       org.scalatra.NotFound()
     } else if (request.hasAttribute(Keys.Request.APIv3)) {
       contentType = formats("json")
-      org.scalatra.NotFound(ApiError("Not Found"))
+      org.scalatra.NotFound(JsonFormat(ApiError("Not Found")))
     } else {
       org.scalatra.NotFound(gitbucket.core.html.error("Not Found"))
     }
@@ -145,7 +143,7 @@ abstract class ControllerBase
       org.scalatra.Unauthorized()
     } else if (request.hasAttribute(Keys.Request.APIv3)) {
       contentType = formats("json")
-      org.scalatra.Unauthorized(ApiError("Requires authentication"))
+      org.scalatra.Unauthorized(JsonFormat(ApiError("Requires authentication")))
     } else if (!isBrowser(request.getHeader("USER-AGENT"))) {
       org.scalatra.Unauthorized()
     } else {
@@ -177,7 +175,7 @@ abstract class ControllerBase
         org.scalatra.InternalServerError()
       } else if (request.hasAttribute(Keys.Request.APIv3)) {
         contentType = formats("json")
-        org.scalatra.InternalServerError(ApiError("Internal Server Error"))
+        org.scalatra.InternalServerError(JsonFormat(ApiError("Internal Server Error")))
       } else {
         org.scalatra.InternalServerError(gitbucket.core.html.error("Internal Server Error", Some(e)))
       }
@@ -256,7 +254,7 @@ abstract class ControllerBase
     repository: RepositoryService.RepositoryInfo
   ): Unit = {
     JGitUtil.getObjectLoaderFromId(git, objectId) { loader =>
-      contentType = FileUtil.getMimeType(path)
+      contentType = FileUtil.getSafeMimeType(path)
 
       if (loader.isLarge) {
         response.setContentLength(loader.getSize.toInt)
@@ -328,28 +326,28 @@ trait AccountManagementControllerBase extends ControllerBase {
 
   protected def updateImage(userName: String, fileId: Option[String], clearImage: Boolean): Unit =
     if (clearImage) {
-      getAccountByUserName(userName).flatMap(_.image).map { image =>
-        new java.io.File(getUserUploadDir(userName), image).delete()
+      getAccountByUserName(userName).flatMap(_.image).foreach { image =>
+        new File(getUserUploadDir(userName), FileUtil.checkFilename(image)).delete()
         updateAvatarImage(userName, None)
       }
     } else {
-      fileId.map { fileId =>
+      fileId.foreach { fileId =>
         val filename = "avatar." + FileUtil.getExtension(session.getAndRemove(Keys.Session.Upload(fileId)).get)
         val uploadDir = getUserUploadDir(userName)
         if (!uploadDir.exists) {
           uploadDir.mkdirs()
         }
         Thumbnails
-          .of(new java.io.File(getTemporaryDir(session.getId), fileId))
+          .of(new File(getTemporaryDir(session.getId), FileUtil.checkFilename(fileId)))
           .size(324, 324)
-          .toFile(new java.io.File(uploadDir, filename))
+          .toFile(new File(uploadDir, FileUtil.checkFilename(filename)))
         updateAvatarImage(userName, Some(filename))
       }
     }
 
   protected def uniqueUserName: Constraint = new Constraint() {
     override def validate(name: String, value: String, messages: Messages): Option[String] =
-      getAccountByUserName(value, true).map { _ =>
+      getAccountByUserNameIgnoreCase(value, true).map { _ =>
         "User already exists."
       }
   }
@@ -361,13 +359,42 @@ trait AccountManagementControllerBase extends ControllerBase {
       params: Map[String, Seq[String]],
       messages: Messages
     ): Option[String] = {
-      getAccountByMailAddress(value, true)
-        .filter { x =>
-          if (paramName.isEmpty) true else Some(x.userName) != params.optionValue(paramName)
-        }
-        .map { _ =>
-          "Mail address is already registered."
-        }
+      val extraMailAddresses = params.filterKeys(k => k.startsWith("extraMailAddresses"))
+      if (extraMailAddresses.exists {
+            case (k, v) =>
+              v.contains(value)
+          }) {
+        Some("These mail addresses are duplicated.")
+      } else {
+        getAccountByMailAddress(value, true)
+          .collect {
+            case x if paramName.isEmpty || Some(x.userName) != params.optionValue(paramName) =>
+              "Mail address is already registered."
+          }
+      }
+    }
+  }
+
+  protected def uniqueExtraMailAddress(paramName: String = ""): Constraint = new Constraint() {
+    override def validate(
+      name: String,
+      value: String,
+      params: Map[String, Seq[String]],
+      messages: Messages
+    ): Option[String] = {
+      val extraMailAddresses = params.filterKeys(k => k.startsWith("extraMailAddresses"))
+      if (Some(value) == params.optionValue("mailAddress") || extraMailAddresses.count {
+            case (k, v) =>
+              v.contains(value)
+          } > 1) {
+        Some("These mail addresses are duplicated.")
+      } else {
+        getAccountByMailAddress(value, true)
+          .collect {
+            case x if paramName.isEmpty || Some(x.userName) != params.optionValue(paramName) =>
+              "Mail address is already registered."
+          }
+      }
     }
   }
 
@@ -386,9 +413,10 @@ trait AccountManagementControllerBase extends ControllerBase {
     "groups",
     "new"
   )
+
   protected def reservedNames(): Constraint = new Constraint() {
     override def validate(name: String, value: String, messages: Messages): Option[String] =
-      if (allReservedNames.contains(value)) {
+      if (allReservedNames.contains(value.toLowerCase)) {
         Some(s"${value} is reserved")
       } else {
         None

src/main/scala/gitbucket/core/controller/DashboardController.scala

@@ -12,15 +12,24 @@ class DashboardController
     with PullRequestService
     with RepositoryService
     with AccountService
+    with ActivityService
     with CommitsService
     with LabelsService
     with PrioritiesService
+    with WebHookService
+    with WebHookPullRequestService
+    with WebHookPullRequestReviewCommentService
     with MilestonesService
     with UsersAuthenticator
 
 trait DashboardControllerBase extends ControllerBase {
   self: IssuesService with PullRequestService with RepositoryService with AccountService with UsersAuthenticator =>
 
+  get("/dashboard/repos")(usersOnly {
+    val repos = getVisibleRepositories(context.loginAccount, withoutPhysicalInfo = true)
+    html.repos(getGroupNames(context.loginAccount.get.userName), repos, repos)
+  })
+
   get("/dashboard/issues")(usersOnly {
     searchIssues("created_by")
   })
@@ -83,8 +92,7 @@ trait DashboardControllerBase extends ControllerBase {
       },
       filter,
       getGroupNames(userName),
-      Nil,
-      getUserRepositories(userName, withoutPhysicalInfo = true)
+      getVisibleRepositories(context.loginAccount, withoutPhysicalInfo = true)
     )
   }
 
@@ -109,8 +117,7 @@ trait DashboardControllerBase extends ControllerBase {
       },
       filter,
       getGroupNames(userName),
-      Nil,
-      getUserRepositories(userName, withoutPhysicalInfo = true)
+      getVisibleRepositories(context.loginAccount, withoutPhysicalInfo = true)
     )
   }
 

src/main/scala/gitbucket/core/controller/FileUploadController.scala

@@ -1,7 +1,9 @@
 package gitbucket.core.controller
 
+import java.io.File
+
 import gitbucket.core.model.Account
-import gitbucket.core.service.{AccountService, RepositoryService, ReleaseService}
+import gitbucket.core.service.{AccountService, ReleaseService, RepositoryService}
 import gitbucket.core.servlet.Database
 import gitbucket.core.util._
 import gitbucket.core.util.SyntaxSugars._
@@ -31,7 +33,8 @@ class FileUploadController
   post("/image") {
     execute(
       { (file, fileId) =>
-        FileUtils.writeByteArrayToFile(new java.io.File(getTemporaryDir(session.getId), fileId), file.get)
+        FileUtils
+          .writeByteArrayToFile(new File(getTemporaryDir(session.getId), FileUtil.checkFilename(fileId)), file.get)
         session += Keys.Session.Upload(fileId) -> file.name
       },
       FileUtil.isImage
@@ -41,7 +44,8 @@ class FileUploadController
   post("/tmp") {
     execute(
       { (file, fileId) =>
-        FileUtils.writeByteArrayToFile(new java.io.File(getTemporaryDir(session.getId), fileId), file.get)
+        FileUtils
+          .writeByteArrayToFile(new File(getTemporaryDir(session.getId), FileUtil.checkFilename(fileId)), file.get)
         session += Keys.Session.Upload(fileId) -> file.name
       },
       _ => true
@@ -52,9 +56,9 @@ class FileUploadController
     execute(
       { (file, fileId) =>
         FileUtils.writeByteArrayToFile(
-          new java.io.File(
+          new File(
             getAttachedDir(params("owner"), params("repository")),
-            fileId + "." + FileUtil.getExtension(file.getName)
+            FileUtil.checkFilename(fileId + "." + FileUtil.getExtension(file.getName))
           ),
           file.get
         )
@@ -129,12 +133,15 @@ class FileUploadController
           val owner = params("owner")
           val repository = params("repository")
           val tag = params("tag")
-          execute({ (file, fileId) =>
-            FileUtils.writeByteArrayToFile(
-              new java.io.File(getReleaseFilesDir(owner, repository), tag + "/" + fileId),
-              file.get
-            )
-          }, _ => true)
+          execute(
+            { (file, fileId) =>
+              FileUtils.writeByteArrayToFile(
+                new File(getReleaseFilesDir(owner, repository), FileUtil.checkFilename(tag + "/" + fileId)),
+                file.get
+              )
+            },
+            _ => true
+          )
       }
       .getOrElse(BadRequest())
   }

src/main/scala/gitbucket/core/controller/IndexController.scala

@@ -9,7 +9,7 @@ import gitbucket.core.model.Account
 import gitbucket.core.service._
 import gitbucket.core.util.Implicits._
 import gitbucket.core.util.SyntaxSugars._
-import gitbucket.core.util.{Keys, LDAPUtil, ReferrerAuthenticator, UsersAuthenticator}
+import gitbucket.core.util._
 import org.scalatra.Ok
 import org.scalatra.forms._
 
@@ -64,8 +64,7 @@ trait IndexControllerBase extends ControllerBase {
         val visibleOwnerSet: Set[String] = Set(account.userName) ++ getGroupsByUserName(account.userName)
         gitbucket.core.html.index(
           getRecentActivitiesByOwners(visibleOwnerSet),
-          Nil,
-          getUserRepositories(account.userName, withoutPhysicalInfo = true),
+          getVisibleRepositories(Some(account), withoutPhysicalInfo = true),
           showBannerToCreatePersonalAccessToken = hasAccountFederation(account.userName) && !hasAccessToken(
             account.userName
           )
@@ -75,7 +74,6 @@ trait IndexControllerBase extends ControllerBase {
         gitbucket.core.html.index(
           getRecentActivities(),
           getVisibleRepositories(None, withoutPhysicalInfo = true),
-          Nil,
           showBannerToCreatePersonalAccessToken = false
         )
       }
@@ -208,7 +206,7 @@ trait IndexControllerBase extends ControllerBase {
             }
             .map { t =>
               Map(
-                "label" -> s"<b>@${t.userName}</b> ${t.fullName}",
+                "label" -> s"<b>@${StringUtil.escapeHtml(t.userName)}</b> ${StringUtil.escapeHtml(t.fullName)}",
                 "value" -> t.userName
               )
             }
@@ -222,7 +220,7 @@ trait IndexControllerBase extends ControllerBase {
    * Returns a single string which is any of "group", "user" or "".
    */
   post("/_user/existence")(usersOnly {
-    getAccountByUserName(params("userName")).map { account =>
+    getAccountByUserNameIgnoreCase(params("userName")).map { account =>
       if (account.isGroupAccount) "group" else "user"
     } getOrElse ""
   })
@@ -239,9 +237,19 @@ trait IndexControllerBase extends ControllerBase {
         }
 
         target.toLowerCase match {
-          case "issue" =>
+          case "issues" =>
             gitbucket.core.search.html.issues(
-              if (query.nonEmpty) searchIssues(repository.owner, repository.name, query) else Nil,
+              if (query.nonEmpty) searchIssues(repository.owner, repository.name, query, false) else Nil,
+              false,
+              query,
+              page,
+              repository
+            )
+
+          case "pulls" =>
+            gitbucket.core.search.html.issues(
+              if (query.nonEmpty) searchIssues(repository.owner, repository.name, query, true) else Nil,
+              true,
               query,
               page,
               repository
@@ -273,18 +281,7 @@ trait IndexControllerBase extends ControllerBase {
     val repositories = visibleRepositories.filter { repository =>
       repository.name.toLowerCase.indexOf(query) >= 0 || repository.owner.toLowerCase.indexOf(query) >= 0
     }
-    context.loginAccount
-      .map { account =>
-        gitbucket.core.search.html.repositories(
-          query,
-          repositories,
-          Nil,
-          getUserRepositories(account.userName, withoutPhysicalInfo = true)
-        )
-      }
-      .getOrElse {
-        gitbucket.core.search.html.repositories(query, repositories, visibleRepositories, Nil)
-      }
+    gitbucket.core.search.html.repositories(query, repositories, visibleRepositories)
   }
 
 }

src/main/scala/gitbucket/core/controller/IssuesController.scala

@@ -26,6 +26,7 @@ class IssuesController
     with WritableUsersAuthenticator
     with PullRequestService
     with WebHookIssueCommentService
+    with WebHookPullRequestReviewCommentService
     with CommitsService
     with PrioritiesService
 
@@ -154,15 +155,25 @@ trait IssuesControllerBase extends ControllerBase {
   ajaxPost("/:owner/:repository/issues/edit_title/:id", issueTitleEditForm)(readableUsersOnly { (title, repository) =>
     defining(repository.owner, repository.name) {
       case (owner, name) =>
-        getIssue(owner, name, params("id")).map { issue =>
-          if (isEditableContent(owner, name, issue.openedUserName)) {
-            // update issue
-            updateIssue(owner, name, issue.issueId, title, issue.content)
-            // extract references and create refer comment
-            createReferComment(owner, name, issue.copy(title = title), title, context.loginAccount.get)
-
-            redirect(s"/${owner}/${name}/issues/_data/${issue.issueId}")
-          } else Unauthorized()
+        getIssue(owner, name, params("id")).map {
+          issue =>
+            if (isEditableContent(owner, name, issue.openedUserName)) {
+              if (issue.title != title) {
+                // update issue
+                updateIssue(owner, name, issue.issueId, title, issue.content)
+                // extract references and create refer comment
+                createReferComment(owner, name, issue.copy(title = title), title, context.loginAccount.get)
+                createComment(
+                  owner,
+                  name,
+                  context.loginAccount.get.userName,
+                  issue.issueId,
+                  issue.title + "\r\n" + title,
+                  "change_title"
+                )
+              }
+              redirect(s"/${owner}/${name}/issues/_data/${issue.issueId}")
+            } else Unauthorized()
         } getOrElse NotFound()
     }
   })
@@ -246,6 +257,7 @@ trait IssuesControllerBase extends ControllerBase {
                 "content" -> Markdown.toHtml(
                   markdown = x.content getOrElse "No description given.",
                   repository = repository,
+                  branch = repository.repository.defaultBranch,
                   enableWikiLink = false,
                   enableRefsLink = true,
                   enableAnchor = true,
@@ -273,6 +285,7 @@ trait IssuesControllerBase extends ControllerBase {
                 "content" -> view.Markdown.toHtml(
                   markdown = x.content,
                   repository = repository,
+                  branch = repository.repository.defaultBranch,
                   enableWikiLink = false,
                   enableRefsLink = true,
                   enableAnchor = true,
@@ -396,7 +409,7 @@ trait IssuesControllerBase extends ControllerBase {
       case dir if (dir.exists && dir.isDirectory) =>
         dir.listFiles.find(_.getName.startsWith(params("file") + ".")).map { file =>
           response.setHeader("Content-Disposition", f"""inline; filename=${file.getName}""")
-          RawData(FileUtil.getMimeType(file.getName), file)
+          RawData(FileUtil.getSafeMimeType(file.getName), file)
         }
       case _ => None
     }) getOrElse NotFound()

src/main/scala/gitbucket/core/controller/PreProcessController.scala

@@ -1,5 +1,6 @@
 package gitbucket.core.controller
 
+import gitbucket.core.plugin.PluginRegistry
 import org.scalatra.MovedPermanently
 
 class PreProcessController extends PreProcessControllerBase
@@ -7,20 +8,21 @@ class PreProcessController extends PreProcessControllerBase
 trait PreProcessControllerBase extends ControllerBase {
 
   /**
-   * Provides GitHub compatible URLs for Git client.
-   *
-   * <ul>
-   *   <li>git clone http://localhost:8080/owner/repo</li>
-   *   <li>git clone http://localhost:8080/owner/repo.git</li>
-   * </ul>
-   *
-   * @see https://git-scm.com/book/en/v2/Git-Internals-Transfer-Protocols
+   * Provides GitHub compatible URLs (e.g. http://localhost:8080/owner/repo.git) for Git client.
    */
   get("/*/*/info/refs") {
     val query = Option(request.getQueryString).map("?" + _).getOrElse("")
     halt(MovedPermanently(baseUrl + "/git" + request.getRequestURI + query))
   }
 
+  /**
+   * Provides GitHub compatible URLs for GitLFS client.
+   */
+  post("/*/*/info/lfs/objects/batch") {
+    val dispatcher = request.getRequestDispatcher("/git" + request.getRequestURI)
+    dispatcher.forward(request, response)
+  }
+
   /**
    * Filter requests from anonymous users.
    *
@@ -29,7 +31,10 @@ trait PreProcessControllerBase extends ControllerBase {
    */
   get(!context.settings.allowAnonymousAccess, context.loginAccount.isEmpty) {
     if (!context.currentPath.startsWith("/assets") && !context.currentPath.startsWith("/signin") &&
-        !context.currentPath.startsWith("/register") && !context.currentPath.endsWith("/info/refs")) {
+        !context.currentPath.startsWith("/register") && !context.currentPath.endsWith("/info/refs") &&
+        !PluginRegistry().getAnonymousAccessiblePaths().exists { path =>
+          context.currentPath.startsWith(path)
+        }) {
       Unauthorized()
     } else {
       pass()

src/main/scala/gitbucket/core/controller/PullRequestsController.scala

@@ -1,6 +1,6 @@
 package gitbucket.core.controller
 
-import gitbucket.core.model.WebHook
+import gitbucket.core.model.{CommitComment, CommitComments, IssueComment, WebHook}
 import gitbucket.core.plugin.PluginRegistry
 import gitbucket.core.pulls.html
 import gitbucket.core.service.CommitStatusService
@@ -15,7 +15,7 @@ import gitbucket.core.util.Implicits._
 import gitbucket.core.util._
 import org.scalatra.forms._
 import org.eclipse.jgit.api.Git
-import org.eclipse.jgit.lib.PersonIdent
+import org.eclipse.jgit.lib.{ObjectId, PersonIdent}
 import org.eclipse.jgit.revwalk.RevWalk
 import org.scalatra.BadRequest
 
@@ -32,6 +32,7 @@ class PullRequestsController
     with CommitsService
     with ActivityService
     with WebHookPullRequestService
+    with WebHookPullRequestReviewCommentService
     with ReadableUsersAuthenticator
     with ReferrerAuthenticator
     with WritableUsersAuthenticator
@@ -113,33 +114,92 @@ trait PullRequestsControllerBase extends ControllerBase {
         val name = repository.name
         getPullRequest(owner, name, issueId) map {
           case (issue, pullreq) =>
-            using(Git.open(getRepositoryDir(owner, name))) {
-              git =>
-                val (commits, diffs) =
-                  getRequestCompareInfo(owner, name, pullreq.commitIdFrom, owner, name, pullreq.commitIdTo)
-                html.pullreq(
-                  issue,
-                  pullreq,
-                  (commits.flatten
-                    .map(commit => getCommitComments(owner, name, commit.id, true))
-                    .flatten
-                    .toList ::: getComments(owner, name, issueId))
-                    .sortWith((a, b) => a.registeredDate before b.registeredDate),
-                  getIssueLabels(owner, name, issueId),
-                  getAssignableUserNames(owner, name),
-                  getMilestonesWithIssueCount(owner, name),
-                  getPriorities(owner, name),
-                  getLabels(owner, name),
-                  commits,
-                  diffs,
-                  isEditable(repository),
-                  isManageable(repository),
-                  hasDeveloperRole(pullreq.requestUserName, pullreq.requestRepositoryName, context.loginAccount),
-                  repository,
-                  getRepository(pullreq.requestUserName, pullreq.requestRepositoryName),
-                  flash.toMap.map(f => f._1 -> f._2.toString)
-                )
-            }
+            val (commits, diffs) =
+              getRequestCompareInfo(owner, name, pullreq.commitIdFrom, owner, name, pullreq.commitIdTo)
+
+            html.conversation(
+              issue,
+              pullreq,
+              commits.flatten,
+              getPullRequestComments(owner, name, issue.issueId, commits.flatten),
+              diffs.size,
+              getIssueLabels(owner, name, issueId),
+              getAssignableUserNames(owner, name),
+              getMilestonesWithIssueCount(owner, name),
+              getPriorities(owner, name),
+              getLabels(owner, name),
+              isEditable(repository),
+              isManageable(repository),
+              hasDeveloperRole(pullreq.requestUserName, pullreq.requestRepositoryName, context.loginAccount),
+              repository,
+              getRepository(pullreq.requestUserName, pullreq.requestRepositoryName),
+              flash.toMap.map(f => f._1 -> f._2.toString)
+            )
+
+//                html.pullreq(
+//                  issue,
+//                  pullreq,
+//                  comments,
+//                  getIssueLabels(owner, name, issueId),
+//                  getAssignableUserNames(owner, name),
+//                  getMilestonesWithIssueCount(owner, name),
+//                  getPriorities(owner, name),
+//                  getLabels(owner, name),
+//                  commits,
+//                  diffs,
+//                  isEditable(repository),
+//                  isManageable(repository),
+//                  hasDeveloperRole(pullreq.requestUserName, pullreq.requestRepositoryName, context.loginAccount),
+//                  repository,
+//                  getRepository(pullreq.requestUserName, pullreq.requestRepositoryName),
+//                  flash.toMap.map(f => f._1 -> f._2.toString)
+//                )
+        }
+    } getOrElse NotFound()
+  })
+
+  get("/:owner/:repository/pull/:id/commits")(referrersOnly { repository =>
+    params("id").toIntOpt.flatMap {
+      issueId =>
+        val owner = repository.owner
+        val name = repository.name
+        getPullRequest(owner, name, issueId) map {
+          case (issue, pullreq) =>
+            val (commits, diffs) =
+              getRequestCompareInfo(owner, name, pullreq.commitIdFrom, owner, name, pullreq.commitIdTo)
+
+            html.commits(
+              issue,
+              pullreq,
+              commits,
+              getPullRequestComments(owner, name, issue.issueId, commits.flatten),
+              diffs.size,
+              isManageable(repository),
+              repository
+            )
+        }
+    } getOrElse NotFound()
+  })
+
+  get("/:owner/:repository/pull/:id/files")(referrersOnly { repository =>
+    params("id").toIntOpt.flatMap {
+      issueId =>
+        val owner = repository.owner
+        val name = repository.name
+        getPullRequest(owner, name, issueId) map {
+          case (issue, pullreq) =>
+            val (commits, diffs) =
+              getRequestCompareInfo(owner, name, pullreq.commitIdFrom, owner, name, pullreq.commitIdTo)
+
+            html.files(
+              issue,
+              pullreq,
+              diffs,
+              commits.flatten,
+              getPullRequestComments(owner, name, issue.issueId, commits.flatten),
+              isManageable(repository),
+              repository
+            )
         }
     } getOrElse NotFound()
   })
@@ -235,11 +295,12 @@ trait PullRequestsControllerBase extends ControllerBase {
       issueId <- params("id").toIntOpt
       loginAccount <- context.loginAccount
       (issue, pullreq) <- getPullRequest(baseRepository.owner, baseRepository.name, issueId)
+      repository <- getRepository(pullreq.requestUserName, pullreq.requestRepositoryName)
+      remoteRepository <- getRepository(pullreq.userName, pullreq.repositoryName)
       owner = pullreq.requestUserName
       name = pullreq.requestRepositoryName
       if hasDeveloperRole(owner, name, context.loginAccount)
     } yield {
-      val repository = getRepository(owner, name).get
       val branchProtection = getProtectedBranchInfo(owner, name, pullreq.requestBranch)
       if (branchProtection.needStatusCheck(loginAccount.userName)) {
         flash += "error" -> s"branch ${pullreq.requestBranch} is protected need status check."
@@ -255,74 +316,19 @@ trait PullRequestsControllerBase extends ControllerBase {
             JGitUtil.getAllCommitIds(git)
           }.toSet
           pullRemote(
-            owner,
-            name,
+            repository,
             pullreq.requestBranch,
-            pullreq.userName,
-            pullreq.repositoryName,
+            remoteRepository,
             pullreq.branch,
             loginAccount,
-            s"Merge branch '${alias}' into ${pullreq.requestBranch}"
+            s"Merge branch '${alias}' into ${pullreq.requestBranch}",
+            Some(pullreq)
           ) match {
             case None => // conflict
               flash += "error" -> s"Can't automatic merging branch '${alias}' into ${pullreq.requestBranch}."
             case Some(oldId) =>
               // update pull request
-              updatePullRequests(owner, name, pullreq.requestBranch)
-
-              using(Git.open(Directory.getRepositoryDir(owner, name))) {
-                git =>
-                  //  after update branch
-                  val newCommitId = git.getRepository.resolve(s"refs/heads/${pullreq.requestBranch}")
-                  val commits = git.log
-                    .addRange(oldId, newCommitId)
-                    .call
-                    .iterator
-                    .asScala
-                    .map(c => new JGitUtil.CommitInfo(c))
-                    .toList
-
-                  commits.foreach { commit =>
-                    if (!existIds.contains(commit.id)) {
-                      createIssueComment(owner, name, commit)
-                    }
-                  }
-
-                  // record activity
-                  recordPushActivity(owner, name, loginAccount.userName, pullreq.branch, commits)
-
-                  // close issue by commit message
-                  if (pullreq.requestBranch == repository.repository.defaultBranch) {
-                    commits.map { commit =>
-                      closeIssuesFromMessage(commit.fullMessage, loginAccount.userName, owner, name)
-                    }
-                  }
-
-                  // call web hook
-                  callPullRequestWebHookByRequestBranch(
-                    "synchronize",
-                    repository,
-                    pullreq.requestBranch,
-                    baseUrl,
-                    loginAccount
-                  )
-                  callWebHookOf(owner, name, WebHook.Push) {
-                    for {
-                      ownerAccount <- getAccountByUserName(owner)
-                    } yield {
-                      WebHookService.WebHookPushPayload(
-                        git,
-                        loginAccount,
-                        pullreq.requestBranch,
-                        repository,
-                        commits,
-                        ownerAccount,
-                        oldId = oldId,
-                        newId = newCommitId
-                      )
-                    }
-                  }
-              }
+              updatePullRequests(owner, name, pullreq.requestBranch, loginAccount, "synchronize")
               flash += "info" -> s"Merge branch '${alias}' into ${pullreq.requestBranch}"
           }
         }
@@ -333,99 +339,14 @@ trait PullRequestsControllerBase extends ControllerBase {
   })
 
   post("/:owner/:repository/pull/:id/merge", mergeForm)(writableUsersOnly { (form, repository) =>
-    params("id").toIntOpt.flatMap {
-      issueId =>
-        val owner = repository.owner
-        val name = repository.name
-        if (repository.repository.options.mergeOptions.split(",").contains(form.strategy)) {
-          LockUtil.lock(s"${owner}/${name}") {
-            getPullRequest(owner, name, issueId).map {
-              case (issue, pullreq) =>
-                using(Git.open(getRepositoryDir(owner, name))) {
-                  git =>
-                    // mark issue as merged and close.
-                    val loginAccount = context.loginAccount.get
-                    val commentId = createComment(owner, name, loginAccount.userName, issueId, form.message, "merge")
-                    createComment(owner, name, loginAccount.userName, issueId, "Close", "close")
-                    updateClosed(owner, name, issueId, true)
+    params("id").toIntOpt.flatMap { issueId =>
+      val owner = repository.owner
+      val name = repository.name
 
-                    // record activity
-                    recordMergeActivity(owner, name, loginAccount.userName, issueId, form.message)
-
-                    val (commits, _) = getRequestCompareInfo(
-                      owner,
-                      name,
-                      pullreq.commitIdFrom,
-                      pullreq.requestUserName,
-                      pullreq.requestRepositoryName,
-                      pullreq.commitIdTo
-                    )
-
-                    val revCommits = using(new RevWalk(git.getRepository)) { revWalk =>
-                      commits.flatten.map { commit =>
-                        revWalk.parseCommit(git.getRepository.resolve(commit.id))
-                      }
-                    }.reverse
-
-                    // merge git repository
-                    form.strategy match {
-                      case "merge-commit" =>
-                        mergePullRequest(
-                          git,
-                          pullreq.branch,
-                          issueId,
-                          s"Merge pull request #${issueId} from ${pullreq.requestUserName}/${pullreq.requestBranch}\n\n" + form.message,
-                          new PersonIdent(loginAccount.fullName, loginAccount.mailAddress)
-                        )
-                      case "rebase" =>
-                        rebasePullRequest(
-                          git,
-                          pullreq.branch,
-                          issueId,
-                          revCommits,
-                          new PersonIdent(loginAccount.fullName, loginAccount.mailAddress)
-                        )
-                      case "squash" =>
-                        squashPullRequest(
-                          git,
-                          pullreq.branch,
-                          issueId,
-                          s"${issue.title} (#${issueId})\n\n" + form.message,
-                          new PersonIdent(loginAccount.fullName, loginAccount.mailAddress)
-                        )
-                    }
-
-                    // close issue by content of pull request
-                    val defaultBranch = getRepository(owner, name).get.repository.defaultBranch
-                    if (pullreq.branch == defaultBranch) {
-                      commits.flatten.foreach { commit =>
-                        closeIssuesFromMessage(commit.fullMessage, loginAccount.userName, owner, name)
-                      }
-                      closeIssuesFromMessage(
-                        issue.title + " " + issue.content.getOrElse(""),
-                        loginAccount.userName,
-                        owner,
-                        name
-                      )
-                      closeIssuesFromMessage(form.message, loginAccount.userName, owner, name)
-                    }
-
-                    updatePullRequests(owner, name, pullreq.branch)
-
-                    // call web hook
-                    callPullRequestWebHook("closed", repository, issueId, context.baseUrl, context.loginAccount.get)
-
-                    // call hooks
-                    PluginRegistry().getPullRequestHooks.foreach { h =>
-                      h.addedComment(commentId, form.message, issue, repository)
-                      h.merged(issue, repository)
-                    }
-
-                    redirect(s"/${owner}/${name}/pull/${issueId}")
-                }
-            }
-          }
-        } else Some(BadRequest())
+      mergePullRequest(repository, issueId, context.loginAccount.get, form.message, form.strategy) match {
+        case Right(objectId) => redirect(s"/${owner}/${name}/pull/${issueId}")
+        case Left(message)   => Some(BadRequest())
+      }
     } getOrElse NotFound()
   })
 
@@ -491,97 +412,68 @@ trait PullRequestsControllerBase extends ControllerBase {
               .map(_.repository.repositoryName)
           };
           originRepository <- getRepository(originOwner, originRepositoryName)) yield {
-      using(
-        Git.open(getRepositoryDir(originRepository.owner, originRepository.name)),
-        Git.open(getRepositoryDir(forkedRepository.owner, forkedRepository.name))
-      ) {
-        case (oldGit, newGit) =>
-          val (oldId, newId) =
-            if (originRepository.branchList.contains(originId)) {
-              val forkedId2 =
-                forkedRepository.tags.collectFirst { case x if x.name == forkedId => x.id }.getOrElse(forkedId)
+      val (oldId, newId) =
+        getPullRequestCommitFromTo(originRepository, forkedRepository, originId, forkedId)
 
-              val originId2 = JGitUtil.getForkedCommitId(
-                oldGit,
-                newGit,
-                originRepository.owner,
-                originRepository.name,
-                originId,
-                forkedRepository.owner,
-                forkedRepository.name,
-                forkedId2
-              )
+      (oldId, newId) match {
+        case (Some(oldId), Some(newId)) => {
+          val (commits, diffs) = getRequestCompareInfo(
+            originRepository.owner,
+            originRepository.name,
+            oldId.getName,
+            forkedRepository.owner,
+            forkedRepository.name,
+            newId.getName
+          )
 
-              (Option(oldGit.getRepository.resolve(originId2)), Option(newGit.getRepository.resolve(forkedId2)))
-
-            } else {
-              val originId2 =
-                originRepository.tags.collectFirst { case x if x.name == originId => x.id }.getOrElse(originId)
-              val forkedId2 =
-                forkedRepository.tags.collectFirst { case x if x.name == forkedId => x.id }.getOrElse(forkedId)
-
-              (Option(oldGit.getRepository.resolve(originId2)), Option(newGit.getRepository.resolve(forkedId2)))
-            }
-
-          (oldId, newId) match {
-            case (Some(oldId), Some(newId)) => {
-              val (commits, diffs) = getRequestCompareInfo(
-                originRepository.owner,
-                originRepository.name,
-                oldId.getName,
-                forkedRepository.owner,
-                forkedRepository.name,
-                newId.getName
-              )
-
-              val title = if (commits.flatten.length == 1) {
-                commits.flatten.head.shortMessage
-              } else {
-                val text = forkedId.replaceAll("[\\-_]", " ")
-                text.substring(0, 1).toUpperCase + text.substring(1)
-              }
-
-              html.compare(
-                title,
-                commits,
-                diffs,
-                ((forkedRepository.repository.originUserName, forkedRepository.repository.originRepositoryName) match {
-                  case (Some(userName), Some(repositoryName)) =>
-                    getRepository(userName, repositoryName) match {
-                      case Some(x) => x.repository :: getForkedRepositories(userName, repositoryName)
-                      case None    => getForkedRepositories(userName, repositoryName)
-                    }
-                  case _ =>
-                    forkedRepository.repository :: getForkedRepositories(forkedRepository.owner, forkedRepository.name)
-                }).map { repository =>
-                  (repository.userName, repository.repositoryName)
-                },
-                commits.flatten
-                  .map(commit => getCommitComments(forkedRepository.owner, forkedRepository.name, commit.id, false))
-                  .flatten
-                  .toList,
-                originId,
-                forkedId,
-                oldId.getName,
-                newId.getName,
-                getContentTemplate(originRepository, "PULL_REQUEST_TEMPLATE"),
-                forkedRepository,
-                originRepository,
-                forkedRepository,
-                hasDeveloperRole(originRepository.owner, originRepository.name, context.loginAccount),
-                getAssignableUserNames(originRepository.owner, originRepository.name),
-                getMilestones(originRepository.owner, originRepository.name),
-                getPriorities(originRepository.owner, originRepository.name),
-                getLabels(originRepository.owner, originRepository.name)
-              )
-            }
-            case (oldId, newId) =>
-              redirect(
-                s"/${forkedRepository.owner}/${forkedRepository.name}/compare/" +
-                  s"${originOwner}:${oldId.map(_ => originId).getOrElse(originRepository.repository.defaultBranch)}..." +
-                  s"${forkedOwner}:${newId.map(_ => forkedId).getOrElse(forkedRepository.repository.defaultBranch)}"
-              )
+          val title = if (commits.flatten.length == 1) {
+            commits.flatten.head.shortMessage
+          } else {
+            val text = forkedId.replaceAll("[\\-_]", " ")
+            text.substring(0, 1).toUpperCase + text.substring(1)
           }
+
+          html.compare(
+            title,
+            commits,
+            diffs,
+            ((forkedRepository.repository.originUserName, forkedRepository.repository.originRepositoryName) match {
+              case (Some(userName), Some(repositoryName)) =>
+                getRepository(userName, repositoryName) match {
+                  case Some(x) => x.repository :: getForkedRepositories(userName, repositoryName)
+                  case None    => getForkedRepositories(userName, repositoryName)
+                }
+              case _ =>
+                forkedRepository.repository :: getForkedRepositories(forkedRepository.owner, forkedRepository.name)
+            }).map { repository =>
+              (repository.userName, repository.repositoryName, repository.defaultBranch)
+            },
+            commits.flatten
+              .map(commit => getCommitComments(forkedRepository.owner, forkedRepository.name, commit.id, false))
+              .flatten
+              .toList,
+            originId,
+            forkedId,
+            oldId.getName,
+            newId.getName,
+            getContentTemplate(originRepository, "PULL_REQUEST_TEMPLATE"),
+            forkedRepository,
+            originRepository,
+            forkedRepository,
+            hasDeveloperRole(originRepository.owner, originRepository.name, context.loginAccount),
+            getAssignableUserNames(originRepository.owner, originRepository.name),
+            getMilestones(originRepository.owner, originRepository.name),
+            getPriorities(originRepository.owner, originRepository.name),
+            getLabels(originRepository.owner, originRepository.name)
+          )
+        }
+        case (oldId, newId) =>
+          redirect(
+            s"/${forkedRepository.owner}/${forkedRepository.name}/compare/" +
+              s"${originOwner}:${oldId.map(_ => originId).getOrElse(originRepository.repository.defaultBranch)}..." +
+              s"${forkedOwner}:${newId.map(_ => forkedId).getOrElse(forkedRepository.repository.defaultBranch)}"
+          )
+
       }
     }) getOrElse NotFound()
   })
@@ -655,7 +547,7 @@ trait PullRequestsControllerBase extends ControllerBase {
 
         // insert labels
         if (manageable) {
-          form.labelNames.map { value =>
+          form.labelNames.foreach { value =>
             val labels = getLabels(owner, name)
             value.split(",").foreach { labelName =>
               labels.find(_.labelName == labelName).map { label =>
@@ -672,7 +564,7 @@ trait PullRequestsControllerBase extends ControllerBase {
         recordPullRequestActivity(owner, name, loginUserName, issueId, form.title)
 
         // call web hook
-        callPullRequestWebHook("opened", repository, issueId, context.baseUrl, context.loginAccount.get)
+        callPullRequestWebHook("opened", repository, issueId, context.loginAccount.get)
 
         getIssue(owner, name, issueId.toString) foreach { issue =>
           // extract references and create refer comment
@@ -693,6 +585,10 @@ trait PullRequestsControllerBase extends ControllerBase {
   })
 
   ajaxGet("/:owner/:repository/pulls/proposals")(readableUsersOnly { repository =>
+    val thresholdTime = System.currentTimeMillis() - (1000 * 60 * 60)
+    val mailAddresses =
+      context.loginAccount.map(x => Seq(x.mailAddress) ++ getAccountExtraMailAddresses(x.userName)).getOrElse(Nil)
+
     val branches = JGitUtil
       .getBranches(
         owner = repository.owner,
@@ -700,8 +596,14 @@ trait PullRequestsControllerBase extends ControllerBase {
         defaultBranch = repository.repository.defaultBranch,
         origin = repository.repository.originUserName.isEmpty
       )
-      .filter(x => x.mergeInfo.map(_.ahead).getOrElse(0) > 0 && x.mergeInfo.map(_.behind).getOrElse(0) == 0)
-      .sortBy(br => (br.mergeInfo.isEmpty, br.commitTime))
+      .filter { x =>
+        x.mergeInfo.map(_.ahead).getOrElse(0) > 0 && x.mergeInfo.map(_.behind).getOrElse(0) == 0 &&
+        x.commitTime.getTime > thresholdTime &&
+        mailAddresses.contains(x.committerEmailAddress)
+      }
+      .sortBy { br =>
+        (br.mergeInfo.isEmpty, br.commitTime)
+      }
       .map(_.name)
       .reverse
 
@@ -722,20 +624,6 @@ trait PullRequestsControllerBase extends ControllerBase {
     html.proposals(proposedBranches, targetRepository, repository)
   })
 
-  /**
-   * Parses branch identifier and extracts owner and branch name as tuple.
-   *
-   * - "owner:branch" to ("owner", "branch")
-   * - "branch" to ("defaultOwner", "branch")
-   */
-  private def parseCompareIdentifier(value: String, defaultOwner: String): (String, String) =
-    if (value.contains(':')) {
-      val array = value.split(":")
-      (array(0), array(1))
-    } else {
-      (defaultOwner, value)
-    }
-
   private def searchPullRequests(userName: Option[String], repository: RepositoryService.RepositoryInfo) =
     defining(repository.owner, repository.name) {
       case (owner, repoName) =>

src/main/scala/gitbucket/core/controller/ReleasesController.scala

@@ -3,13 +3,14 @@ package gitbucket.core.controller
 import java.io.File
 
 import gitbucket.core.service.{AccountService, ActivityService, ReleaseService, RepositoryService}
-import gitbucket.core.util.{FileUtil, ReadableUsersAuthenticator, ReferrerAuthenticator, WritableUsersAuthenticator}
+import gitbucket.core.util._
 import gitbucket.core.util.Directory._
 import gitbucket.core.util.Implicits._
 import org.scalatra.forms._
 import gitbucket.core.releases.html
+import gitbucket.core.util.SyntaxSugars.using
 import org.apache.commons.io.FileUtils
-import scala.collection.JavaConverters._
+import org.eclipse.jgit.api.Git
 
 class ReleaseController
     extends ReleaseControllerBase
@@ -79,18 +80,20 @@ trait ReleaseControllerBase extends ControllerBase {
     } yield {
       response.setHeader("Content-Disposition", s"attachment; filename=${asset.label}")
       RawData(
-        FileUtil.getMimeType(asset.label),
-        new File(getReleaseFilesDir(repository.owner, repository.name), tagName + "/" + fileId)
+        FileUtil.getSafeMimeType(asset.label),
+        new File(getReleaseFilesDir(repository.owner, repository.name), FileUtil.checkFilename(tagName + "/" + fileId))
       )
     }).getOrElse(NotFound())
   })
 
   get("/:owner/:repository/releases/:tag/create")(writableUsersOnly { repository =>
     val tagName = params("tag")
+    val previousTags = repository.tags.takeWhile(_.name != tagName).reverse
+
     repository.tags
       .find(_.name == tagName)
       .map { tag =>
-        html.form(repository, tag, None)
+        html.form(repository, tag, previousTags.map(_.name), tag.message, None)
       }
       .getOrElse(NotFound())
   })
@@ -111,7 +114,10 @@ trait ReleaseControllerBase extends ControllerBase {
     files.foreach {
       case (fileId, fileName) =>
         val size =
-          new java.io.File(getReleaseFilesDir(repository.owner, repository.name), tagName + "/" + fileId).length
+          new File(
+            getReleaseFilesDir(repository.owner, repository.name),
+            FileUtil.checkFilename(tagName + "/" + fileId)
+          ).length
         createReleaseAsset(repository.owner, repository.name, tagName, fileId, fileName, size, loginAccount)
     }
 
@@ -120,14 +126,37 @@ trait ReleaseControllerBase extends ControllerBase {
     redirect(s"/${repository.owner}/${repository.name}/releases/${tagName}")
   })
 
+  get("/:owner/:repository/changelog/*...*")(writableUsersOnly { repository =>
+    val Seq(previousTag, currentTag) = multiParams("splat")
+    val previousTagId = repository.tags.collectFirst { case x if x.name == previousTag => x.id }.getOrElse("")
+
+    val commitLog = using(Git.open(getRepositoryDir(repository.owner, repository.name))) { git =>
+      val commits = JGitUtil.getCommitLog(git, previousTagId, currentTag).reverse
+      commits
+        .map { commit =>
+          s"- ${commit.shortMessage} ${commit.id}"
+        }
+        .mkString("\n")
+    }
+
+    commitLog
+  })
+
   get("/:owner/:repository/releases/:tag/edit")(writableUsersOnly { repository =>
     val tagName = params("tag")
+    val previousTags = repository.tags.takeWhile(_.name != tagName).reverse
 
     (for {
       release <- getRelease(repository.owner, repository.name, tagName)
       tag <- repository.tags.find(_.name == tagName)
     } yield {
-      html.form(repository, tag, Some(release, getReleaseAssets(repository.owner, repository.name, tagName)))
+      html.form(
+        repository,
+        tag,
+        previousTags.map(_.name),
+        release.content.getOrElse(""),
+        Some(release, getReleaseAssets(repository.owner, repository.name, tagName))
+      )
     }).getOrElse(NotFound())
   })
 
@@ -153,15 +182,18 @@ trait ReleaseControllerBase extends ControllerBase {
           files.foreach {
             case (fileId, fileName) =>
               val size =
-                new java.io.File(getReleaseFilesDir(repository.owner, repository.name), tagName + "/" + fileId).length
+                new File(
+                  getReleaseFilesDir(repository.owner, repository.name),
+                  FileUtil.checkFilename(tagName + "/" + fileId)
+                ).length
               createReleaseAsset(repository.owner, repository.name, tagName, fileId, fileName, size, loginAccount)
           }
 
           assets.foreach { asset =>
             if (!files.exists { case (fileId, _) => fileId == asset.fileName }) {
-              val file = new java.io.File(
+              val file = new File(
                 getReleaseFilesDir(repository.owner, repository.name),
-                release.tag + "/" + asset.fileName
+                FileUtil.checkFilename(release.tag + "/" + asset.fileName)
               )
               FileUtils.forceDelete(file)
             }
@@ -175,7 +207,9 @@ trait ReleaseControllerBase extends ControllerBase {
   post("/:owner/:repository/releases/:tag/delete")(writableUsersOnly { repository =>
     val tagName = params("tag")
     getRelease(repository.owner, repository.name, tagName).foreach { release =>
-      FileUtils.deleteDirectory(new File(getReleaseFilesDir(repository.owner, repository.name), release.tag))
+      FileUtils.deleteDirectory(
+        new File(getReleaseFilesDir(repository.owner, repository.name), FileUtil.checkFilename(release.tag))
+      )
     }
     deleteRelease(repository.owner, repository.name, tagName)
     redirect(s"/${repository.owner}/${repository.name}/releases")

src/main/scala/gitbucket/core/controller/RepositorySettingsController.scala

@@ -13,13 +13,11 @@ import gitbucket.core.util.SyntaxSugars._
 import gitbucket.core.util.Implicits._
 import gitbucket.core.util.Directory._
 import org.scalatra.forms._
-import org.apache.commons.io.FileUtils
 import org.scalatra.i18n.Messages
 import org.eclipse.jgit.api.Git
 import org.eclipse.jgit.lib.Constants
 import org.eclipse.jgit.lib.ObjectId
 import gitbucket.core.model.WebHookContentType
-import gitbucket.core.plugin.PluginRegistry
 
 class RepositorySettingsController
     extends RepositorySettingsControllerBase
@@ -148,29 +146,6 @@ trait RepositorySettingsControllerBase extends ControllerBase {
     if (repository.name != form.repositoryName) {
       // Update database
       renameRepository(repository.owner, repository.name, repository.owner, form.repositoryName)
-      // Move git repository
-      defining(getRepositoryDir(repository.owner, repository.name)) { dir =>
-        if (dir.isDirectory) {
-          FileUtils.moveDirectory(dir, getRepositoryDir(repository.owner, form.repositoryName))
-        }
-      }
-      // Move wiki repository
-      defining(getWikiRepositoryDir(repository.owner, repository.name)) { dir =>
-        if (dir.isDirectory) {
-          FileUtils.moveDirectory(dir, getWikiRepositoryDir(repository.owner, form.repositoryName))
-        }
-      }
-      // Move files directory
-      defining(getRepositoryFilesDir(repository.owner, repository.name)) { dir =>
-        if (dir.isDirectory) {
-          FileUtils.moveDirectory(dir, getRepositoryFilesDir(repository.owner, form.repositoryName))
-        }
-      }
-      // Delete parent directory
-      FileUtil.deleteDirectoryIfEmpty(getRepositoryFilesDir(repository.owner, repository.name))
-
-      // Call hooks
-      PluginRegistry().getRepositoryHooks.foreach(_.renamed(repository.owner, repository.name, form.repositoryName))
     }
     flash += "info" -> "Repository settings has been updated."
     redirect(s"/${repository.owner}/${form.repositoryName}/settings/options")
@@ -229,7 +204,7 @@ trait RepositorySettingsControllerBase extends ControllerBase {
   post("/:owner/:repository/settings/collaborators")(ownerOnly { repository =>
     val collaborators = params("collaborators")
     removeCollaborators(repository.owner, repository.name)
-    collaborators.split(",").withFilter(_.nonEmpty).map { collaborator =>
+    collaborators.split(",").withFilter(_.nonEmpty).foreach { collaborator =>
       val userName :: role :: Nil = collaborator.split(":").toList
       addCollaborator(repository.owner, repository.name, userName, role)
     }
@@ -392,31 +367,7 @@ trait RepositorySettingsControllerBase extends ControllerBase {
   post("/:owner/:repository/settings/transfer", transferForm)(ownerOnly { (form, repository) =>
     // Change repository owner
     if (repository.owner != form.newOwner) {
-      LockUtil.lock(s"${repository.owner}/${repository.name}") {
-        // Update database
-        renameRepository(repository.owner, repository.name, form.newOwner, repository.name)
-        // Move git repository
-        defining(getRepositoryDir(repository.owner, repository.name)) { dir =>
-          if (dir.isDirectory) {
-            FileUtils.moveDirectory(dir, getRepositoryDir(form.newOwner, repository.name))
-          }
-        }
-        // Move wiki repository
-        defining(getWikiRepositoryDir(repository.owner, repository.name)) { dir =>
-          if (dir.isDirectory) {
-            FileUtils.moveDirectory(dir, getWikiRepositoryDir(form.newOwner, repository.name))
-          }
-        }
-        // Move files directory
-        defining(getRepositoryFilesDir(repository.owner, repository.name)) { dir =>
-          if (dir.isDirectory) {
-            FileUtils.moveDirectory(dir, getRepositoryFilesDir(form.newOwner, repository.name))
-          }
-        }
-
-        // Call hooks
-        PluginRegistry().getRepositoryHooks.foreach(_.transferred(repository.owner, form.newOwner, repository.name))
-      }
+      renameRepository(repository.owner, repository.name, form.newOwner, repository.name)
     }
     redirect(s"/${form.newOwner}/${repository.name}")
   })
@@ -425,19 +376,8 @@ trait RepositorySettingsControllerBase extends ControllerBase {
    * Delete the repository.
    */
   post("/:owner/:repository/settings/delete")(ownerOnly { repository =>
-    LockUtil.lock(s"${repository.owner}/${repository.name}") {
-      // Delete the repository and related files
-      deleteRepository(repository.owner, repository.name)
-
-      FileUtils.deleteDirectory(getRepositoryDir(repository.owner, repository.name))
-      FileUtils.deleteDirectory(getWikiRepositoryDir(repository.owner, repository.name))
-      FileUtils.deleteDirectory(getTemporaryDir(repository.owner, repository.name))
-      FileUtils.deleteDirectory(getRepositoryFilesDir(repository.owner, repository.name))
-
-      // Call hooks
-      PluginRegistry().getRepositoryHooks.foreach(_.deleted(repository.owner, repository.name))
-    }
-
+    // Delete the repository and related files
+    deleteRepository(repository.repository)
     redirect(s"/${repository.owner}")
   })
 
@@ -572,10 +512,10 @@ trait RepositorySettingsControllerBase extends ControllerBase {
 
   private def mergeOptions = new ValueType[Seq[String]] {
     override def convert(name: String, params: Map[String, Seq[String]], messages: Messages): Seq[String] = {
-      params.get("mergeOptions").getOrElse(Nil)
+      params.getOrElse("mergeOptions", Nil)
     }
     override def validate(name: String, params: Map[String, Seq[String]], messages: Messages): Seq[(String, String)] = {
-      val mergeOptions = params.get("mergeOptions").getOrElse(Nil)
+      val mergeOptions = params.getOrElse("mergeOptions", Nil)
       if (mergeOptions.isEmpty) {
         Seq("mergeOptions" -> "At least one option must be enabled.")
       } else if (!mergeOptions.forall(x => Seq("merge-commit", "squash", "rebase").contains(x))) {

src/main/scala/gitbucket/core/controller/RepositoryViewerController.scala

@@ -1,30 +1,36 @@
 package gitbucket.core.controller
 
 import java.io.File
-import javax.servlet.http.{HttpServletRequest, HttpServletResponse}
 
+import javax.servlet.http.{HttpServletRequest, HttpServletResponse}
 import gitbucket.core.plugin.PluginRegistry
 import gitbucket.core.repo.html
 import gitbucket.core.helper
 import gitbucket.core.service._
+import gitbucket.core.service.RepositoryCommitFileService.CommitFile
 import gitbucket.core.util._
-import gitbucket.core.util.JGitUtil._
 import gitbucket.core.util.StringUtil._
 import gitbucket.core.util.SyntaxSugars._
 import gitbucket.core.util.Implicits._
 import gitbucket.core.util.Directory._
-import gitbucket.core.model.{Account, CommitState, CommitStatus, WebHook}
-import gitbucket.core.service.WebHookService._
+import gitbucket.core.model.{Account, CommitState, CommitStatus}
 import gitbucket.core.view
 import gitbucket.core.view.helpers
-import org.scalatra.forms._
+import org.apache.commons.compress.archivers.{ArchiveEntry, ArchiveOutputStream}
+import org.apache.commons.compress.archivers.tar.{TarArchiveEntry, TarArchiveOutputStream}
+import org.apache.commons.compress.archivers.zip.{ZipArchiveEntry, ZipArchiveOutputStream}
+import org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream
+import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream
+import org.apache.commons.compress.compressors.xz.XZCompressorOutputStream
+import org.apache.commons.compress.utils.IOUtils
 import org.apache.commons.io.FileUtils
+import org.scalatra.forms._
 import org.eclipse.jgit.api.{ArchiveCommand, Git}
 import org.eclipse.jgit.archive.{TgzFormat, ZipFormat}
-import org.eclipse.jgit.dircache.{DirCache, DirCacheBuilder}
 import org.eclipse.jgit.errors.MissingObjectException
 import org.eclipse.jgit.lib._
-import org.eclipse.jgit.transport.{ReceiveCommand, ReceivePack}
+import org.eclipse.jgit.treewalk.TreeWalk
+import org.eclipse.jgit.treewalk.filter.PathFilter
 import org.json4s.jackson.Serialization
 import org.scalatra._
 import org.scalatra.i18n.Messages
@@ -32,6 +38,7 @@ import org.scalatra.i18n.Messages
 class RepositoryViewerController
     extends RepositoryViewerControllerBase
     with RepositoryService
+    with RepositoryCommitFileService
     with AccountService
     with ActivityService
     with IssuesService
@@ -54,6 +61,7 @@ class RepositoryViewerController
  */
 trait RepositoryViewerControllerBase extends ControllerBase {
   self: RepositoryService
+    with RepositoryCommitFileService
     with AccountService
     with ActivityService
     with IssuesService
@@ -103,7 +111,14 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     oldLineNumber: Option[Int],
     newLineNumber: Option[Int],
     content: String,
-    issueId: Option[Int]
+    issueId: Option[Int],
+    diff: Option[String]
+  )
+
+  case class TagForm(
+    commitId: String,
+    tagName: String,
+    message: Option[String]
   )
 
   val uploadForm = mapping(
@@ -138,9 +153,16 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     "oldLineNumber" -> trim(label("Old line number", optional(number()))),
     "newLineNumber" -> trim(label("New line number", optional(number()))),
     "content" -> trim(label("Content", text(required))),
-    "issueId" -> trim(label("Issue Id", optional(number())))
+    "issueId" -> trim(label("Issue Id", optional(number()))),
+    "diff" -> optional(text())
   )(CommentForm.apply)
 
+  val tagForm = mapping(
+    "commitId" -> trim(label("Commit id", text(required))),
+    "tagName" -> trim(label("Tag name", text(required))),
+    "message" -> trim(label("Message", optional(text())))
+  )(TagForm.apply)
+
   /**
    * Returns converted HTML from Markdown for preview.
    */
@@ -152,7 +174,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
         helpers.renderMarkup(
           filePath = List(f),
           fileContent = params("content"),
-          branch = "master",
+          branch = repository.repository.defaultBranch,
           repository = repository,
           enableWikiLink = params("enableWikiLink").toBoolean,
           enableRefsLink = params("enableRefsLink").toBoolean,
@@ -162,6 +184,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
         helpers.markdown(
           markdown = params("content"),
           repository = repository,
+          branch = repository.repository.defaultBranch,
           enableWikiLink = params("enableWikiLink").toBoolean,
           enableRefsLink = params("enableRefsLink").toBoolean,
           enableLineBreaks = params("enableLineBreaks").toBoolean,
@@ -237,6 +260,10 @@ trait RepositoryViewerControllerBase extends ControllerBase {
 
     using(Git.open(getRepositoryDir(repository.owner, repository.name))) {
       git =>
+        def getTags(sha: String): List[String] = {
+          JGitUtil.getTagsOnCommit(git, sha)
+        }
+
         JGitUtil.getCommitLog(git, branchName, page, 30, path) match {
           case Right((logs, hasNext)) =>
             html.commits(
@@ -250,7 +277,8 @@ trait RepositoryViewerControllerBase extends ControllerBase {
               hasNext,
               hasDeveloperRole(repository.owner, repository.name, context.loginAccount),
               getStatuses,
-              getSummary
+              getSummary,
+              getTags
             )
           case Left(_) => NotFound()
         }
@@ -290,13 +318,34 @@ trait RepositoryViewerControllerBase extends ControllerBase {
       CommitFile(line.substring(0, i).trim, line.substring(i + 1).trim)
     }
 
+    val newFiles = files.map { file =>
+      file.copy(name = if (form.path.length == 0) file.name else s"${form.path}/${file.name}")
+    }
+
     commitFiles(
       repository = repository,
       branch = form.branch,
       path = form.path,
       files = files,
-      message = form.message.getOrElse("Add files via upload")
-    )
+      message = form.message.getOrElse("Add files via upload"),
+      loginAccount = context.loginAccount.get
+    ) {
+      case (git, headTip, builder, inserter) =>
+        JGitUtil.processTree(git, headTip) { (path, tree) =>
+          if (!newFiles.exists(_.name.contains(path))) {
+            builder.add(JGitUtil.createDirCacheEntry(path, tree.getEntryFileMode, tree.getEntryObjectId))
+          }
+        }
+
+        newFiles.foreach { file =>
+          val bytes =
+            FileUtils.readFileToByteArray(new File(getTemporaryDir(session.getId), FileUtil.checkFilename(file.id)))
+          builder.add(
+            JGitUtil.createDirCacheEntry(file.name, FileMode.REGULAR_FILE, inserter.insert(Constants.OBJ_BLOB, bytes))
+          )
+          builder.finish()
+        }
+    }
 
     if (form.path.length == 0) {
       redirect(s"/${repository.owner}/${repository.name}/tree/${form.branch}")
@@ -314,17 +363,23 @@ trait RepositoryViewerControllerBase extends ControllerBase {
       git =>
         val revCommit = JGitUtil.getRevCommitFromId(git, git.getRepository.resolve(branch))
 
-        getPathObjectId(git, path, revCommit).map { objectId =>
-          val paths = path.split("/")
-          html.editor(
-            branch = branch,
-            repository = repository,
-            pathList = paths.take(paths.size - 1).toList,
-            fileName = Some(paths.last),
-            content = JGitUtil.getContentInfo(git, path, objectId),
-            protectedBranch = protectedBranch,
-            commit = revCommit.getName
-          )
+        getPathObjectId(git, path, revCommit).map {
+          objectId =>
+            val paths = path.split("/")
+            val info = EditorConfigUtil.getEditorConfigInfo(git, branch, path)
+
+            html.editor(
+              branch = branch,
+              repository = repository,
+              pathList = paths.take(paths.size - 1).toList,
+              fileName = Some(paths.last),
+              content = JGitUtil.getContentInfo(git, path, objectId),
+              protectedBranch = protectedBranch,
+              commit = revCommit.getName,
+              newLineMode = info.newLineMode,
+              useSoftTabs = info.useSoftTabs,
+              tabSize = info.tabSize
+            )
         } getOrElse NotFound()
     }
   })
@@ -359,7 +414,8 @@ trait RepositoryViewerControllerBase extends ControllerBase {
       content = appendNewLine(convertLineSeparator(form.content, form.lineSeparator), form.lineSeparator),
       charset = form.charset,
       message = form.message.getOrElse(s"Create ${form.newFileName}"),
-      commit = form.commit
+      commit = form.commit,
+      loginAccount = context.loginAccount.get
     )
 
     redirect(
@@ -382,7 +438,8 @@ trait RepositoryViewerControllerBase extends ControllerBase {
       } else {
         form.message.getOrElse(s"Rename ${form.oldFileName.get} to ${form.newFileName}")
       },
-      commit = form.commit
+      commit = form.commit,
+      loginAccount = context.loginAccount.get
     )
 
     redirect(
@@ -401,11 +458,14 @@ trait RepositoryViewerControllerBase extends ControllerBase {
       content = "",
       charset = "",
       message = form.message.getOrElse(s"Delete ${form.fileName}"),
-      commit = form.commit
+      commit = form.commit,
+      loginAccount = context.loginAccount.get
     )
 
+    println(form.path)
+
     redirect(
-      s"/${repository.owner}/${repository.name}/tree/${form.branch}${if (form.path.length == 0) "" else form.path}"
+      s"/${repository.owner}/${repository.name}/tree/${form.branch}${if (form.path.length == 0) "" else "/" + form.path}"
     )
   })
 
@@ -435,6 +495,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
               // Download (This route is left for backword compatibility)
               responseRawFile(git, objectId, path, repository)
             } else {
+              val info = EditorConfigUtil.getEditorConfigInfo(git, id, path)
               html.blob(
                 branch = id,
                 repository = repository,
@@ -443,7 +504,8 @@ trait RepositoryViewerControllerBase extends ControllerBase {
                 latestCommit = new JGitUtil.CommitInfo(JGitUtil.getLastModifiedCommit(git, revCommit, path)),
                 hasWritePermission = hasDeveloperRole(repository.owner, repository.name, context.loginAccount),
                 isBlame = request.paths(2) == "blame",
-                isLfsFile = isLfsFile(git, objectId)
+                isLfsFile = isLfsFile(git, objectId),
+                tabSize = info.tabSize
               )
             }
         } getOrElse NotFound()
@@ -515,7 +577,9 @@ trait RepositoryViewerControllerBase extends ControllerBase {
                 repository,
                 diffs,
                 oldCommitId,
-                hasDeveloperRole(repository.owner, repository.name, context.loginAccount)
+                hasDeveloperRole(repository.owner, repository.name, context.loginAccount),
+                flash.get("info"),
+                flash.get("error")
               )
           }
       }
@@ -552,34 +616,17 @@ trait RepositoryViewerControllerBase extends ControllerBase {
   post("/:owner/:repository/commit/:id/comment/new", commentForm)(readableUsersOnly { (form, repository) =>
     val id = params("id")
     createCommitComment(
-      repository.owner,
-      repository.name,
+      repository,
       id,
-      context.loginAccount.get.userName,
+      context.loginAccount.get,
       form.content,
       form.fileName,
       form.oldLineNumber,
       form.newLineNumber,
+      form.diff,
       form.issueId
     )
-    form.issueId match {
-      case Some(issueId) =>
-        recordCommentPullRequestActivity(
-          repository.owner,
-          repository.name,
-          context.loginAccount.get.userName,
-          issueId,
-          form.content
-        )
-      case None =>
-        recordCommentCommitActivity(
-          repository.owner,
-          repository.name,
-          context.loginAccount.get.userName,
-          id,
-          form.content
-        )
-    }
+
     redirect(s"/${repository.owner}/${repository.name}/commit/${id}")
   })
 
@@ -596,55 +643,26 @@ trait RepositoryViewerControllerBase extends ControllerBase {
       newLineNumber,
       issueId,
       hasWritePermission = hasDeveloperRole(repository.owner, repository.name, context.loginAccount),
-      repository = repository
+      repository = repository,
+      focus = true
     )
   })
 
   ajaxPost("/:owner/:repository/commit/:id/comment/_data/new", commentForm)(readableUsersOnly { (form, repository) =>
     val id = params("id")
     val commentId = createCommitComment(
-      repository.owner,
-      repository.name,
+      repository,
       id,
-      context.loginAccount.get.userName,
+      context.loginAccount.get,
       form.content,
       form.fileName,
       form.oldLineNumber,
       form.newLineNumber,
+      form.diff,
       form.issueId
     )
+
     val comment = getCommitComment(repository.owner, repository.name, commentId.toString).get
-    form.issueId match {
-      case Some(issueId) =>
-        getPullRequest(repository.owner, repository.name, issueId).foreach {
-          case (issue, pullRequest) =>
-            recordCommentPullRequestActivity(
-              repository.owner,
-              repository.name,
-              context.loginAccount.get.userName,
-              issueId,
-              form.content
-            )
-            PluginRegistry().getPullRequestHooks.foreach(_.addedComment(commentId, form.content, issue, repository))
-            callPullRequestReviewCommentWebHook(
-              "create",
-              comment,
-              repository,
-              issue,
-              pullRequest,
-              context.baseUrl,
-              context.loginAccount.get
-            )
-        }
-      case None =>
-        recordCommentCommitActivity(
-          repository.owner,
-          repository.name,
-          context.loginAccount.get.userName,
-          id,
-          form.content
-        )
-    }
     helper.html
       .commitcomment(comment, hasDeveloperRole(repository.owner, repository.name, context.loginAccount), repository)
   })
@@ -662,10 +680,12 @@ trait RepositoryViewerControllerBase extends ControllerBase {
                 "content" -> view.Markdown.toHtml(
                   markdown = x.content,
                   repository = repository,
+                  branch = repository.repository.defaultBranch,
                   enableWikiLink = false,
                   enableRefsLink = true,
                   enableAnchor = true,
                   enableLineBreaks = true,
+                  enableTaskList = true,
                   hasWritePermission = true
                 )
               )
@@ -730,6 +750,29 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     html.branches(branches, hasDeveloperRole(repository.owner, repository.name, context.loginAccount), repository)
   })
 
+  /**
+   * Displays the create tag dialog.
+   */
+  get("/:owner/:repository/tag/:id")(writableUsersOnly { repository =>
+    html.tag(params("id"), repository)
+  })
+
+  /**
+   * Creates a tag.
+   */
+  post("/:owner/:repository/tag", tagForm)(writableUsersOnly { (form, repository) =>
+    using(Git.open(getRepositoryDir(repository.owner, repository.name))) { git =>
+      JGitUtil.createTag(git, form.tagName, form.message, form.commitId)
+    } match {
+      case Right(message) =>
+        flash += "info" -> message
+        redirect(s"/${repository.owner}/${repository.name}/commit/${form.commitId}")
+      case Left(message) =>
+        flash += "error" -> message
+        redirect(s"/${repository.owner}/${repository.name}/commit/${form.commitId}")
+    }
+  })
+
   /**
    * Creates a branch.
    */
@@ -772,17 +815,15 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     redirect(s"${repository.owner}/${repository.name}/releases")
   })
 
-  /**
-   * Download repository contents as an archive.
-   */
-  get("/:owner/:repository/archive/*")(referrersOnly { repository =>
-    multiParams("splat").head match {
-      case name if name.endsWith(".zip") =>
-        archiveRepository(name, ".zip", repository)
-      case name if name.endsWith(".tar.gz") =>
-        archiveRepository(name, ".tar.gz", repository)
-      case _ => BadRequest()
-    }
+  get("/:owner/:repository/archive/:name")(referrersOnly { repository =>
+    val name = params("name")
+    archiveRepository(name, repository, "")
+  })
+
+  get("/:owner/:repository/archive/*/:name")(referrersOnly { repository =>
+    val name = params("name")
+    val path = multiParams("splat").head
+    archiveRepository(name, repository, path)
   })
 
   get("/:owner/:repository/network/members")(referrersOnly { repository =>
@@ -834,175 +875,6 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     lazy val isValid: Boolean = fileIds.nonEmpty
   }
 
-  case class CommitFile(id: String, name: String)
-
-  private def commitFiles(
-    repository: RepositoryService.RepositoryInfo,
-    files: Seq[CommitFile],
-    branch: String,
-    path: String,
-    message: String
-  ) = {
-    // prepend path to the filename
-    val newFiles = files.map { file =>
-      file.copy(name = if (path.length == 0) file.name else s"${path}/${file.name}")
-    }
-
-    _commitFile(repository, branch, message) {
-      case (git, headTip, builder, inserter) =>
-        JGitUtil.processTree(git, headTip) { (path, tree) =>
-          if (!newFiles.exists(_.name.contains(path))) {
-            builder.add(JGitUtil.createDirCacheEntry(path, tree.getEntryFileMode, tree.getEntryObjectId))
-          }
-        }
-
-        newFiles.foreach { file =>
-          val bytes = FileUtils.readFileToByteArray(new File(getTemporaryDir(session.getId), file.id))
-          builder.add(
-            JGitUtil.createDirCacheEntry(file.name, FileMode.REGULAR_FILE, inserter.insert(Constants.OBJ_BLOB, bytes))
-          )
-          builder.finish()
-        }
-    }
-  }
-
-  private def commitFile(
-    repository: RepositoryService.RepositoryInfo,
-    branch: String,
-    path: String,
-    newFileName: Option[String],
-    oldFileName: Option[String],
-    content: String,
-    charset: String,
-    message: String,
-    commit: String
-  ) = {
-
-    val newPath = newFileName.map { newFileName =>
-      if (path.length == 0) newFileName else s"${path}/${newFileName}"
-    }
-    val oldPath = oldFileName.map { oldFileName =>
-      if (path.length == 0) oldFileName else s"${path}/${oldFileName}"
-    }
-
-    _commitFile(repository, branch, message) {
-      case (git, headTip, builder, inserter) =>
-        if (headTip.getName == commit) {
-          val permission = JGitUtil
-            .processTree(git, headTip) { (path, tree) =>
-              // Add all entries except the editing file
-              if (!newPath.contains(path) && !oldPath.contains(path)) {
-                builder.add(JGitUtil.createDirCacheEntry(path, tree.getEntryFileMode, tree.getEntryObjectId))
-              }
-              // Retrieve permission if file exists to keep it
-              oldPath.collect { case x if x == path => tree.getEntryFileMode.getBits }
-            }
-            .flatten
-            .headOption
-
-          newPath.foreach { newPath =>
-            builder.add(JGitUtil.createDirCacheEntry(newPath, permission.map { bits =>
-              FileMode.fromBits(bits)
-            } getOrElse FileMode.REGULAR_FILE, inserter.insert(Constants.OBJ_BLOB, content.getBytes(charset))))
-          }
-          builder.finish()
-        }
-    }
-  }
-
-  private def _commitFile(repository: RepositoryService.RepositoryInfo, branch: String, message: String)(
-    f: (Git, ObjectId, DirCacheBuilder, ObjectInserter) => Unit
-  ) = {
-
-    LockUtil.lock(s"${repository.owner}/${repository.name}") {
-      using(Git.open(getRepositoryDir(repository.owner, repository.name))) { git =>
-        val loginAccount = context.loginAccount.get
-        val builder = DirCache.newInCore.builder()
-        val inserter = git.getRepository.newObjectInserter()
-        val headName = s"refs/heads/${branch}"
-        val headTip = git.getRepository.resolve(headName)
-
-        f(git, headTip, builder, inserter)
-
-        val commitId = JGitUtil.createNewCommit(
-          git,
-          inserter,
-          headTip,
-          builder.getDirCache.writeTree(inserter),
-          headName,
-          loginAccount.fullName,
-          loginAccount.mailAddress,
-          message
-        )
-
-        inserter.flush()
-        inserter.close()
-
-        val receivePack = new ReceivePack(git.getRepository)
-        val receiveCommand = new ReceiveCommand(headTip, commitId, headName)
-
-        // call post commit hook
-        val error = PluginRegistry().getReceiveHooks.flatMap { hook =>
-          hook.preReceive(repository.owner, repository.name, receivePack, receiveCommand, loginAccount.userName)
-        }.headOption
-
-        error match {
-          case Some(error) =>
-            // commit is rejected
-            // TODO Notify commit failure to edited user
-            val refUpdate = git.getRepository.updateRef(headName)
-            refUpdate.setNewObjectId(headTip)
-            refUpdate.setForceUpdate(true)
-            refUpdate.update()
-
-          case None =>
-            // update refs
-            val refUpdate = git.getRepository.updateRef(headName)
-            refUpdate.setNewObjectId(commitId)
-            refUpdate.setForceUpdate(false)
-            refUpdate.setRefLogIdent(new PersonIdent(loginAccount.fullName, loginAccount.mailAddress))
-            refUpdate.update()
-
-            // update pull request
-            updatePullRequests(repository.owner, repository.name, branch)
-
-            // record activity
-            val commitInfo = new CommitInfo(JGitUtil.getRevCommitFromId(git, commitId))
-            recordPushActivity(repository.owner, repository.name, loginAccount.userName, branch, List(commitInfo))
-
-            // create issue comment by commit message
-            createIssueComment(repository.owner, repository.name, commitInfo)
-
-            // close issue by commit message
-            closeIssuesFromMessage(message, loginAccount.userName, repository.owner, repository.name)
-
-            // call post commit hook
-            PluginRegistry().getReceiveHooks.foreach { hook =>
-              hook.postReceive(repository.owner, repository.name, receivePack, receiveCommand, loginAccount.userName)
-            }
-
-            //call web hook
-            callPullRequestWebHookByRequestBranch("synchronize", repository, branch, context.baseUrl, loginAccount)
-            val commit = new JGitUtil.CommitInfo(JGitUtil.getRevCommitFromId(git, commitId))
-            callWebHookOf(repository.owner, repository.name, WebHook.Push) {
-              getAccountByUserName(repository.owner).map { ownerAccount =>
-                WebHookPushPayload(
-                  git,
-                  loginAccount,
-                  headName,
-                  repository,
-                  List(commit),
-                  ownerAccount,
-                  oldId = headTip,
-                  newId = commitId
-                )
-              }
-            }
-        }
-      }
-    }
-  }
-
   private val readmeFiles = PluginRegistry().renderableExtensions.map { extension =>
     s"readme.${extension}"
   } ++ Seq("readme.txt", "readme")
@@ -1067,26 +939,99 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     }
   }
 
-  private def archiveRepository(name: String, suffix: String, repository: RepositoryService.RepositoryInfo): Unit = {
-    val revision = name.stripSuffix(suffix)
+  private def archiveRepository(
+    filename: String,
+    repository: RepositoryService.RepositoryInfo,
+    path: String
+  ) = {
+    def archive(revision: String, archiveFormat: String, archive: ArchiveOutputStream)(
+      entryCreator: (String, Long, java.util.Date, Int) => ArchiveEntry
+    ): Unit = {
+      using(Git.open(getRepositoryDir(repository.owner, repository.name))) { git =>
+        val oid = git.getRepository.resolve(revision)
+        val commit = JGitUtil.getRevCommitFromId(git, oid)
+        val date = commit.getCommitterIdent.getWhen
+        val sha1 = oid.getName()
+        val repositorySuffix = (if (sha1.startsWith(revision)) sha1 else revision).replace('/', '-')
+        val pathSuffix = if (path.isEmpty) "" else '-' + path.replace('/', '-')
+        val baseName = repository.name + "-" + repositorySuffix + pathSuffix
 
-    using(Git.open(getRepositoryDir(repository.owner, repository.name))) { git =>
-      val oid = git.getRepository.resolve(revision)
-      val revCommit = JGitUtil.getRevCommitFromId(git, oid)
-      val sha1 = oid.getName()
-      val repositorySuffix = (if (sha1.startsWith(revision)) sha1 else revision).replace('/', '-')
-      val filename = repository.name + "-" + repositorySuffix + suffix
+        using(new TreeWalk(git.getRepository)) { treeWalk =>
+          treeWalk.addTree(commit.getTree)
+          treeWalk.setRecursive(true)
+          if (!path.isEmpty) {
+            treeWalk.setFilter(PathFilter.create(path))
+          }
+          if (treeWalk != null) {
+            while (treeWalk.next()) {
+              val entryPath =
+                if (path.isEmpty) baseName + "/" + treeWalk.getPathString
+                else path.split("/").last + treeWalk.getPathString.substring(path.length)
+              val size = JGitUtil.getFileSize(git, repository, treeWalk)
+              val mode = treeWalk.getFileMode.getBits
+              val entry: ArchiveEntry = entryCreator(entryPath, size, date, mode)
+              JGitUtil.openFile(git, repository, commit.getTree, treeWalk.getPathString) { in =>
+                archive.putArchiveEntry(entry)
+                IOUtils.copy(in, archive)
+                archive.closeArchiveEntry()
+              }
+            }
+          }
+        }
+      }
+    }
 
-      contentType = "application/octet-stream"
-      response.setHeader("Content-Disposition", s"attachment; filename=${filename}")
-      response.setBufferSize(1024 * 1024);
+    val suffix =
+      path.split("/").lastOption.collect { case x if x.length > 0 => "-" + x.replace('/', '_') }.getOrElse("")
+    val zipRe = """(.+)\.zip$""".r
+    val tarRe = """(.+)\.tar\.(gz|bz2|xz)$""".r
 
-      git.archive
-        .setFormat(suffix.tail)
-        .setPrefix(repository.name + "-" + repositorySuffix + "/")
-        .setTree(revCommit)
-        .setOutputStream(response.getOutputStream)
-        .call()
+    filename match {
+      case zipRe(revision) =>
+        response.setHeader(
+          "Content-Disposition",
+          s"attachment; filename=${repository.name}-${revision}${suffix}.zip"
+        )
+        contentType = "application/octet-stream"
+        response.setBufferSize(1024 * 1024)
+        using(new ZipArchiveOutputStream(response.getOutputStream)) { zip =>
+          archive(revision, ".zip", zip) { (path, size, date, mode) =>
+            val entry = new ZipArchiveEntry(path)
+            entry.setSize(size)
+            entry.setUnixMode(mode)
+            entry.setTime(date.getTime)
+            entry
+          }
+        }
+        ()
+      case tarRe(revision, compressor) =>
+        response.setHeader(
+          "Content-Disposition",
+          s"attachment; filename=${repository.name}-${revision}${suffix}.tar.${compressor}"
+        )
+        contentType = "application/octet-stream"
+        response.setBufferSize(1024 * 1024)
+        using(compressor match {
+          case "gz"  => new GzipCompressorOutputStream(response.getOutputStream)
+          case "bz2" => new BZip2CompressorOutputStream(response.getOutputStream)
+          case "xz"  => new XZCompressorOutputStream(response.getOutputStream)
+        }) { compressorOutputStream =>
+          using(new TarArchiveOutputStream(compressorOutputStream)) { tar =>
+            tar.setBigNumberMode(TarArchiveOutputStream.BIGNUMBER_STAR)
+            tar.setLongFileMode(TarArchiveOutputStream.LONGFILE_GNU)
+            tar.setAddPaxHeadersForNonAsciiNames(true)
+            archive(revision, ".tar.gz", tar) { (path, size, date, mode) =>
+              val entry = new TarArchiveEntry(path)
+              entry.setSize(size)
+              entry.setModTime(date)
+              entry.setMode(mode)
+              entry
+            }
+          }
+        }
+        ()
+      case _ =>
+        NotFound()
     }
   }
 

src/main/scala/gitbucket/core/controller/SystemSettingsController.scala

@@ -15,6 +15,7 @@ import gitbucket.core.util.StringUtil._
 import gitbucket.core.util.SyntaxSugars._
 import gitbucket.core.util.{AdminAuthenticator, Mailer}
 import org.apache.commons.io.IOUtils
+import org.apache.commons.mail.EmailException
 import org.json4s.jackson.Serialization
 import org.scalatra._
 import org.scalatra.forms._
@@ -44,9 +45,11 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
     "gravatar" -> trim(label("Gravatar", boolean())),
     "notification" -> trim(label("Notification", boolean())),
     "activityLogLimit" -> trim(label("Limit of activity logs", optional(number()))),
-    "ssh" -> trim(label("SSH access", boolean())),
-    "sshHost" -> trim(label("SSH host", optional(text()))),
-    "sshPort" -> trim(label("SSH port", optional(number()))),
+    "ssh" -> mapping(
+      "enabled" -> trim(label("SSH access", boolean())),
+      "host" -> trim(label("SSH host", optional(text()))),
+      "port" -> trim(label("SSH port", optional(number()))),
+    )(Ssh.apply),
     "useSMTP" -> trim(label("SMTP", boolean())),
     "smtp" -> optionalIfNotChecked(
       "useSMTP",
@@ -89,13 +92,24 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
         "jwsAlgorithm" -> trim(label("Signature algorithm", optional(text())))
       )(OIDC.apply)
     ),
-    "skinName" -> trim(label("AdminLTE skin name", text(required)))
+    "skinName" -> trim(label("AdminLTE skin name", text(required))),
+    "showMailAddress" -> trim(label("Show mail address", boolean())),
+    "pluginNetworkInstall" -> trim(label("Network plugin installation", boolean())),
+    "proxy" -> optionalIfNotChecked(
+      "useProxy",
+      mapping(
+        "host" -> trim(label("Proxy host", text(required))),
+        "port" -> trim(label("Proxy port", number())),
+        "user" -> trim(label("Keystore", optional(text()))),
+        "password" -> trim(label("Keystore", optional(text())))
+      )(Proxy.apply)
+    )
   )(SystemSettings.apply).verifying { settings =>
     Vector(
-      if (settings.ssh && settings.baseUrl.isEmpty) {
+      if (settings.ssh.enabled && settings.baseUrl.isEmpty) {
         Some("baseUrl" -> "Base URL is required if SSH access is enabled.")
       } else None,
-      if (settings.ssh && settings.sshHost.isEmpty) {
+      if (settings.ssh.enabled && settings.ssh.sshHost.isEmpty) {
         Some("sshHost" -> "SSH host is required if SSH access is enabled.")
       } else None
     ).flatten
@@ -124,6 +138,7 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
     password: String,
     fullName: String,
     mailAddress: String,
+    extraMailAddresses: List[String],
     isAdmin: Boolean,
     description: Option[String],
     url: Option[String],
@@ -135,6 +150,7 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
     password: Option[String],
     fullName: String,
     mailAddress: String,
+    extraMailAddresses: List[String],
     isAdmin: Boolean,
     description: Option[String],
     url: Option[String],
@@ -166,6 +182,9 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
     "password" -> trim(label("Password", text(required, maxlength(20), password))),
     "fullName" -> trim(label("Full Name", text(required, maxlength(100)))),
     "mailAddress" -> trim(label("Mail Address", text(required, maxlength(100), uniqueMailAddress()))),
+    "extraMailAddresses" -> list(
+      trim(label("Additional Mail Address", text(maxlength(100), uniqueExtraMailAddress("userName"))))
+    ),
     "isAdmin" -> trim(label("User Type", boolean())),
     "description" -> trim(label("bio", optional(text()))),
     "url" -> trim(label("URL", optional(text(maxlength(200))))),
@@ -177,6 +196,9 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
     "password" -> trim(label("Password", optional(text(maxlength(20), password)))),
     "fullName" -> trim(label("Full Name", text(required, maxlength(100)))),
     "mailAddress" -> trim(label("Mail Address", text(required, maxlength(100), uniqueMailAddress("userName")))),
+    "extraMailAddresses" -> list(
+      trim(label("Additional Mail Address", text(maxlength(100), uniqueExtraMailAddress("userName"))))
+    ),
     "isAdmin" -> trim(label("User Type", boolean())),
     "description" -> trim(label("bio", optional(text()))),
     "url" -> trim(label("URL", optional(text(maxlength(200))))),
@@ -304,42 +326,62 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
       "Test mail has been sent to: " + form.testAddress
 
     } catch {
-      case e: Exception => "[Error] " + e.toString
+      case e: EmailException => s"[Error] ${e.getCause}"
+      case e: Exception      => s"[Error] ${e.toString}"
     }
   })
 
   get("/admin/plugins")(adminOnly {
     // Installed plugins
     val enabledPlugins = PluginRegistry().getPlugins()
+    val gitbucketVersion = GitBucketCoreModule.getVersions.asScala.last.getVersion
+    val gitbucketSemver = Semver.valueOf(gitbucketVersion)
 
-    val gitbucketVersion = Semver.valueOf(GitBucketCoreModule.getVersions.asScala.last.getVersion)
-
-    // Plugins in the local repository
-    val repositoryPlugins = PluginRepository
-      .getPlugins()
-      .filterNot { meta =>
-        enabledPlugins.exists { plugin =>
-          plugin.pluginId == meta.id &&
-          Semver.valueOf(plugin.pluginVersion).greaterThanOrEqualTo(Semver.valueOf(meta.latestVersion.version))
+    // Plugins in the remote repository
+    val repositoryPlugins = if (context.settings.pluginNetworkInstall) {
+      PluginRepository
+        .getPlugins()
+        .map {
+          meta =>
+            (meta, meta.versions.reverse.find {
+              version =>
+                val semver = Semver.valueOf(version.version)
+                gitbucketVersion == version.gitbucketVersion && !enabledPlugins.exists { plugin =>
+                  if (plugin.pluginId == meta.id) {
+                    Semver.valueOf(plugin.pluginVersion) match {
+                      case x if x.greaterThan(semver) => true
+                      case x if x.equals(semver) =>
+                        plugin.gitbucketVersion match {
+                          case None    => true
+                          case Some(x) => Semver.valueOf(x).greaterThanOrEqualTo(gitbucketSemver)
+                        }
+                      case _ => false
+                    }
+                  } else false
+                }
+            })
         }
-      }
-      .map { meta =>
-        (meta, meta.versions.reverse.find { version =>
-          gitbucketVersion.satisfies(version.range)
-        })
-      }
-      .collect {
-        case (meta, Some(version)) =>
-          new PluginInfoBase(
-            pluginId = meta.id,
-            pluginName = meta.name,
-            pluginVersion = version.version,
-            description = meta.description
-          )
-      }
+        .collect {
+          case (meta, Some(version)) =>
+            new PluginInfoBase(
+              pluginId = meta.id,
+              pluginName = meta.name,
+              pluginVersion = version.version,
+              gitbucketVersion = Some(version.gitbucketVersion),
+              description = meta.description
+            )
+        }
+    } else Nil
 
     // Merge
-    val plugins = enabledPlugins.map((_, true)) ++ repositoryPlugins.map((_, false))
+    val plugins = (enabledPlugins.map((_, true)) ++ repositoryPlugins.map((_, false)))
+      .groupBy(_._1.pluginId)
+      .map {
+        case (pluginId, plugins) =>
+          val (plugin, enabled) = plugins.head
+          (plugin, enabled, if (plugins.length > 1) plugins.last._1.pluginVersion else "")
+      }
+      .toList
 
     html.plugins(plugins, flash.get("info"))
   })
@@ -350,40 +392,45 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
     redirect("/admin/plugins")
   })
 
-  post("/admin/plugins/:pluginId/:version/_uninstall")(adminOnly {
+  post("/admin/plugins/:pluginId/_uninstall")(adminOnly {
     val pluginId = params("pluginId")
-    val version = params("version")
-    PluginRegistry()
-      .getPlugins()
-      .collect { case plugin if (plugin.pluginId == pluginId && plugin.pluginVersion == version) => plugin }
-      .foreach { _ =>
-        PluginRegistry
-          .uninstall(pluginId, request.getServletContext, loadSystemSettings(), request2Session(request).conn)
-        flash += "info" -> s"${pluginId} was uninstalled."
-      }
+
+    if (PluginRegistry().getPlugins().exists(_.pluginId == pluginId)) {
+      PluginRegistry
+        .uninstall(pluginId, request.getServletContext, loadSystemSettings(), request2Session(request).conn)
+      flash += "info" -> s"${pluginId} was uninstalled."
+    }
+
     redirect("/admin/plugins")
   })
 
   post("/admin/plugins/:pluginId/:version/_install")(adminOnly {
-    val pluginId = params("pluginId")
-    val version = params("version")
-    /// TODO!!!!
-    PluginRepository
-      .getPlugins()
-      .collect { case meta if meta.id == pluginId => (meta, meta.versions.find(_.version == version)) }
-      .foreach {
-        case (meta, version) =>
-          version.foreach { version =>
-            // TODO Install version!
-            PluginRegistry.install(
-              new java.io.File(PluginHome, s".repository/${version.file}"),
-              request.getServletContext,
-              loadSystemSettings(),
-              request2Session(request).conn
-            )
-            flash += "info" -> s"${pluginId} was installed."
-          }
-      }
+    if (context.settings.pluginNetworkInstall) {
+      val pluginId = params("pluginId")
+      val version = params("version")
+      val gitbucketVersion = GitBucketCoreModule.getVersions.asScala.last.getVersion
+
+      PluginRepository
+        .getPlugins()
+        .collectFirst {
+          case meta if meta.id == pluginId =>
+            (meta, meta.versions.find(x => x.gitbucketVersion == gitbucketVersion && x.version == version))
+        }
+        .foreach {
+          case (meta, version) =>
+            version.foreach { version =>
+              PluginRegistry.install(
+                pluginId,
+                new java.net.URL(version.url),
+                request.getServletContext,
+                loadSystemSettings(),
+                request2Session(request).conn
+              )
+              flash += "info" -> s"${pluginId}:${version.version} was installed."
+            }
+        }
+    }
+
     redirect("/admin/plugins")
   })
 
@@ -400,13 +447,13 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
   })
 
   get("/admin/users/_newuser")(adminOnly {
-    html.user(None)
+    html.user(None, Nil)
   })
 
   post("/admin/users/_newuser", newUserForm)(adminOnly { form =>
     createAccount(
       form.userName,
-      sha1(form.password),
+      pbkdf2_sha256(form.password),
       form.fullName,
       form.mailAddress,
       form.isAdmin,
@@ -414,12 +461,14 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
       form.url
     )
     updateImage(form.userName, form.fileId, false)
+    updateAccountExtraMailAddresses(form.userName, form.extraMailAddresses.filter(_ != ""))
     redirect("/admin/users")
   })
 
   get("/admin/users/:userName/_edituser")(adminOnly {
     val userName = params("userName")
-    html.user(getAccountByUserName(userName, true), flash.get("error"))
+    val extraMails = getAccountExtraMailAddresses(userName)
+    html.user(getAccountByUserName(userName, true), extraMails, flash.get("error"))
   })
 
   post("/admin/users/:name/_edituser", editUserForm)(adminOnly { form =>
@@ -444,7 +493,7 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
 
           updateAccount(
             account.copy(
-              password = form.password.map(sha1).getOrElse(account.password),
+              password = form.password.map(pbkdf2_sha256).getOrElse(account.password),
               fullName = form.fullName,
               mailAddress = form.mailAddress,
               isAdmin = form.isAdmin,
@@ -455,6 +504,7 @@ trait SystemSettingsControllerBase extends AccountManagementControllerBase {
           )
 
           updateImage(userName, form.fileId, form.clearImage)
+          updateAccountExtraMailAddresses(userName, form.extraMailAddresses.filter(_ != ""))
 
           // call hooks
           if (form.isRemoved) PluginRegistry().getAccountHooks.foreach(_.deleted(userName))

src/main/scala/gitbucket/core/controller/WikiController.scala

@@ -180,7 +180,7 @@ trait WikiControllerBase extends ControllerBase {
             loginAccount,
             form.message.getOrElse(""),
             Some(form.id)
-          ).map {
+          ).foreach {
             commitId =>
               updateLastActivityDate(repository.owner, repository.name)
               recordEditWikiPageActivity(
@@ -224,7 +224,7 @@ trait WikiControllerBase extends ControllerBase {
             loginAccount,
             form.message.getOrElse(""),
             None
-          ).map {
+          ).foreach {
             commitId =>
               updateLastActivityDate(repository.owner, repository.name)
               recordCreateWikiPageActivity(repository.owner, repository.name, loginAccount.userName, form.pageName)

src/main/scala/gitbucket/core/controller/api/ApiGitReferenceControllerBase.scala

@@ -0,0 +1,60 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api.{ApiObject, ApiRef, JsonFormat}
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.util.Directory.getRepositoryDir
+import gitbucket.core.util.ReferrerAuthenticator
+import gitbucket.core.util.SyntaxSugars.using
+import gitbucket.core.util.Implicits._
+import org.eclipse.jgit.api.Git
+import scala.collection.JavaConverters._
+
+trait ApiGitReferenceControllerBase extends ControllerBase {
+  self: ReferrerAuthenticator =>
+
+  /*
+   * i. Get a reference
+   * https://developer.github.com/v3/git/refs/#get-a-reference
+   */
+  get("/api/v3/repos/:owner/:repository/git/refs/*")(referrersOnly { repository =>
+    val revstr = multiParams("splat").head
+    using(Git.open(getRepositoryDir(params("owner"), params("repository")))) { git =>
+      val ref = git.getRepository().findRef(revstr)
+
+      if (ref != null) {
+        val sha = ref.getObjectId().name()
+        JsonFormat(ApiRef(revstr, ApiObject(sha)))
+
+      } else {
+        val refs = git
+          .getRepository()
+          .getRefDatabase()
+          .getRefsByPrefix("refs/")
+          .asScala
+
+        JsonFormat(refs.map { ref =>
+          val sha = ref.getObjectId().name()
+          ApiRef(revstr, ApiObject(sha))
+        })
+      }
+    }
+  })
+  /*
+   * ii. Get all references
+   * https://developer.github.com/v3/git/refs/#get-all-references
+   */
+
+  /*
+   * iii. Create a reference
+   * https://developer.github.com/v3/git/refs/#create-a-reference
+   */
+
+  /*
+   * iv. Update a reference
+   * https://developer.github.com/v3/git/refs/#update-a-reference
+   */
+
+  /*
+ * v. Delete a reference
+ * https://developer.github.com/v3/git/refs/#delete-a-reference
+ */
+}

src/main/scala/gitbucket/core/controller/api/ApiIssueCommentControllerBase.scala

@@ -0,0 +1,79 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api.{ApiComment, ApiUser, CreateAComment, JsonFormat}
+import gitbucket.core.controller.{Context, ControllerBase}
+import gitbucket.core.service._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.{ReadableUsersAuthenticator, ReferrerAuthenticator, RepositoryName}
+
+trait ApiIssueCommentControllerBase extends ControllerBase {
+  self: AccountService
+    with IssuesService
+    with RepositoryService
+    with HandleCommentService
+    with MilestonesService
+    with ReadableUsersAuthenticator
+    with ReferrerAuthenticator =>
+  /*
+   * i. List comments on an issue
+   * https://developer.github.com/v3/issues/comments/#list-comments-on-an-issue
+   */
+  get("/api/v3/repos/:owner/:repository/issues/:id/comments")(referrersOnly { repository =>
+    (for {
+      issueId <- params("id").toIntOpt
+      comments = getCommentsForApi(repository.owner, repository.name, issueId)
+    } yield {
+      JsonFormat(comments.map {
+        case (issueComment, user, issue) =>
+          ApiComment(issueComment, RepositoryName(repository), issueId, ApiUser(user), issue.isPullRequest)
+      })
+    }) getOrElse NotFound()
+  })
+
+  /*
+   * ii. List comments in a repository
+   * https://developer.github.com/v3/issues/comments/#list-comments-in-a-repository
+   */
+
+  /*
+   * iii. Get a single comment
+   * https://developer.github.com/v3/issues/comments/#get-a-single-comment
+   */
+
+  /*
+   * iv. Create a comment
+   * https://developer.github.com/v3/issues/comments/#create-a-comment
+   */
+  post("/api/v3/repos/:owner/:repository/issues/:id/comments")(readableUsersOnly { repository =>
+    (for {
+      issueId <- params("id").toIntOpt
+      issue <- getIssue(repository.owner, repository.name, issueId.toString)
+      body <- extractFromJsonBody[CreateAComment].map(_.body) if !body.isEmpty
+      action = params.get("action").filter(_ => isEditable(issue.userName, issue.repositoryName, issue.openedUserName))
+      (issue, id) <- handleComment(issue, Some(body), repository, action)
+      issueComment <- getComment(repository.owner, repository.name, id.toString())
+    } yield {
+      JsonFormat(
+        ApiComment(
+          issueComment,
+          RepositoryName(repository),
+          issueId,
+          ApiUser(context.loginAccount.get),
+          issue.isPullRequest
+        )
+      )
+    }) getOrElse NotFound()
+  })
+
+  /*
+   * v. Edit a comment
+   * https://developer.github.com/v3/issues/comments/#edit-a-comment
+   */
+
+  /*
+   * vi. Delete a comment
+   * https://developer.github.com/v3/issues/comments/#delete-a-comment
+   */
+
+  private def isEditable(owner: String, repository: String, author: String)(implicit context: Context): Boolean =
+    hasDeveloperRole(owner, repository, context.loginAccount) || author == context.loginAccount.get.userName
+}

src/main/scala/gitbucket/core/controller/api/ApiIssueControllerBase.scala

@@ -0,0 +1,122 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api._
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.model.{Account, Issue}
+import gitbucket.core.service.{AccountService, IssueCreationService, IssuesService, MilestonesService}
+import gitbucket.core.service.IssuesService.IssueSearchCondition
+import gitbucket.core.service.PullRequestService.PullRequestLimit
+import gitbucket.core.util.{ReadableUsersAuthenticator, ReferrerAuthenticator, RepositoryName, UsersAuthenticator}
+import gitbucket.core.util.Implicits._
+
+trait ApiIssueControllerBase extends ControllerBase {
+  self: AccountService
+    with IssuesService
+    with IssueCreationService
+    with MilestonesService
+    with ReadableUsersAuthenticator
+    with ReferrerAuthenticator =>
+  /*
+   * i. List issues
+   * https://developer.github.com/v3/issues/#list-issues
+   * requested: 1743
+   */
+
+  /*
+   * ii. List issues for a repository
+   * https://developer.github.com/v3/issues/#list-issues-for-a-repository
+   */
+  get("/api/v3/repos/:owner/:repository/issues")(referrersOnly { repository =>
+    val page = IssueSearchCondition.page(request)
+    // TODO: more api spec condition
+    val condition = IssueSearchCondition(request)
+    val baseOwner = getAccountByUserName(repository.owner).get
+
+    val issues: List[(Issue, Account)] =
+      searchIssueByApi(
+        condition = condition,
+        offset = (page - 1) * PullRequestLimit,
+        limit = PullRequestLimit,
+        repos = repository.owner -> repository.name
+      )
+
+    JsonFormat(issues.map {
+      case (issue, issueUser) =>
+        ApiIssue(
+          issue = issue,
+          repositoryName = RepositoryName(repository),
+          user = ApiUser(issueUser),
+          labels = getIssueLabels(repository.owner, repository.name, issue.issueId)
+            .map(ApiLabel(_, RepositoryName(repository)))
+        )
+    })
+  })
+
+  /*
+   * iii. Get a single issue
+   * https://developer.github.com/v3/issues/#get-a-single-issue
+   */
+  get("/api/v3/repos/:owner/:repository/issues/:id")(referrersOnly { repository =>
+    (for {
+      issueId <- params("id").toIntOpt
+      issue <- getIssue(repository.owner, repository.name, issueId.toString)
+      openedUser <- getAccountByUserName(issue.openedUserName)
+    } yield {
+      JsonFormat(
+        ApiIssue(
+          issue,
+          RepositoryName(repository),
+          ApiUser(openedUser),
+          getIssueLabels(repository.owner, repository.name, issue.issueId).map(ApiLabel(_, RepositoryName(repository)))
+        )
+      )
+    }) getOrElse NotFound()
+  })
+
+  /*
+   * iv. Create an issue
+   * https://developer.github.com/v3/issues/#create-an-issue
+   */
+  post("/api/v3/repos/:owner/:repository/issues")(readableUsersOnly { repository =>
+    if (isIssueEditable(repository)) { // TODO Should this check is provided by authenticator?
+      (for {
+        data <- extractFromJsonBody[CreateAnIssue]
+        loginAccount <- context.loginAccount
+      } yield {
+        val milestone = data.milestone.flatMap(getMilestone(repository.owner, repository.name, _))
+        val issue = createIssue(
+          repository,
+          data.title,
+          data.body,
+          data.assignees.headOption,
+          milestone.map(_.milestoneId),
+          None,
+          data.labels,
+          loginAccount
+        )
+        JsonFormat(
+          ApiIssue(
+            issue,
+            RepositoryName(repository),
+            ApiUser(loginAccount),
+            getIssueLabels(repository.owner, repository.name, issue.issueId)
+              .map(ApiLabel(_, RepositoryName(repository)))
+          )
+        )
+      }) getOrElse NotFound()
+    } else Unauthorized()
+  })
+  /*
+   * v. Edit an issue
+   * https://developer.github.com/v3/issues/#edit-an-issue
+   */
+
+  /*
+   * vi. Lock an issue
+   * https://developer.github.com/v3/issues/#lock-an-issue
+   */
+
+  /*
+ * vii. Unlock an issue
+ * https://developer.github.com/v3/issues/#unlock-an-issue
+ */
+}

src/main/scala/gitbucket/core/controller/api/ApiIssueLabelControllerBase.scala

@@ -0,0 +1,195 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api.{ApiError, ApiLabel, CreateALabel, JsonFormat}
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.service._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util._
+import org.scalatra.{Created, NoContent, UnprocessableEntity}
+
+trait ApiIssueLabelControllerBase extends ControllerBase {
+  self: AccountService
+    with IssuesService
+    with LabelsService
+    with ReferrerAuthenticator
+    with WritableUsersAuthenticator =>
+
+  /*
+   * i. List all labels for this repository
+   * https://developer.github.com/v3/issues/labels/#list-all-labels-for-this-repository
+   */
+  get("/api/v3/repos/:owner/:repository/labels")(referrersOnly { repository =>
+    JsonFormat(getLabels(repository.owner, repository.name).map { label =>
+      ApiLabel(label, RepositoryName(repository))
+    })
+  })
+
+  /*
+   * ii. Get a single label
+   * https://developer.github.com/v3/issues/labels/#get-a-single-label
+   */
+  get("/api/v3/repos/:owner/:repository/labels/:labelName")(referrersOnly { repository =>
+    getLabel(repository.owner, repository.name, params("labelName")).map { label =>
+      JsonFormat(ApiLabel(label, RepositoryName(repository)))
+    } getOrElse NotFound()
+  })
+
+  /*
+   * iii. Create a label
+   * https://developer.github.com/v3/issues/labels/#create-a-label
+   */
+  post("/api/v3/repos/:owner/:repository/labels")(writableUsersOnly { repository =>
+    (for {
+      data <- extractFromJsonBody[CreateALabel] if data.isValid
+    } yield {
+      LockUtil.lock(RepositoryName(repository).fullName) {
+        if (getLabel(repository.owner, repository.name, data.name).isEmpty) {
+          val labelId = createLabel(repository.owner, repository.name, data.name, data.color)
+          getLabel(repository.owner, repository.name, labelId).map { label =>
+            Created(JsonFormat(ApiLabel(label, RepositoryName(repository))))
+          } getOrElse NotFound()
+        } else {
+          // TODO ApiError should support errors field to enhance compatibility of GitHub API
+          UnprocessableEntity(
+            ApiError(
+              "Validation Failed",
+              Some("https://developer.github.com/v3/issues/labels/#create-a-label")
+            )
+          )
+        }
+      }
+    }) getOrElse NotFound()
+  })
+
+  /*
+   * iv. Update a label
+   * https://developer.github.com/v3/issues/labels/#update-a-label
+   */
+  patch("/api/v3/repos/:owner/:repository/labels/:labelName")(writableUsersOnly { repository =>
+    (for {
+      data <- extractFromJsonBody[CreateALabel] if data.isValid
+    } yield {
+      LockUtil.lock(RepositoryName(repository).fullName) {
+        getLabel(repository.owner, repository.name, params("labelName")).map {
+          label =>
+            if (getLabel(repository.owner, repository.name, data.name).isEmpty) {
+              updateLabel(repository.owner, repository.name, label.labelId, data.name, data.color)
+              JsonFormat(
+                ApiLabel(
+                  getLabel(repository.owner, repository.name, label.labelId).get,
+                  RepositoryName(repository)
+                )
+              )
+            } else {
+              // TODO ApiError should support errors field to enhance compatibility of GitHub API
+              UnprocessableEntity(
+                ApiError(
+                  "Validation Failed",
+                  Some("https://developer.github.com/v3/issues/labels/#create-a-label")
+                )
+              )
+            }
+        } getOrElse NotFound()
+      }
+    }) getOrElse NotFound()
+  })
+
+  /*
+   * v. Delete a label
+   * https://developer.github.com/v3/issues/labels/#delete-a-label
+   */
+  delete("/api/v3/repos/:owner/:repository/labels/:labelName")(writableUsersOnly { repository =>
+    LockUtil.lock(RepositoryName(repository).fullName) {
+      getLabel(repository.owner, repository.name, params("labelName")).map { label =>
+        deleteLabel(repository.owner, repository.name, label.labelId)
+        NoContent()
+      } getOrElse NotFound()
+    }
+  })
+  /*
+   * vi. List labels on an issue
+   * https://developer.github.com/v3/issues/labels/#list-labels-on-an-issue
+   */
+  get("/api/v3/repos/:owner/:repository/issues/:id/labels")(referrersOnly { repository =>
+    JsonFormat(getIssueLabels(repository.owner, repository.name, params("id").toInt).map { l =>
+      ApiLabel(l, RepositoryName(repository.owner, repository.name))
+    })
+  })
+
+  /*
+   * vii. Add labels to an issue
+   * https://developer.github.com/v3/issues/labels/#add-labels-to-an-issue
+   */
+  post("/api/v3/repos/:owner/:repository/issues/:id/labels")(writableUsersOnly { repository =>
+    JsonFormat(for {
+      data <- extractFromJsonBody[Seq[String]];
+      issueId <- params("id").toIntOpt
+    } yield {
+      data.map { labelName =>
+        val label = getLabel(repository.owner, repository.name, labelName).getOrElse(
+          getLabel(
+            repository.owner,
+            repository.name,
+            createLabel(repository.owner, repository.name, labelName)
+          ).get
+        )
+        registerIssueLabel(repository.owner, repository.name, issueId, label.labelId, true)
+        ApiLabel(label, RepositoryName(repository.owner, repository.name))
+      }
+    })
+  })
+
+  /*
+   * viii. Remove a label from an issue
+   * https://developer.github.com/v3/issues/labels/#remove-a-label-from-an-issue
+   */
+  delete("/api/v3/repos/:owner/:repository/issues/:id/labels/:name")(writableUsersOnly { repository =>
+    val issueId = params("id").toInt
+    val labelName = params("name")
+    getLabel(repository.owner, repository.name, labelName) match {
+      case Some(label) =>
+        deleteIssueLabel(repository.owner, repository.name, issueId, label.labelId, true)
+        JsonFormat(Seq(label))
+      case None =>
+        NotFound()
+    }
+  })
+
+  /*
+   * ix. Replace all labels for an issue
+   * https://developer.github.com/v3/issues/labels/#replace-all-labels-for-an-issue
+   */
+  put("/api/v3/repos/:owner/:repository/issues/:id/labels")(writableUsersOnly { repository =>
+    JsonFormat(for {
+      data <- extractFromJsonBody[Seq[String]];
+      issueId <- params("id").toIntOpt
+    } yield {
+      deleteAllIssueLabels(repository.owner, repository.name, issueId, true)
+      data.map { labelName =>
+        val label = getLabel(repository.owner, repository.name, labelName).getOrElse(
+          getLabel(
+            repository.owner,
+            repository.name,
+            createLabel(repository.owner, repository.name, labelName)
+          ).get
+        )
+        registerIssueLabel(repository.owner, repository.name, issueId, label.labelId, true)
+        ApiLabel(label, RepositoryName(repository.owner, repository.name))
+      }
+    })
+  })
+
+  /*
+   * x. Remove all labels from an issue
+   * https://developer.github.com/v3/issues/labels/#remove-all-labels-from-an-issue
+   */
+  delete("/api/v3/repos/:owner/:repository/issues/:id/labels")(writableUsersOnly { repository =>
+    val issueId = params("id").toInt
+    deleteAllIssueLabels(repository.owner, repository.name, issueId, true)
+    NoContent()
+  })
+
+  /*
+ * xi Get labels for every issue in a milestone
+ * https://developer.github.com/v3/issues/labels/#get-labels-for-every-issue-in-a-milestone
+ */
+}

src/main/scala/gitbucket/core/controller/api/ApiOrganizationControllerBase.scala

@@ -0,0 +1,63 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api.{ApiGroup, ApiRepository, ApiUser, JsonFormat}
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.service.{AccountService, RepositoryService}
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.UsersAuthenticator
+
+trait ApiOrganizationControllerBase extends ControllerBase {
+  self: RepositoryService with AccountService with UsersAuthenticator =>
+
+  /*
+   * i. List your organizations
+   * https://developer.github.com/v3/orgs/#list-your-organizations
+   */
+  get("/api/v3/user/orgs")(usersOnly {
+    JsonFormat(getGroupsByUserName(context.loginAccount.get.userName).flatMap(getAccountByUserName(_)).map(ApiGroup(_)))
+  })
+
+  /*
+   * ii. List all organizations
+   * https://developer.github.com/v3/orgs/#list-all-organizations
+   */
+  get("/api/v3/organizations") {
+    JsonFormat(getAllUsers(false, true).filter(a => a.isGroupAccount).map(ApiGroup(_)))
+  }
+
+  /*
+   * iii. List user organizations
+   * https://developer.github.com/v3/orgs/#list-user-organizations
+   */
+  get("/api/v3/users/:userName/orgs") {
+    JsonFormat(getGroupsByUserName(params("userName")).flatMap(getAccountByUserName(_)).map(ApiGroup(_)))
+  }
+
+  /**
+   * iv. Get an organization
+   * https://developer.github.com/v3/orgs/#get-an-organization
+   */
+  get("/api/v3/orgs/:groupName") {
+    getAccountByUserName(params("groupName")).filter(account => account.isGroupAccount).map { account =>
+      JsonFormat(ApiGroup(account))
+    } getOrElse NotFound()
+  }
+
+  /*
+   * v. Edit an organization
+   * https://developer.github.com/v3/orgs/#edit-an-organization
+   */
+
+  /*
+   * ghe: i. Create an organization
+   * https://developer.github.com/enterprise/2.14/v3/enterprise-admin/orgs/#create-an-organization
+   */
+
+  /*
+   * ghe: ii. Rename an organization
+   * https://developer.github.com/enterprise/2.14/v3/enterprise-admin/orgs/#rename-an-organization
+   */
+
+  /*
+ * should implement delete an organization API?
+ */
+}

src/main/scala/gitbucket/core/controller/api/ApiPullRequestControllerBase.scala

@@ -0,0 +1,252 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api._
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.model.{Account, Issue, PullRequest, Repository}
+import gitbucket.core.service._
+import gitbucket.core.service.IssuesService.IssueSearchCondition
+import gitbucket.core.service.PullRequestService.PullRequestLimit
+import gitbucket.core.util.Directory.getRepositoryDir
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.JGitUtil.CommitInfo
+import gitbucket.core.util.SyntaxSugars.using
+import gitbucket.core.util._
+import org.eclipse.jgit.api.Git
+import org.scalatra.NoContent
+
+import scala.collection.JavaConverters._
+
+trait ApiPullRequestControllerBase extends ControllerBase {
+  self: AccountService
+    with IssuesService
+    with PullRequestService
+    with RepositoryService
+    with MergeService
+    with ReferrerAuthenticator
+    with ReadableUsersAuthenticator
+    with WritableUsersAuthenticator =>
+
+  /*
+   * i. Link Relations
+   * https://developer.github.com/v3/pulls/#link-relations
+   */
+
+  /*
+   * ii. List pull requests
+   * https://developer.github.com/v3/pulls/#list-pull-requests
+   */
+  get("/api/v3/repos/:owner/:repository/pulls")(referrersOnly { repository =>
+    val page = IssueSearchCondition.page(request)
+    // TODO: more api spec condition
+    val condition = IssueSearchCondition(request)
+    val baseOwner = getAccountByUserName(repository.owner).get
+
+    val issues: List[(Issue, Account, Int, PullRequest, Repository, Account, Option[Account])] =
+      searchPullRequestByApi(
+        condition = condition,
+        offset = (page - 1) * PullRequestLimit,
+        limit = PullRequestLimit,
+        repos = repository.owner -> repository.name
+      )
+
+    JsonFormat(issues.map {
+      case (issue, issueUser, commentCount, pullRequest, headRepo, headOwner, assignee) =>
+        ApiPullRequest(
+          issue = issue,
+          pullRequest = pullRequest,
+          headRepo = ApiRepository(headRepo, ApiUser(headOwner)),
+          baseRepo = ApiRepository(repository, ApiUser(baseOwner)),
+          user = ApiUser(issueUser),
+          labels = getIssueLabels(repository.owner, repository.name, issue.issueId)
+            .map(ApiLabel(_, RepositoryName(repository))),
+          assignee = assignee.map(ApiUser.apply),
+          mergedComment = getMergedComment(repository.owner, repository.name, issue.issueId)
+        )
+    })
+  })
+
+  /*
+   * iii. Get a single pull request
+   * https://developer.github.com/v3/pulls/#get-a-single-pull-request
+   */
+  get("/api/v3/repos/:owner/:repository/pulls/:id")(referrersOnly { repository =>
+    (for {
+      issueId <- params("id").toIntOpt
+    } yield {
+      JsonFormat(getApiPullRequest(repository, issueId))
+    }) getOrElse NotFound()
+  })
+
+  /*
+   * iv. Create a pull request
+   * https://developer.github.com/v3/pulls/#create-a-pull-request
+   * requested #1843
+   */
+  post("/api/v3/repos/:owner/:repository/pulls")(readableUsersOnly { repository =>
+    (for {
+      data <- extractFromJsonBody[Either[CreateAPullRequest, CreateAPullRequestAlt]]
+    } yield {
+      data match {
+        case Left(createPullReq) =>
+          val (reqOwner, reqBranch) = parseCompareIdentifier(createPullReq.head, repository.owner)
+          getRepository(reqOwner, repository.name)
+            .flatMap {
+              forkedRepository =>
+                getPullRequestCommitFromTo(repository, forkedRepository, createPullReq.base, reqBranch) match {
+                  case (Some(commitIdFrom), Some(commitIdTo)) =>
+                    val issueId = insertIssue(
+                      owner = repository.owner,
+                      repository = repository.name,
+                      loginUser = context.loginAccount.get.userName,
+                      title = createPullReq.title,
+                      content = createPullReq.body,
+                      assignedUserName = None,
+                      milestoneId = None,
+                      priorityId = None,
+                      isPullRequest = true
+                    )
+
+                    createPullRequest(
+                      originUserName = repository.owner,
+                      originRepositoryName = repository.name,
+                      issueId = issueId,
+                      originBranch = createPullReq.base,
+                      requestUserName = reqOwner,
+                      requestRepositoryName = repository.name,
+                      requestBranch = reqBranch,
+                      commitIdFrom = commitIdFrom.getName,
+                      commitIdTo = commitIdTo.getName
+                    )
+                    getApiPullRequest(repository, issueId).map(JsonFormat(_))
+                  case _ =>
+                    None
+                }
+            }
+            .getOrElse {
+              NotFound()
+            }
+        case Right(createPullReqAlt) =>
+          val (reqOwner, reqBranch) = parseCompareIdentifier(createPullReqAlt.head, repository.owner)
+          getRepository(reqOwner, repository.name)
+            .flatMap {
+              forkedRepository =>
+                getPullRequestCommitFromTo(repository, forkedRepository, createPullReqAlt.base, reqBranch) match {
+                  case (Some(commitIdFrom), Some(commitIdTo)) =>
+                    changeIssueToPullRequest(repository.owner, repository.name, createPullReqAlt.issue)
+                    createPullRequest(
+                      originUserName = repository.owner,
+                      originRepositoryName = repository.name,
+                      issueId = createPullReqAlt.issue,
+                      originBranch = createPullReqAlt.base,
+                      requestUserName = reqOwner,
+                      requestRepositoryName = repository.name,
+                      requestBranch = reqBranch,
+                      commitIdFrom = commitIdFrom.getName,
+                      commitIdTo = commitIdTo.getName
+                    )
+                    getApiPullRequest(repository, createPullReqAlt.issue).map(JsonFormat(_))
+                  case _ =>
+                    None
+                }
+            }
+            .getOrElse {
+              NotFound()
+            }
+      }
+    })
+  })
+
+  /*
+   * v. Update a pull request
+   * https://developer.github.com/v3/pulls/#update-a-pull-request
+   */
+
+  /*
+   * vi. List commits on a pull request
+   * https://developer.github.com/v3/pulls/#list-commits-on-a-pull-request
+   */
+  get("/api/v3/repos/:owner/:repository/pulls/:id/commits")(referrersOnly { repository =>
+    val owner = repository.owner
+    val name = repository.name
+    params("id").toIntOpt.flatMap {
+      issueId =>
+        getPullRequest(owner, name, issueId) map {
+          case (issue, pullreq) =>
+            using(Git.open(getRepositoryDir(owner, name))) { git =>
+              val oldId = git.getRepository.resolve(pullreq.commitIdFrom)
+              val newId = git.getRepository.resolve(pullreq.commitIdTo)
+              val repoFullName = RepositoryName(repository)
+              val commits = git.log
+                .addRange(oldId, newId)
+                .call
+                .iterator
+                .asScala
+                .map { c =>
+                  ApiCommitListItem(new CommitInfo(c), repoFullName)
+                }
+                .toList
+              JsonFormat(commits)
+            }
+        }
+    } getOrElse NotFound()
+  })
+  /*
+   * vii. List pull requests files
+   * https://developer.github.com/v3/pulls/#list-pull-requests-files
+   */
+
+  /*
+   * viii. Get if a pull request has been merged
+   * https://developer.github.com/v3/pulls/#get-if-a-pull-request-has-been-merged
+   */
+  get("/api/v3/repos/:owner/:repository/pulls/:id/merge")(referrersOnly { repository =>
+    (for {
+      issueId <- params("id").toIntOpt
+      (issue, pullReq) <- getPullRequest(repository.owner, repository.name, issueId)
+    } yield {
+      if (checkConflict(repository.owner, repository.name, pullReq.branch, issueId).isDefined) {
+        NoContent
+      } else {
+        NotFound
+      }
+    }).getOrElse(NotFound)
+  })
+
+  /*
+   * ix. Merge a pull request (Merge Button)
+   * https://developer.github.com/v3/pulls/#merge-a-pull-request-merge-button
+   */
+
+  /*
+   * x. Labels, assignees, and milestones
+   * https://developer.github.com/v3/pulls/#labels-assignees-and-milestones
+   */
+
+  private def getApiPullRequest(repository: RepositoryService.RepositoryInfo, issueId: Int): Option[ApiPullRequest] = {
+    for {
+      (issue, pullRequest) <- getPullRequest(repository.owner, repository.name, issueId)
+      users = getAccountsByUserNames(
+        Set(repository.owner, pullRequest.requestUserName, issue.openedUserName),
+        Set.empty
+      )
+      baseOwner <- users.get(repository.owner)
+      headOwner <- users.get(pullRequest.requestUserName)
+      issueUser <- users.get(issue.openedUserName)
+      assignee = issue.assignedUserName.flatMap { userName =>
+        getAccountByUserName(userName, false)
+      }
+      headRepo <- getRepository(pullRequest.requestUserName, pullRequest.requestRepositoryName)
+    } yield {
+      ApiPullRequest(
+        issue = issue,
+        pullRequest = pullRequest,
+        headRepo = ApiRepository(headRepo, ApiUser(headOwner)),
+        baseRepo = ApiRepository(repository, ApiUser(baseOwner)),
+        user = ApiUser(issueUser),
+        labels = getIssueLabels(repository.owner, repository.name, issue.issueId)
+          .map(ApiLabel(_, RepositoryName(repository))),
+        assignee = assignee.map(ApiUser.apply),
+        mergedComment = getMergedComment(repository.owner, repository.name, issue.issueId)
+      )
+    }
+  }
+}

src/main/scala/gitbucket/core/controller/api/ApiRepositoryBranchControllerBase.scala

@@ -0,0 +1,236 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api._
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.service.{AccountService, ProtectedBranchService, RepositoryService}
+import gitbucket.core.util._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.JGitUtil.getBranches
+
+trait ApiRepositoryBranchControllerBase extends ControllerBase {
+  self: RepositoryService
+    with AccountService
+    with OwnerAuthenticator
+    with UsersAuthenticator
+    with GroupManagerAuthenticator
+    with ProtectedBranchService
+    with ReferrerAuthenticator
+    with ReadableUsersAuthenticator
+    with WritableUsersAuthenticator =>
+
+  /**
+   * i. List branches
+   * https://developer.github.com/v3/repos/branches/#list-branches
+   */
+  get("/api/v3/repos/:owner/:repository/branches")(referrersOnly { repository =>
+    JsonFormat(
+      JGitUtil
+        .getBranches(
+          owner = repository.owner,
+          name = repository.name,
+          defaultBranch = repository.repository.defaultBranch,
+          origin = repository.repository.originUserName.isEmpty
+        )
+        .map { br =>
+          ApiBranchForList(br.name, ApiBranchCommit(br.commitId))
+        }
+    )
+  })
+
+  /**
+   * ii. Get branch
+   * https://developer.github.com/v3/repos/branches/#get-branch
+   */
+  get("/api/v3/repos/:owner/:repository/branches/*")(referrersOnly { repository =>
+    //import gitbucket.core.api._
+    (for {
+      branch <- params.get("splat") if repository.branchList.contains(branch)
+      br <- getBranches(
+        repository.owner,
+        repository.name,
+        repository.repository.defaultBranch,
+        repository.repository.originUserName.isEmpty
+      ).find(_.name == branch)
+    } yield {
+      val protection = getProtectedBranchInfo(repository.owner, repository.name, branch)
+      JsonFormat(
+        ApiBranch(branch, ApiBranchCommit(br.commitId), ApiBranchProtection(protection))(RepositoryName(repository))
+      )
+    }) getOrElse NotFound()
+  })
+
+  /*
+   * iii. Get branch protection
+   * https://developer.github.com/v3/repos/branches/#get-branch-protection
+   */
+
+  /*
+   * iv. Update branch protection
+   * https://developer.github.com/v3/repos/branches/#update-branch-protection
+   */
+
+  /*
+   * v. Remove branch protection
+   * https://developer.github.com/v3/repos/branches/#remove-branch-protection
+   */
+
+  /*
+   * vi. Get required status checks of protected branch
+   * https://developer.github.com/v3/repos/branches/#get-required-status-checks-of-protected-branch
+   */
+
+  /*
+   * vii. Update required status checks of protected branch
+   * https://developer.github.com/v3/repos/branches/#update-required-status-checks-of-protected-branch
+   */
+
+  /*
+   * viii. Remove required status checks of protected branch
+   * https://developer.github.com/v3/repos/branches/#remove-required-status-checks-of-protected-branch
+   */
+
+  /*
+   * ix. List required status checks contexts of protected branch
+   * https://developer.github.com/v3/repos/branches/#list-required-status-checks-contexts-of-protected-branch
+   */
+
+  /*
+   * x. Replace required status checks contexts of protected branch
+   * https://developer.github.com/v3/repos/branches/#replace-required-status-checks-contexts-of-protected-branch
+   */
+
+  /*
+   * xi. Add required status checks contexts of protected branch
+   * https://developer.github.com/v3/repos/branches/#remove-required-status-checks-contexts-of-protected-branch
+   */
+
+  /*
+   * xii. Remove required status checks contexts of protected branch
+   * https://developer.github.com/v3/repos/branches/#remove-required-status-checks-contexts-of-protected-branch
+   */
+
+  /*
+   * xiii. Get pull request review enforcement of protected branch
+   * https://developer.github.com/v3/repos/branches/#get-pull-request-review-enforcement-of-protected-branch
+   */
+
+  /*
+   * xiv. Update pull request review enforcement of protected branch
+   * https://developer.github.com/v3/repos/branches/#update-pull-request-review-enforcement-of-protected-branch
+   */
+
+  /*
+   * xv. Remove pull request review enforcement of protected branch
+   * https://developer.github.com/v3/repos/branches/#remove-pull-request-review-enforcement-of-protected-branch
+   */
+
+  /*
+   * xvi. Get required signatures of protected branch
+   * https://developer.github.com/v3/repos/branches/#get-required-signatures-of-protected-branch
+   */
+
+  /*
+   * xvii. Add required signatures of protected branch
+   * https://developer.github.com/v3/repos/branches/#add-required-signatures-of-protected-branch
+   */
+
+  /*
+   * xviii. Remove required signatures of protected branch
+   * https://developer.github.com/v3/repos/branches/#remove-required-signatures-of-protected-branch
+   */
+
+  /*
+   * xix. Get admin enforcement of protected branch
+   * https://developer.github.com/v3/repos/branches/#get-admin-enforcement-of-protected-branch
+   */
+
+  /*
+   * xx. Add admin enforcement of protected branch
+   * https://developer.github.com/v3/repos/branches/#add-admin-enforcement-of-protected-branch
+   */
+
+  /*
+   * xxi. Remove admin enforcement of protected branch
+   * https://developer.github.com/v3/repos/branches/#remove-admin-enforcement-of-protected-branch
+   */
+
+  /*
+   * xxii. Get restrictions of protected branch
+   * https://developer.github.com/v3/repos/branches/#get-restrictions-of-protected-branch
+   */
+
+  /*
+   * xxiii. Remove restrictions of protected branch
+   * https://developer.github.com/v3/repos/branches/#remove-restrictions-of-protected-branch
+   */
+
+  /*
+   * xxiv. List team restrictions of protected branch
+   * https://developer.github.com/v3/repos/branches/#list-team-restrictions-of-protected-branch
+   */
+
+  /*
+   * xxv. Replace team restrictions of protected branch
+   * https://developer.github.com/v3/repos/branches/#replace-team-restrictions-of-protected-branch
+   */
+
+  /*
+   * xxvi. Add team restrictions of protected branch
+   * https://developer.github.com/v3/repos/branches/#add-team-restrictions-of-protected-branch
+   */
+
+  /*
+   * xxvii. Remove team restrictions of protected branch
+   * https://developer.github.com/v3/repos/branches/#remove-team-restrictions-of-protected-branch
+   */
+
+  /*
+   * xxviii. List user restrictions of protected branch
+   * https://developer.github.com/v3/repos/branches/#list-user-restrictions-of-protected-branch
+   */
+
+  /*
+   * xxix. Replace user restrictions of protected branch
+   * https://developer.github.com/v3/repos/branches/#replace-user-restrictions-of-protected-branch
+   */
+
+  /*
+   * xxx. Add user restrictions of protected branch
+   * https://developer.github.com/v3/repos/branches/#add-user-restrictions-of-protected-branch
+   */
+
+  /*
+   * xxxi. Remove user restrictions of protected branch
+   * https://developer.github.com/v3/repos/branches/#remove-user-restrictions-of-protected-branch
+   */
+
+  /**
+   * Enabling and disabling branch protection: deprecated?
+   * https://developer.github.com/v3/repos/#enabling-and-disabling-branch-protection
+   */
+  patch("/api/v3/repos/:owner/:repository/branches/*")(ownerOnly { repository =>
+    import gitbucket.core.api._
+    (for {
+      branch <- params.get("splat") if repository.branchList.contains(branch)
+      protection <- extractFromJsonBody[ApiBranchProtection.EnablingAndDisabling].map(_.protection)
+      br <- getBranches(
+        repository.owner,
+        repository.name,
+        repository.repository.defaultBranch,
+        repository.repository.originUserName.isEmpty
+      ).find(_.name == branch)
+    } yield {
+      if (protection.enabled) {
+        enableBranchProtection(
+          repository.owner,
+          repository.name,
+          branch,
+          protection.status.enforcement_level == ApiBranchProtection.Everyone,
+          protection.status.contexts
+        )
+      } else {
+        disableBranchProtection(repository.owner, repository.name, branch)
+      }
+      JsonFormat(ApiBranch(branch, ApiBranchCommit(br.commitId), protection)(RepositoryName(repository)))
+    }) getOrElse NotFound()
+  })
+}

src/main/scala/gitbucket/core/controller/api/ApiRepositoryCollaboratorControllerBase.scala

@@ -0,0 +1,55 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api.{AddACollaborator, ApiUser, JsonFormat}
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.service.{AccountService, RepositoryService}
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.{OwnerAuthenticator, ReferrerAuthenticator}
+import org.scalatra.NoContent
+
+trait ApiRepositoryCollaboratorControllerBase extends ControllerBase {
+  self: RepositoryService with AccountService with ReferrerAuthenticator with OwnerAuthenticator =>
+
+  /*
+   * i. List collaborators
+   * https://developer.github.com/v3/repos/collaborators/#list-collaborators
+   */
+  get("/api/v3/repos/:owner/:repository/collaborators")(referrersOnly { repository =>
+    // TODO Should ApiUser take permission? getCollaboratorUserNames does not return owner group members.
+    JsonFormat(
+      getCollaboratorUserNames(params("owner"), params("repository")).map(u => ApiUser(getAccountByUserName(u).get))
+    )
+  })
+  /*
+   * ii. Check if a user is a collaborator
+   * https://developer.github.com/v3/repos/collaborators/#check-if-a-user-is-a-collaborator
+   */
+
+  /*
+   * iii. Review a user's permission level
+   * https://developer.github.com/v3/repos/collaborators/#review-a-users-permission-level
+   */
+
+  /*
+   * iv. Add user as a collaborator
+   * https://developer.github.com/v3/repos/collaborators/#add-user-as-a-collaborator
+   * requested #1586
+   */
+  put("/api/v3/repos/:owner/:repository/collaborators/:userName")(ownerOnly { repository =>
+    for {
+      data <- extractFromJsonBody[AddACollaborator]
+    } yield {
+      addCollaborator(repository.owner, repository.name, params("userName"), data.role)
+      NoContent()
+    }
+  })
+
+  /*
+   * v. Remove user as a collaborator
+   * https://developer.github.com/v3/repos/collaborators/#remove-user-as-a-collaborator
+   * requested #1586
+   */
+  delete("/api/v3/repos/:owner/:repository/collaborators/:userName")(ownerOnly { repository =>
+    removeCollaborator(repository.owner, repository.name, params("userName"))
+    NoContent()
+  })
+}

src/main/scala/gitbucket/core/controller/api/ApiRepositoryCommitControllerBase.scala

@@ -0,0 +1,85 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api.{ApiCommits, JsonFormat}
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.model.Account
+import gitbucket.core.service.{AccountService, CommitsService}
+import gitbucket.core.util.Directory.getRepositoryDir
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.JGitUtil.CommitInfo
+import gitbucket.core.util.{JGitUtil, ReferrerAuthenticator, RepositoryName}
+import gitbucket.core.util.SyntaxSugars.using
+import org.eclipse.jgit.api.Git
+import org.eclipse.jgit.revwalk.RevWalk
+
+trait ApiRepositoryCommitControllerBase extends ControllerBase {
+  self: AccountService with CommitsService with ReferrerAuthenticator =>
+  /*
+   * i. List commits on a repository
+   * https://developer.github.com/v3/repos/commits/#list-commits-on-a-repository
+   */
+
+  /*
+   * ii. Get a single commit
+   * https://developer.github.com/v3/repos/commits/#get-a-single-commit
+   */
+  get("/api/v3/repos/:owner/:repository/commits/:sha")(referrersOnly { repository =>
+    val owner = repository.owner
+    val name = repository.name
+    val sha = params("sha")
+
+    using(Git.open(getRepositoryDir(owner, name))) {
+      git =>
+        val repo = git.getRepository
+        val objectId = repo.resolve(sha)
+        val commitInfo = using(new RevWalk(repo)) { revWalk =>
+          new CommitInfo(revWalk.parseCommit(objectId))
+        }
+
+        JsonFormat(
+          ApiCommits(
+            repositoryName = RepositoryName(repository),
+            commitInfo = commitInfo,
+            diffs = JGitUtil.getDiffs(git, commitInfo.parents.headOption, commitInfo.id, false, true),
+            author = getAccount(commitInfo.authorName, commitInfo.authorEmailAddress),
+            committer = getAccount(commitInfo.committerName, commitInfo.committerEmailAddress),
+            commentCount = getCommitComment(repository.owner, repository.name, sha).size
+          )
+        )
+    }
+  })
+
+  private def getAccount(userName: String, email: String): Account = {
+    getAccountByMailAddress(email).getOrElse {
+      Account(
+        userName = userName,
+        fullName = userName,
+        mailAddress = email,
+        password = "xxx",
+        isAdmin = false,
+        url = None,
+        registeredDate = new java.util.Date(),
+        updatedDate = new java.util.Date(),
+        lastLoginDate = None,
+        image = None,
+        isGroupAccount = false,
+        isRemoved = true,
+        description = None
+      )
+    }
+  }
+
+  /*
+   * iii. Get the SHA-1 of a commit reference
+   * https://developer.github.com/v3/repos/commits/#get-the-sha-1-of-a-commit-reference
+   */
+
+  /*
+   * iv. Compare two commits
+   * https://developer.github.com/v3/repos/commits/#compare-two-commits
+   */
+
+  /*
+ * v. Commit signature verification
+ * https://developer.github.com/v3/repos/commits/#commit-signature-verification
+ */
+}

src/main/scala/gitbucket/core/controller/api/ApiRepositoryContentsControllerBase.scala

@@ -0,0 +1,126 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api.{ApiContents, JsonFormat}
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.service.{AccountService, ProtectedBranchService, RepositoryService}
+import gitbucket.core.util.Directory.getRepositoryDir
+import gitbucket.core.util.JGitUtil.{FileInfo, getContentFromId, getFileList}
+import gitbucket.core.util._
+import gitbucket.core.util.SyntaxSugars.using
+import gitbucket.core.view.helpers.{isRenderable, renderMarkup}
+import gitbucket.core.util.Implicits._
+import org.eclipse.jgit.api.Git
+
+trait ApiRepositoryContentsControllerBase extends ControllerBase {
+  self: ReferrerAuthenticator =>
+
+  /*
+   * i. Get the README
+   * https://developer.github.com/v3/repos/contents/#get-the-readme
+   */
+
+  /**
+   * ii. Get contents
+   * https://developer.github.com/v3/repos/contents/#get-contents
+   */
+  get("/api/v3/repos/:owner/:repository/contents")(referrersOnly { repository =>
+    getContents(repository, ".", params.getOrElse("ref", repository.repository.defaultBranch))
+  })
+
+  /**
+   * ii. Get contents
+   * https://developer.github.com/v3/repos/contents/#get-contents
+   */
+  get("/api/v3/repos/:owner/:repository/contents/*")(referrersOnly { repository =>
+    getContents(repository, multiParams("splat").head, params.getOrElse("ref", repository.repository.defaultBranch))
+  })
+
+  private def getContents(repository: RepositoryService.RepositoryInfo, path: String, refStr: String) = {
+    def getFileInfo(git: Git, revision: String, pathStr: String): Option[FileInfo] = {
+      val (dirName, fileName) = pathStr.lastIndexOf('/') match {
+        case -1 =>
+          (".", pathStr)
+        case n =>
+          (pathStr.take(n), pathStr.drop(n + 1))
+      }
+      getFileList(git, revision, dirName).find(f => f.name.equals(fileName))
+    }
+
+    using(Git.open(getRepositoryDir(params("owner"), params("repository")))) { git =>
+      val fileList = getFileList(git, refStr, path)
+      if (fileList.isEmpty) { // file or NotFound
+        getFileInfo(git, refStr, path)
+          .flatMap { f =>
+            val largeFile = params.get("large_file").exists(s => s.equals("true"))
+            val content = getContentFromId(git, f.id, largeFile)
+            request.getHeader("Accept") match {
+              case "application/vnd.github.v3.raw" => {
+                contentType = "application/vnd.github.v3.raw"
+                content
+              }
+              case "application/vnd.github.v3.html" if isRenderable(f.name) => {
+                contentType = "application/vnd.github.v3.html"
+                content.map { c =>
+                  List(
+                    "<div data-path=\"",
+                    path,
+                    "\" id=\"file\">",
+                    "<article>",
+                    renderMarkup(path.split("/").toList, new String(c), refStr, repository, false, false, true).body,
+                    "</article>",
+                    "</div>"
+                  ).mkString
+                }
+              }
+              case "application/vnd.github.v3.html" => {
+                contentType = "application/vnd.github.v3.html"
+                content.map { c =>
+                  List(
+                    "<div data-path=\"",
+                    path,
+                    "\" id=\"file\">",
+                    "<div class=\"plain\">",
+                    "<pre>",
+                    play.twirl.api.HtmlFormat.escape(new String(c)).body,
+                    "</pre>",
+                    "</div>",
+                    "</div>"
+                  ).mkString
+                }
+              }
+              case _ =>
+                Some(JsonFormat(ApiContents(f, RepositoryName(repository), content)))
+            }
+          }
+          .getOrElse(NotFound())
+
+      } else { // directory
+        JsonFormat(fileList.map { f =>
+          ApiContents(f, RepositoryName(repository), None)
+        })
+      }
+    }
+  }
+  /*
+   * iii. Create a file
+   * https://developer.github.com/v3/repos/contents/#create-a-file
+   * requested #2112
+   */
+
+  /*
+   * iv. Update a file
+   * https://developer.github.com/v3/repos/contents/#update-a-file
+   * requested #2112
+   */
+
+  /*
+   * v. Delete a file
+   * https://developer.github.com/v3/repos/contents/#delete-a-file
+   * should be implemented
+   */
+
+  /*
+ * vi. Get archive link
+ * https://developer.github.com/v3/repos/contents/#get-archive-link
+ */
+
+}

src/main/scala/gitbucket/core/controller/api/ApiRepositoryControllerBase.scala

@@ -0,0 +1,204 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api._
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.service.{AccountService, RepositoryCreationService, RepositoryService}
+import gitbucket.core.servlet.Database
+import gitbucket.core.util.Directory.getRepositoryDir
+import gitbucket.core.util._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.SyntaxSugars.using
+import gitbucket.core.model.Profile.profile.blockingApi._
+import org.eclipse.jgit.api.Git
+
+import scala.concurrent.Await
+import scala.concurrent.duration.Duration
+
+trait ApiRepositoryControllerBase extends ControllerBase {
+  self: RepositoryService
+    with RepositoryCreationService
+    with AccountService
+    with OwnerAuthenticator
+    with UsersAuthenticator
+    with GroupManagerAuthenticator
+    with ReferrerAuthenticator
+    with ReadableUsersAuthenticator
+    with WritableUsersAuthenticator =>
+
+  /**
+   * i. List your repositories
+   * https://developer.github.com/v3/repos/#list-your-repositories
+   */
+  get("/api/v3/user/repos")(usersOnly {
+    JsonFormat(getVisibleRepositories(context.loginAccount, Option(context.loginAccount.get.userName)).map { r =>
+      ApiRepository(r, getAccountByUserName(r.owner).get)
+    })
+  })
+
+  /**
+   * ii. List user repositories
+   * https://developer.github.com/v3/repos/#list-user-repositories
+   */
+  get("/api/v3/users/:userName/repos") {
+    JsonFormat(getVisibleRepositories(context.loginAccount, Some(params("userName"))).map { r =>
+      ApiRepository(r, getAccountByUserName(r.owner).get)
+    })
+  }
+
+  /**
+   * iii. List organization repositories
+   * https://developer.github.com/v3/repos/#list-organization-repositories
+   */
+  get("/api/v3/orgs/:orgName/repos") {
+    JsonFormat(getVisibleRepositories(context.loginAccount, Some(params("orgName"))).map { r =>
+      ApiRepository(r, getAccountByUserName(r.owner).get)
+    })
+  }
+
+  /*
+   * iv. List all public repositories
+   * https://developer.github.com/v3/repos/#list-all-public-repositories
+   * Not implemented
+   */
+
+  /*
+   * v. Create
+   * https://developer.github.com/v3/repos/#create
+   * Implemented with two methods (user/orgs)
+   */
+
+  /**
+   * Create user repository
+   * https://developer.github.com/v3/repos/#create
+   */
+  post("/api/v3/user/repos")(usersOnly {
+    val owner = context.loginAccount.get.userName
+    (for {
+      data <- extractFromJsonBody[CreateARepository] if data.isValid
+    } yield {
+      LockUtil.lock(s"${owner}/${data.name}") {
+        if (getRepository(owner, data.name).isEmpty) {
+          val f = createRepository(
+            context.loginAccount.get,
+            owner,
+            data.name,
+            data.description,
+            data.`private`,
+            data.auto_init
+          )
+          Await.result(f, Duration.Inf)
+
+          val repository = Database() withTransaction { session =>
+            getRepository(owner, data.name)(session).get
+          }
+          JsonFormat(ApiRepository(repository, ApiUser(getAccountByUserName(owner).get)))
+        } else {
+          ApiError(
+            "A repository with this name already exists on this account",
+            Some("https://developer.github.com/v3/repos/#create")
+          )
+        }
+      }
+    }) getOrElse NotFound()
+  })
+
+  /**
+   * Create group repository
+   * https://developer.github.com/v3/repos/#create
+   */
+  post("/api/v3/orgs/:org/repos")(managersOnly {
+    val groupName = params("org")
+    (for {
+      data <- extractFromJsonBody[CreateARepository] if data.isValid
+    } yield {
+      LockUtil.lock(s"${groupName}/${data.name}") {
+        if (getRepository(groupName, data.name).isEmpty) {
+          val f = createRepository(
+            context.loginAccount.get,
+            groupName,
+            data.name,
+            data.description,
+            data.`private`,
+            data.auto_init
+          )
+          Await.result(f, Duration.Inf)
+          val repository = Database() withTransaction { session =>
+            getRepository(groupName, data.name).get
+          }
+          JsonFormat(ApiRepository(repository, ApiUser(getAccountByUserName(groupName).get)))
+        } else {
+          ApiError(
+            "A repository with this name already exists for this group",
+            Some("https://developer.github.com/v3/repos/#create")
+          )
+        }
+      }
+    }) getOrElse NotFound()
+  })
+
+  /*
+   * vi. Get
+   * https://developer.github.com/v3/repos/#get
+   */
+  get("/api/v3/repos/:owner/:repository")(referrersOnly { repository =>
+    JsonFormat(ApiRepository(repository, ApiUser(getAccountByUserName(repository.owner).get)))
+  })
+
+  /*
+   * vii. Edit
+   * https://developer.github.com/v3/repos/#edit
+   */
+
+  /*
+   * viii. List all topics for a repository
+   * https://developer.github.com/v3/repos/#list-all-topics-for-a-repository
+   */
+
+  /*
+   * ix. Replace all topics for a repository
+   * https://developer.github.com/v3/repos/#replace-all-topics-for-a-repository
+   */
+
+  /*
+   * x. List contributors
+   * https://developer.github.com/v3/repos/#list-contributors
+   */
+
+  /*
+   * xi. List languages
+   * https://developer.github.com/v3/repos/#list-languages
+   */
+
+  /*
+   * xii. List teams
+   * https://developer.github.com/v3/repos/#list-teams
+   */
+
+  /*
+   * xiii. List tags
+   * https://developer.github.com/v3/repos/#list-tags
+   */
+
+  /*
+   * xiv. Delete a repository
+   * https://developer.github.com/v3/repos/#delete-a-repository
+   */
+
+  /*
+   * xv. Transfer a repository
+   * https://developer.github.com/v3/repos/#transfer-a-repository
+   */
+
+  /**
+   * non-GitHub compatible API for Jenkins-Plugin
+   */
+  get("/api/v3/repos/:owner/:repository/raw/*")(referrersOnly { repository =>
+    val (id, path) = repository.splitPath(multiParams("splat").head)
+    using(Git.open(getRepositoryDir(repository.owner, repository.name))) { git =>
+      val revCommit = JGitUtil.getRevCommitFromId(git, git.getRepository.resolve(id))
+
+      getPathObjectId(git, path, revCommit).map { objectId =>
+        responseRawFile(git, objectId, path, repository)
+      } getOrElse NotFound()
+    }
+  })
+}

src/main/scala/gitbucket/core/controller/api/ApiRepositoryStatusControllerBase.scala

@@ -0,0 +1,80 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api._
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.model.CommitState
+import gitbucket.core.service.{AccountService, CommitStatusService}
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.{JGitUtil, ReferrerAuthenticator, WritableUsersAuthenticator}
+
+trait ApiRepositoryStatusControllerBase extends ControllerBase {
+  self: AccountService with CommitStatusService with ReferrerAuthenticator with WritableUsersAuthenticator =>
+
+  /*
+   * i. Create a status
+   * https://developer.github.com/v3/repos/statuses/#create-a-status
+   */
+  post("/api/v3/repos/:owner/:repository/statuses/:sha")(writableUsersOnly { repository =>
+    (for {
+      ref <- params.get("sha")
+      sha <- JGitUtil.getShaByRef(repository.owner, repository.name, ref)
+      data <- extractFromJsonBody[CreateAStatus] if data.isValid
+      creator <- context.loginAccount
+      state <- CommitState.valueOf(data.state)
+      statusId = createCommitStatus(
+        repository.owner,
+        repository.name,
+        sha,
+        data.context.getOrElse("default"),
+        state,
+        data.target_url,
+        data.description,
+        new java.util.Date(),
+        creator
+      )
+      status <- getCommitStatus(repository.owner, repository.name, statusId)
+    } yield {
+      JsonFormat(ApiCommitStatus(status, ApiUser(creator)))
+    }) getOrElse NotFound()
+  })
+
+  /*
+   * ii. List statuses for a specific ref
+   * https://developer.github.com/v3/repos/statuses/#list-statuses-for-a-specific-ref
+   * ref is Ref to list the statuses from. It can be a SHA, a branch name, or a tag name.
+   */
+  val listStatusesRoute = get("/api/v3/repos/:owner/:repository/commits/:ref/statuses")(referrersOnly { repository =>
+    (for {
+      ref <- params.get("ref")
+      sha <- JGitUtil.getShaByRef(repository.owner, repository.name, ref)
+    } yield {
+      JsonFormat(getCommitStatuesWithCreator(repository.owner, repository.name, sha).map {
+        case (status, creator) =>
+          ApiCommitStatus(status, ApiUser(creator))
+      })
+    }) getOrElse NotFound()
+  })
+
+  /**
+   * https://developer.github.com/v3/repos/statuses/#list-statuses-for-a-specific-ref
+   * legacy route
+   */
+  get("/api/v3/repos/:owner/:repository/statuses/:ref") {
+    listStatusesRoute.action()
+  }
+
+  /*
+   * iii. Get the combined status for a specific ref
+   * https://developer.github.com/v3/repos/statuses/#get-the-combined-status-for-a-specific-ref
+   * ref is Ref to list the statuses from. It can be a SHA, a branch name, or a tag name.
+   */
+  get("/api/v3/repos/:owner/:repository/commits/:ref/status")(referrersOnly { repository =>
+    (for {
+      ref <- params.get("ref")
+      owner <- getAccountByUserName(repository.owner)
+      sha <- JGitUtil.getShaByRef(repository.owner, repository.name, ref)
+    } yield {
+      val statuses = getCommitStatuesWithCreator(repository.owner, repository.name, sha)
+      JsonFormat(ApiCombinedCommitStatus(sha, statuses, ApiRepository(repository, owner)))
+    }) getOrElse NotFound()
+  })
+}

src/main/scala/gitbucket/core/controller/api/ApiUserControllerBase.scala

@@ -0,0 +1,114 @@
+package gitbucket.core.controller.api
+import gitbucket.core.api.{ApiUser, CreateAUser, JsonFormat, UpdateAUser}
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.service.{AccountService, RepositoryService}
+import gitbucket.core.util.{AdminAuthenticator, UsersAuthenticator}
+import gitbucket.core.util.Implicits._
+import org.scalatra.NoContent
+
+trait ApiUserControllerBase extends ControllerBase {
+  self: RepositoryService with AccountService with AdminAuthenticator with UsersAuthenticator =>
+
+  /**
+   * i. Get a single user
+   * https://developer.github.com/v3/users/#get-a-single-user
+   * This API also returns group information (as GitHub).
+   */
+  get("/api/v3/users/:userName") {
+    getAccountByUserName(params("userName")).map { account =>
+      JsonFormat(ApiUser(account))
+    } getOrElse NotFound()
+  }
+
+  /**
+   * ii. Get the authenticated user
+   * https://developer.github.com/v3/users/#get-the-authenticated-user
+   */
+  get("/api/v3/user") {
+    context.loginAccount.map { account =>
+      JsonFormat(ApiUser(account))
+    } getOrElse Unauthorized()
+  }
+
+  /*
+   * iii. Update the authenticated user
+   * https://developer.github.com/v3/users/#update-the-authenticated-user
+   */
+  patch("/api/v3/user")(usersOnly {
+    (for {
+      data <- extractFromJsonBody[UpdateAUser]
+    } yield {
+      val loginAccount = context.loginAccount.get
+      val updatedAccount = loginAccount.copy(
+        mailAddress = data.email.getOrElse(loginAccount.mailAddress)
+      )
+      updateAccount(updatedAccount)
+      JsonFormat(ApiUser(updatedAccount))
+    })
+  })
+
+  /*
+   * iv. Get contextual information about a user
+   * https://developer.github.com/v3/users/#get-contextual-information-about-a-user
+   */
+
+  /*
+   * v. Get all users
+   * https://developer.github.com/v3/users/#get-all-users
+   */
+  get("/api/v3/users") {
+    JsonFormat(getAllUsers(false, false).map(a => ApiUser(a)))
+  }
+
+  /*
+   * ghe: i. Create a new user
+   * https://developer.github.com/enterprise/2.14/v3/enterprise-admin/users/#create-a-new-user
+   */
+  post("/api/v3/admin/users")(adminOnly {
+    for {
+      data <- extractFromJsonBody[CreateAUser]
+    } yield {
+      val user = createAccount(
+        data.login,
+        data.password,
+        data.fullName.getOrElse(data.login),
+        data.email,
+        data.isAdmin.getOrElse(false),
+        data.description,
+        data.url
+      )
+      JsonFormat(ApiUser(user))
+    }
+  })
+
+  /*
+   * ghe: vii. Suspend a user
+   * https://developer.github.com/enterprise/2.14/v3/enterprise-admin/users/#suspend-a-user
+   */
+  put("/api/v3/users/:userName/suspended")(adminOnly {
+    val userName = params("userName")
+    getAccountByUserName(userName) match {
+      case Some(targetAccount) =>
+        removeUserRelatedData(userName)
+        updateAccount(targetAccount.copy(isRemoved = true))
+        NoContent()
+      case None =>
+        NotFound()
+    }
+  })
+
+  /*
+   * ghe: vii. Unsuspend a user
+   * https://developer.github.com/enterprise/2.14/v3/enterprise-admin/users/#unsuspend-a-user
+   */
+  delete("/api/v3/users/:userName/suspended")(adminOnly {
+    val userName = params("userName")
+    getAccountByUserName(userName) match {
+      case Some(targetAccount) =>
+        updateAccount(targetAccount.copy(isRemoved = false))
+        NoContent()
+      case None =>
+        NotFound()
+    }
+  })
+}

src/main/scala/gitbucket/core/model/AccountExtraMailAddress.scala

@@ -0,0 +1,19 @@
+package gitbucket.core.model
+
+trait AccountExtraMailAddressComponent { self: Profile =>
+  import profile.api._
+
+  lazy val AccountExtraMailAddresses = TableQuery[AccountExtraMailAddresses]
+
+  class AccountExtraMailAddresses(tag: Tag) extends Table[AccountExtraMailAddress](tag, "ACCOUNT_EXTRA_MAIL_ADDRESS") {
+    val userName = column[String]("USER_NAME", O PrimaryKey)
+    val extraMailAddress = column[String]("EXTRA_MAIL_ADDRESS", O PrimaryKey)
+    def * =
+      (userName, extraMailAddress) <> (AccountExtraMailAddress.tupled, AccountExtraMailAddress.unapply)
+  }
+}
+
+case class AccountExtraMailAddress(
+  userName: String,
+  extraMailAddress: String
+)

src/main/scala/gitbucket/core/model/Comment.scala

@@ -1,6 +1,7 @@
 package gitbucket.core.model
+import java.util.Date
 
-trait Comment {
+sealed trait Comment {
   val commentedUserName: String
   val registeredDate: java.util.Date
 }
@@ -53,6 +54,9 @@ trait CommitCommentComponent extends TemplateComponent { self: Profile =>
     val registeredDate = column[java.util.Date]("REGISTERED_DATE")
     val updatedDate = column[java.util.Date]("UPDATED_DATE")
     val issueId = column[Option[Int]]("ISSUE_ID")
+    val originalCommitId = column[String]("ORIGINAL_COMMIT_ID")
+    val originalOldLine = column[Option[Int]]("ORIGINAL_OLD_LINE")
+    val originalNewLine = column[Option[Int]]("ORIGINAL_NEW_LINE")
     def * =
       (
         userName,
@@ -66,7 +70,10 @@ trait CommitCommentComponent extends TemplateComponent { self: Profile =>
         newLine,
         registeredDate,
         updatedDate,
-        issueId
+        issueId,
+        originalCommitId,
+        originalOldLine,
+        originalNewLine
       ) <> (CommitComment.tupled, CommitComment.unapply)
 
     def byPrimaryKey(commentId: Int) = this.commentId === commentId.bind
@@ -85,5 +92,16 @@ case class CommitComment(
   newLine: Option[Int],
   registeredDate: java.util.Date,
   updatedDate: java.util.Date,
-  issueId: Option[Int]
+  issueId: Option[Int],
+  originalCommitId: String,
+  originalOldLine: Option[Int],
+  originalNewLine: Option[Int]
+) extends Comment
+
+case class CommitComments(
+  fileName: String,
+  commentedUserName: String,
+  registeredDate: Date,
+  comments: Seq[CommitComment],
+  diff: Option[String]
 ) extends Comment

src/main/scala/gitbucket/core/model/Profile.scala

@@ -68,5 +68,6 @@ trait CoreProfile
     with DeployKeyComponent
     with ReleaseTagComponent
     with ReleaseAssetComponent
+    with AccountExtraMailAddressComponent
 
 object Profile extends CoreProfile

src/main/scala/gitbucket/core/plugin/IssueHook.scala

@@ -1,7 +1,7 @@
 package gitbucket.core.plugin
 
 import gitbucket.core.controller.Context
-import gitbucket.core.model.Issue
+import gitbucket.core.model.{Account, Issue}
 import gitbucket.core.service.RepositoryService.RepositoryInfo
 import gitbucket.core.model.Profile._
 import profile.api._
@@ -15,6 +15,19 @@ trait IssueHook {
   ): Unit = ()
   def closed(issue: Issue, repository: RepositoryInfo)(implicit session: Session, context: Context): Unit = ()
   def reopened(issue: Issue, repository: RepositoryInfo)(implicit session: Session, context: Context): Unit = ()
+  def assigned(
+    issue: Issue,
+    repository: RepositoryInfo,
+    assigner: Option[String],
+    assigned: Option[String],
+    oldAssigned: Option[String]
+  )(
+    implicit session: Session,
+    context: Context
+  ): Unit = ()
+  def closedByCommitComment(issue: Issue, repository: RepositoryInfo, message: String, pusher: Account)(
+    implicit session: Session
+  ): Unit = ()
 
 }
 

src/main/scala/gitbucket/core/plugin/Plugin.scala

@@ -8,7 +8,7 @@ import gitbucket.core.service.RepositoryService.RepositoryInfo
 import gitbucket.core.service.SystemSettingsService.SystemSettings
 import gitbucket.core.util.SyntaxSugars._
 import io.github.gitbucket.solidbase.model.Version
-import org.apache.sshd.server.Command
+import org.apache.sshd.server.command.Command
 import play.twirl.api.Html
 
 /**
@@ -47,6 +47,20 @@ abstract class Plugin {
     settings: SystemSettings
   ): Seq[(String, ControllerBase)] = Nil
 
+  /**
+   * Override to declare this plug-in provides anonymous accessible paths.
+   */
+  val anonymousAccessiblePaths: Seq[String] = Nil
+
+  /**
+   * Override to declare this plug-in provides anonymous accessible paths.
+   */
+  def anonymousAccessiblePaths(
+    registry: PluginRegistry,
+    context: ServletContext,
+    settings: SystemSettings
+  ): Seq[String] = Nil
+
   /**
    * Override to declare this plug-in provides JavaScript.
    */
@@ -333,6 +347,10 @@ abstract class Plugin {
       case (path, controller) =>
         registry.addController(path, controller)
     }
+    (anonymousAccessiblePaths ++ anonymousAccessiblePaths(registry, context, settings)).foreach {
+      case (path) =>
+        registry.addAnonymousAccessiblePath(path)
+    }
     (javaScripts ++ javaScripts(registry, context, settings)).foreach {
       case (path, script) =>
         registry.addJavaScript(path, script)

src/main/scala/gitbucket/core/plugin/PluginRegistry.scala

@@ -1,28 +1,29 @@
 package gitbucket.core.plugin
 
-import java.io.{File, FilenameFilter, InputStream}
+import java.io.{File, FilenameFilter}
 import java.net.URLClassLoader
 import java.nio.file.{Files, Paths, StandardWatchEventKinds}
 import java.util.Base64
-import java.util.concurrent.atomic.AtomicBoolean
 import java.util.concurrent.ConcurrentLinkedQueue
 import java.util.concurrent.ConcurrentHashMap
-import javax.servlet.ServletContext
 
+import javax.servlet.ServletContext
+import com.github.zafarkhaja.semver.Version
 import gitbucket.core.controller.{Context, ControllerBase}
 import gitbucket.core.model.{Account, Issue}
 import gitbucket.core.service.ProtectedBranchService.ProtectedBranchReceiveHook
 import gitbucket.core.service.RepositoryService.RepositoryInfo
 import gitbucket.core.service.SystemSettingsService
 import gitbucket.core.service.SystemSettingsService.SystemSettings
-import gitbucket.core.util.SyntaxSugars._
 import gitbucket.core.util.DatabaseConfig
 import gitbucket.core.util.Directory._
+import gitbucket.core.util.HttpClientUtil._
 import io.github.gitbucket.solidbase.Solidbase
 import io.github.gitbucket.solidbase.manager.JDBCVersionManager
 import io.github.gitbucket.solidbase.model.Module
 import org.apache.commons.io.FileUtils
-import org.apache.sshd.server.Command
+import org.apache.http.client.methods.HttpGet
+import org.apache.sshd.server.command.Command
 import org.slf4j.LoggerFactory
 import play.twirl.api.Html
 
@@ -33,6 +34,7 @@ class PluginRegistry {
   private val plugins = new ConcurrentLinkedQueue[PluginInfo]
   private val javaScripts = new ConcurrentLinkedQueue[(String, String)]
   private val controllers = new ConcurrentLinkedQueue[(ControllerBase, String)]
+  private val anonymousAccessiblePaths = new ConcurrentLinkedQueue[String]
   private val images = new ConcurrentHashMap[String, String]
   private val renderers = new ConcurrentHashMap[String, Renderer]
   renderers.put("md", MarkdownRenderer)
@@ -68,25 +70,16 @@ class PluginRegistry {
     images.put(id, encoded)
   }
 
-  @deprecated("Use addImage(id: String, bytes: Array[Byte]) instead", "3.4.0")
-  def addImage(id: String, in: InputStream): Unit = {
-    val bytes = using(in) { in =>
-      val bytes = new Array[Byte](in.available)
-      in.read(bytes)
-      bytes
-    }
-    addImage(id, bytes)
-  }
-
   def getImage(id: String): String = images.get(id)
 
   def addController(path: String, controller: ControllerBase): Unit = controllers.add((controller, path))
 
-  @deprecated("Use addController(path: String, controller: ControllerBase) instead", "3.4.0")
-  def addController(controller: ControllerBase, path: String): Unit = addController(path, controller)
-
   def getControllers(): Seq[(ControllerBase, String)] = controllers.asScala.toSeq
 
+  def addAnonymousAccessiblePath(path: String): Unit = anonymousAccessiblePaths.add(path)
+
+  def getAnonymousAccessiblePaths(): Seq[String] = anonymousAccessiblePaths.asScala.toSeq
+
   def addJavaScript(path: String, script: String): Unit =
     javaScripts.add((path, script)) //javaScripts += ((path, script))
 
@@ -202,7 +195,6 @@ object PluginRegistry {
 
   private var watcher: PluginWatchThread = null
   private var extraWatcher: PluginWatchThread = null
-  private val initializing = new AtomicBoolean(false)
 
   /**
    * Returns the PluginRegistry singleton instance.
@@ -223,30 +215,48 @@ object PluginRegistry {
    */
   def uninstall(pluginId: String, context: ServletContext, settings: SystemSettings, conn: java.sql.Connection): Unit =
     synchronized {
-      instance
-        .getPlugins()
-        .collect { case plugin if plugin.pluginId == pluginId => plugin }
-        .foreach { plugin =>
-//      try {
-//        plugin.pluginClass.uninstall(instance, context, settings)
-//      } catch {
-//        case e: Exception =>
-//          logger.error(s"Error during uninstalling plugin: ${plugin.pluginJar.getName}", e)
-//      }
-          shutdown(context, settings)
-          plugin.pluginJar.delete()
-          instance = new PluginRegistry()
-          initialize(context, settings, conn)
-        }
+      shutdown(context, settings)
+
+      new File(PluginHome)
+        .listFiles((_: File, name: String) => {
+          name.startsWith(s"gitbucket-${pluginId}-plugin") && name.endsWith(".jar")
+        })
+        .foreach(_.delete())
+
+      instance = new PluginRegistry()
+      initialize(context, settings, conn)
     }
 
   /**
    * Install a plugin from a specified jar file.
    */
-  def install(file: File, context: ServletContext, settings: SystemSettings, conn: java.sql.Connection): Unit =
+  def install(
+    pluginId: String,
+    url: java.net.URL,
+    context: ServletContext,
+    settings: SystemSettings,
+    conn: java.sql.Connection
+  ): Unit =
     synchronized {
       shutdown(context, settings)
-      FileUtils.copyFile(file, new File(PluginHome, file.getName))
+
+      new File(PluginHome)
+        .listFiles((_: File, name: String) => {
+          name.startsWith(s"gitbucket-${pluginId}-plugin") && name.endsWith(".jar")
+        })
+        .foreach(_.delete())
+
+      withHttpClient(settings.pluginProxy) { httpClient =>
+        val httpGet = new HttpGet(url.toString)
+        try {
+          val response = httpClient.execute(httpGet)
+          val in = response.getEntity.getContent
+          FileUtils.copyToFile(in, new File(PluginHome, new File(url.getFile).getName))
+        } finally {
+          httpGet.releaseConnection()
+        }
+      }
+
       instance = new PluginRegistry()
       initialize(context, settings, conn)
     }
@@ -257,12 +267,33 @@ object PluginRegistry {
         override def accept(dir: File, name: String): Boolean = name.endsWith(".jar")
       })
       .toSeq
-      .sortBy(_.getName)
+      .sortBy(x => Version.valueOf(getPluginVersion(x.getName)))
       .reverse
   }
 
   lazy val extraPluginDir: Option[String] = Option(System.getProperty("gitbucket.pluginDir"))
 
+  def getGitBucketVersion(pluginJarFileName: String): Option[String] = {
+    val regex = ".+-gitbucket\\_(\\d+\\.\\d+\\.\\d+(-SNAPSHOT)?)-.+".r
+    pluginJarFileName match {
+      case regex(all, _) => Some(all)
+      case _             => None
+    }
+  }
+
+  def getPluginVersion(pluginJarFileName: String): String = {
+    val regex = ".+-((\\d+)\\.(\\d+)(\\.(\\d+))?(-SNAPSHOT)?)\\.jar$".r
+    pluginJarFileName match {
+      case regex(all, major, minor, _, patch, modifier) => {
+        if (patch != null) all
+        else {
+          s"${major}.${minor}.0" + (if (modifier == null) "" else modifier)
+        }
+      }
+      case _ => "0.0.0"
+    }
+  }
+
   /**
    * Initializes all installed plugins.
    */
@@ -278,6 +309,7 @@ object PluginRegistry {
     installedDir.mkdirs()
 
     val pluginJars = listPluginJars(pluginDir)
+
     val extraJars = extraPluginDir
       .map { extraDir =>
         listPluginJars(new File(extraDir))
@@ -288,9 +320,9 @@ object PluginRegistry {
       val installedJar = new File(installedDir, pluginJar.getName)
 
       FileUtils.copyFile(pluginJar, installedJar)
-
       logger.info(s"Initialize ${pluginJar.getName}")
-      val classLoader = new URLClassLoader(Array(installedJar.toURI.toURL), Thread.currentThread.getContextClassLoader)
+      val classLoader =
+        new URLClassLoader(Array(installedJar.toURI.toURL), Thread.currentThread.getContextClassLoader)
       try {
         val plugin = classLoader.loadClass("Plugin").getDeclaredConstructor().newInstance().asInstanceOf[Plugin]
         val pluginId = plugin.pluginId
@@ -304,7 +336,12 @@ object PluginRegistry {
             // Migration
             val solidbase = new Solidbase()
             solidbase
-              .migrate(conn, classLoader, DatabaseConfig.liquiDriver, new Module(plugin.pluginId, plugin.versions: _*))
+              .migrate(
+                conn,
+                classLoader,
+                DatabaseConfig.liquiDriver,
+                new Module(plugin.pluginId, plugin.versions: _*)
+              )
             conn.commit()
 
             // Check database version
@@ -323,6 +360,7 @@ object PluginRegistry {
                 pluginId = plugin.pluginId,
                 pluginName = plugin.pluginName,
                 pluginVersion = plugin.versions.last.getVersion,
+                gitbucketVersion = getGitBucketVersion(installedJar.getName),
                 description = plugin.description,
                 pluginClass = plugin,
                 pluginJar = pluginJar,
@@ -384,6 +422,7 @@ class PluginInfoBase(
   val pluginId: String,
   val pluginName: String,
   val pluginVersion: String,
+  val gitbucketVersion: Option[String],
   val description: String
 )
 
@@ -391,11 +430,12 @@ case class PluginInfo(
   override val pluginId: String,
   override val pluginName: String,
   override val pluginVersion: String,
+  override val gitbucketVersion: Option[String],
   override val description: String,
   pluginClass: Plugin,
   pluginJar: File,
   classLoader: URLClassLoader
-) extends PluginInfoBase(pluginId, pluginName, pluginVersion, description)
+) extends PluginInfoBase(pluginId, pluginName, pluginVersion, gitbucketVersion, description)
 
 class PluginWatchThread(context: ServletContext, dir: String) extends Thread with SystemSettingsService {
   import gitbucket.core.model.Profile.profile.blockingApi._

src/main/scala/gitbucket/core/plugin/PluginRepository.scala

@@ -1,25 +1,44 @@
 package gitbucket.core.plugin
 
+import gitbucket.core.controller.Context
+import gitbucket.core.util.SyntaxSugars.using
+import gitbucket.core.util.HttpClientUtil._
 import org.json4s._
-import gitbucket.core.util.Directory._
-import org.apache.commons.io.FileUtils
+import org.apache.commons.io.IOUtils
+
+import org.apache.http.client.methods.HttpGet
+import org.slf4j.LoggerFactory
 
 object PluginRepository {
+  private val logger = LoggerFactory.getLogger(getClass)
   implicit val formats = DefaultFormats
 
   def parsePluginJson(json: String): Seq[PluginMetadata] = {
     org.json4s.jackson.JsonMethods.parse(json).extract[Seq[PluginMetadata]]
   }
 
-  lazy val LocalRepositoryDir = new java.io.File(PluginHome, ".repository")
-  lazy val LocalRepositoryIndexFile = new java.io.File(LocalRepositoryDir, "plugins.json")
+  def getPlugins()(implicit context: Context): Seq[PluginMetadata] = {
+    try {
+      val url = new java.net.URL("https://plugins.gitbucket-community.org/releases/plugins.json")
 
-  def getPlugins(): Seq[PluginMetadata] = {
-    if (LocalRepositoryIndexFile.exists) {
-      parsePluginJson(FileUtils.readFileToString(LocalRepositoryIndexFile, "UTF-8"))
-    } else Nil
+      withHttpClient(context.settings.pluginProxy) { httpClient =>
+        val httpGet = new HttpGet(url.toString)
+        try {
+          val response = httpClient.execute(httpGet)
+          using(response.getEntity.getContent) { in =>
+            val str = IOUtils.toString(in, "UTF-8")
+            parsePluginJson(str)
+          }
+        } finally {
+          httpGet.releaseConnection()
+        }
+      }
+    } catch {
+      case t: Throwable =>
+        logger.warn("Failed to access to the plugin repository: " + t.toString)
+        Nil
+    }
   }
-
 }
 
 // Mapped from plugins.json
@@ -36,7 +55,5 @@ case class PluginMetadata(
 case class VersionDef(
   version: String,
   url: String,
-  range: String
-) {
-  lazy val file = url.substring(url.lastIndexOf("/") + 1)
-}
+  gitbucketVersion: String
+)

src/main/scala/gitbucket/core/plugin/Renderer.scala

@@ -25,10 +25,13 @@ object MarkdownRenderer extends Renderer {
       Markdown.toHtml(
         markdown = fileContent,
         repository = repository,
+        branch = branch,
         enableWikiLink = enableWikiLink,
         enableRefsLink = enableRefsLink,
         enableAnchor = enableAnchor,
-        enableLineBreaks = false
+        enableLineBreaks = false,
+        enableTaskList = true,
+        hasWritePermission = false
       )(context)
     )
   }

src/main/scala/gitbucket/core/service/AccessTokenService.scala

@@ -5,13 +5,13 @@ import gitbucket.core.model.Profile.profile.blockingApi._
 import gitbucket.core.model.{AccessToken, Account}
 import gitbucket.core.util.StringUtil
 
-import scala.util.Random
+import java.security.SecureRandom
 
 trait AccessTokenService {
 
   def makeAccessTokenString: String = {
     val bytes = new Array[Byte](20)
-    Random.nextBytes(bytes)
+    AccessTokenService.secureRandom.nextBytes(bytes)
     bytes.map("%02x".format(_)).mkString
   }
 
@@ -55,4 +55,6 @@ trait AccessTokenService {
 
 }
 
-object AccessTokenService extends AccessTokenService
+object AccessTokenService extends AccessTokenService {
+  private val secureRandom = new SecureRandom()
+}

src/main/scala/gitbucket/core/service/AccountService.scala

@@ -1,12 +1,13 @@
 package gitbucket.core.service
 
 import org.slf4j.LoggerFactory
-import gitbucket.core.model.{GroupMember, Account}
+import gitbucket.core.model.{Account, AccountExtraMailAddress, GroupMember}
 import gitbucket.core.model.Profile._
 import gitbucket.core.model.Profile.profile.blockingApi._
 import gitbucket.core.model.Profile.dateColumnType
-import gitbucket.core.util.{StringUtil, LDAPUtil}
+import gitbucket.core.util.{LDAPUtil, StringUtil}
 import StringUtil._
+import gitbucket.core.plugin.PluginRegistry
 import gitbucket.core.service.SystemSettingsService.SystemSettings
 
 trait AccountService {
@@ -33,7 +34,16 @@ trait AccountService {
    * Authenticate by internal database.
    */
   private def defaultAuthentication(userName: String, password: String)(implicit s: Session) = {
+    val pbkdf2re = """^\$pbkdf2-sha256\$(\d+)\$([0-9a-zA-Z+/=]+)\$([0-9a-zA-Z+/=]+)$""".r
     getAccountByUserName(userName).collect {
+      case account if !account.isGroupAccount =>
+        account.password match {
+          case pbkdf2re(iter, salt, hash) if (pbkdf2_sha256(iter.toInt, salt, password) == hash) => Some(account)
+          case p if p == sha1(password) =>
+            updateAccount(account.copy(password = pbkdf2_sha256(password)))
+            Some(account)
+          case _ => None
+        }
       case account if (!account.isGroupAccount && account.password == sha1(password)) => Some(account)
     } getOrElse None
   }
@@ -95,6 +105,13 @@ trait AccountService {
   def getAccountByUserName(userName: String, includeRemoved: Boolean = false)(implicit s: Session): Option[Account] =
     Accounts filter (t => (t.userName === userName.bind) && (t.removed === false.bind, !includeRemoved)) firstOption
 
+  def getAccountByUserNameIgnoreCase(userName: String, includeRemoved: Boolean = false)(
+    implicit s: Session
+  ): Option[Account] =
+    Accounts filter (
+      t => (t.userName.toLowerCase === userName.toLowerCase.bind) && (t.removed === false.bind, !includeRemoved)
+    ) firstOption
+
   def getAccountsByUserNames(userNames: Set[String], knowns: Set[Account], includeRemoved: Boolean = false)(
     implicit s: Session
   ): Map[String, Account] = {
@@ -114,9 +131,16 @@ trait AccountService {
   def getAccountByMailAddress(mailAddress: String, includeRemoved: Boolean = false)(
     implicit s: Session
   ): Option[Account] =
-    Accounts filter (
-      t => (t.mailAddress.toLowerCase === mailAddress.toLowerCase.bind) && (t.removed === false.bind, !includeRemoved)
-    ) firstOption
+    (Accounts joinLeft AccountExtraMailAddresses on { case (a, e) => a.userName === e.userName })
+      .filter {
+        case (a, x) =>
+          ((a.mailAddress.toLowerCase === mailAddress.toLowerCase.bind) ||
+            (x.map { e =>
+                e.extraMailAddress.toLowerCase === mailAddress.toLowerCase.bind
+              }
+              .getOrElse(false.bind))) && (a.removed === false.bind, !includeRemoved)
+      }
+      .map { case (a, e) => a } firstOption
 
   def getAllUsers(includeRemoved: Boolean = true, includeGroups: Boolean = true)(implicit s: Session): List[Account] = {
     Accounts filter { t =>
@@ -140,8 +164,8 @@ trait AccountService {
     isAdmin: Boolean,
     description: Option[String],
     url: Option[String]
-  )(implicit s: Session): Unit =
-    Accounts insert Account(
+  )(implicit s: Session): Account = {
+    val account = Account(
       userName = userName,
       password = password,
       fullName = fullName,
@@ -156,6 +180,18 @@ trait AccountService {
       isRemoved = false,
       description = description
     )
+    Accounts insert account
+    account
+  }
+
+  def suspendAccount(account: Account)(implicit s: Session): Unit = {
+    // Remove from GROUP_MEMBER and COLLABORATOR
+    removeUserRelatedData(account.userName)
+    updateAccount(account.copy(isRemoved = true))
+
+    // call hooks
+    PluginRegistry().getAccountHooks.foreach(_.deleted(account.userName))
+  }
 
   def updateAccount(account: Account)(implicit s: Session): Unit =
     Accounts
@@ -192,6 +228,15 @@ trait AccountService {
   def updateAvatarImage(userName: String, image: Option[String])(implicit s: Session): Unit =
     Accounts.filter(_.userName === userName.bind).map(_.image.?).update(image)
 
+  def getAccountExtraMailAddresses(userName: String)(implicit s: Session): List[String] = {
+    AccountExtraMailAddresses.filter(_.userName === userName.bind).map(_.extraMailAddress) list
+  }
+
+  def updateAccountExtraMailAddresses(userName: String, mails: List[String])(implicit s: Session): Unit = {
+    AccountExtraMailAddresses.filter(_.userName === userName.bind).delete
+    mails.map(AccountExtraMailAddresses insert AccountExtraMailAddress(userName, _))
+  }
+
   def updateLastLoginDate(userName: String)(implicit s: Session): Unit =
     Accounts.filter(_.userName === userName.bind).map(_.lastLoginDate).update(currentDate)
 
@@ -246,6 +291,15 @@ trait AccountService {
     Collaborators.filter(_.collaboratorName === userName.bind).delete
   }
 
+  def removeUser(account: Account)(implicit s: Session): Unit = {
+    // Remove from GROUP_MEMBER and COLLABORATOR
+    removeUserRelatedData(account.userName)
+    updateAccount(account.copy(isRemoved = true))
+
+    // call hooks
+    PluginRegistry().getAccountHooks.foreach(_.deleted(account.userName))
+  }
+
   def getGroupNames(userName: String)(implicit s: Session): List[String] = {
     List(userName) ++
       Collaborators.filter(_.collaboratorName === userName.bind).sortBy(_.userName).map(_.userName).list.distinct

src/main/scala/gitbucket/core/service/ActivityService.scala

@@ -360,7 +360,7 @@ trait ActivityService {
       repositoryName,
       activityUserName,
       "release",
-      s"[user:${activityUserName}] released ${name} at [repo:${userName}/${repositoryName}]",
+      s"[user:${activityUserName}] released [release:${userName}/${repositoryName}/${name}] at [repo:${userName}/${repositoryName}]",
       None,
       currentDate
     )

src/main/scala/gitbucket/core/service/CommitsService.scala

@@ -1,11 +1,21 @@
 package gitbucket.core.service
 
-import gitbucket.core.model.CommitComment
+import java.io.File
+
+import gitbucket.core.api.JsonFormat
+import gitbucket.core.controller.Context
+import gitbucket.core.model.{Account, CommitComment}
 import gitbucket.core.model.Profile._
 import gitbucket.core.model.Profile.profile.blockingApi._
 import gitbucket.core.model.Profile.dateColumnType
+import gitbucket.core.plugin.PluginRegistry
+import gitbucket.core.service.RepositoryService.RepositoryInfo
+import gitbucket.core.util.Directory._
+import gitbucket.core.util.{FileUtil, StringUtil}
+import org.apache.commons.io.FileUtils
 
 trait CommitsService {
+  self: ActivityService with PullRequestService with WebHookPullRequestReviewCommentService =>
 
   def getCommitComments(owner: String, repository: String, commitId: String, includePullRequest: Boolean)(
     implicit s: Session
@@ -23,30 +33,83 @@ trait CommitsService {
       None
 
   def createCommitComment(
-    owner: String,
-    repository: String,
+    repository: RepositoryInfo,
     commitId: String,
-    loginUser: String,
+    loginAccount: Account,
     content: String,
     fileName: Option[String],
     oldLine: Option[Int],
     newLine: Option[Int],
+    diff: Option[String],
     issueId: Option[Int]
-  )(implicit s: Session): Int =
-    CommitComments returning CommitComments.map(_.commentId) insert CommitComment(
-      userName = owner,
-      repositoryName = repository,
+  )(implicit s: Session, c: JsonFormat.Context, context: Context): Int = {
+    val commentId = CommitComments returning CommitComments.map(_.commentId) insert CommitComment(
+      userName = repository.owner,
+      repositoryName = repository.name,
       commitId = commitId,
-      commentedUserName = loginUser,
+      commentedUserName = loginAccount.userName,
       content = content,
       fileName = fileName,
       oldLine = oldLine,
       newLine = newLine,
       registeredDate = currentDate,
       updatedDate = currentDate,
-      issueId = issueId
+      issueId = issueId,
+      originalCommitId = commitId,
+      originalOldLine = oldLine,
+      originalNewLine = newLine
     )
 
+    for {
+      fileName <- fileName
+      diff <- diff
+    } {
+      saveCommitCommentDiff(
+        repository.owner,
+        repository.name,
+        commitId,
+        fileName,
+        oldLine,
+        newLine,
+        diff
+      )
+    }
+
+    val comment = getCommitComment(repository.owner, repository.name, commentId.toString).get
+    issueId match {
+      case Some(issueId) =>
+        getPullRequest(repository.owner, repository.name, issueId).foreach {
+          case (issue, pullRequest) =>
+            recordCommentPullRequestActivity(
+              repository.owner,
+              repository.name,
+              loginAccount.userName,
+              issueId,
+              content
+            )
+            PluginRegistry().getPullRequestHooks.foreach(_.addedComment(commentId, content, issue, repository))
+            callPullRequestReviewCommentWebHook(
+              "create",
+              comment,
+              repository,
+              issue,
+              pullRequest,
+              loginAccount
+            )
+        }
+      case None =>
+        recordCommentCommitActivity(
+          repository.owner,
+          repository.name,
+          loginAccount.userName,
+          commitId,
+          content
+        )
+    }
+
+    commentId
+  }
+
   def updateCommitCommentPosition(commentId: Int, commitId: String, oldLine: Option[Int], newLine: Option[Int])(
     implicit s: Session
   ): Unit =
@@ -68,4 +131,48 @@ trait CommitsService {
 
   def deleteCommitComment(commentId: Int)(implicit s: Session) =
     CommitComments filter (_.byPrimaryKey(commentId)) delete
+
+  def saveCommitCommentDiff(
+    owner: String,
+    repository: String,
+    commitId: String,
+    fileName: String,
+    oldLine: Option[Int],
+    newLine: Option[Int],
+    diffJson: String
+  ): Unit = {
+    val dir = new File(getDiffDir(owner, repository), FileUtil.checkFilename(commitId))
+    if (!dir.exists) {
+      dir.mkdirs()
+    }
+    val file = diffFile(dir, fileName, oldLine, newLine)
+    FileUtils.write(file, diffJson, "UTF-8")
+  }
+
+  def loadCommitCommentDiff(
+    owner: String,
+    repository: String,
+    commitId: String,
+    fileName: String,
+    oldLine: Option[Int],
+    newLine: Option[Int]
+  ): Option[String] = {
+    val dir = new File(getDiffDir(owner, repository), FileUtil.checkFilename(commitId))
+    val file = diffFile(dir, fileName, oldLine, newLine)
+    if (file.exists) {
+      Option(FileUtils.readFileToString(file, "UTF-8"))
+    } else None
+  }
+
+  private def diffFile(dir: java.io.File, fileName: String, oldLine: Option[Int], newLine: Option[Int]): File = {
+    new File(
+      dir,
+      StringUtil.sha1(
+        fileName +
+          "_oldLine:" + oldLine.map(_.toString).getOrElse("") +
+          "_newLine:" + newLine.map(_.toString).getOrElse("")
+      )
+    )
+  }
+
 }

src/main/scala/gitbucket/core/service/HandleCommentService.scala

@@ -87,9 +87,9 @@ trait HandleCommentService {
                 case "reopen" => "reopened"
               }
               if (issue.isPullRequest)
-                callPullRequestWebHook(webHookAction, repository, issue.issueId, context.baseUrl, loginAccount)
+                callPullRequestWebHook(webHookAction, repository, issue.issueId, loginAccount)
               else
-                callIssuesWebHook(webHookAction, repository, issue, context.baseUrl, loginAccount)
+                callIssuesWebHook(webHookAction, repository, issue, loginAccount)
           }
 
           // call hooks

src/main/scala/gitbucket/core/service/IssueCreationService.scala

@@ -57,7 +57,7 @@ trait IssueCreationService {
     createReferComment(owner, name, issue, title + " " + body.getOrElse(""), loginAccount)
 
     // call web hooks
-    callIssuesWebHook("opened", repository, issue, context.baseUrl, loginAccount)
+    callIssuesWebHook("opened", repository, issue, loginAccount)
 
     // call hooks
     PluginRegistry().getIssueHooks.foreach(_.created(issue, repository))

src/main/scala/gitbucket/core/service/IssuesService.scala

@@ -6,20 +6,21 @@ import gitbucket.core.util.Implicits._
 import gitbucket.core.util.SyntaxSugars._
 import gitbucket.core.controller.Context
 import gitbucket.core.model.{
+  Account,
+  CommitState,
   Issue,
-  PullRequest,
   IssueComment,
   IssueLabel,
   Label,
-  Account,
+  PullRequest,
   Repository,
-  CommitState,
   Role
 }
 import gitbucket.core.model.Profile._
 import gitbucket.core.model.Profile.profile._
 import gitbucket.core.model.Profile.profile.blockingApi._
 import gitbucket.core.model.Profile.dateColumnType
+import gitbucket.core.plugin.PluginRegistry
 
 trait IssuesService {
   self: AccountService with RepositoryService with LabelsService with PrioritiesService with MilestonesService =>
@@ -350,9 +351,11 @@ trait IssuesService {
     implicit s: Session
   ) =
     Issues filter { t1 =>
-      repos
-        .map { case (owner, repository) => t1.byRepository(owner, repository) }
-        .foldLeft[Rep[Boolean]](false)(_ || _) &&
+      (if (repos.size == 1) {
+         t1.byRepository(repos.head._1, repos.head._2)
+       } else {
+         ((t1.userName ++ "/" ++ t1.repositoryName) inSetBind (repos.map { case (owner, repo) => s"$owner/$repo" }))
+       }) &&
       (t1.closed === (condition.state == "closed").bind) &&
       (t1.milestoneId.? isEmpty, condition.milestone == Some(None)) &&
       (t1.priorityId.? isEmpty, condition.priority == Some(None)) &&
@@ -472,6 +475,25 @@ trait IssuesService {
     IssueLabels filter (_.byPrimaryKey(owner, repository, issueId, labelId)) delete
   }
 
+  def deleteAllIssueLabels(owner: String, repository: String, issueId: Int, insertComment: Boolean = false)(
+    implicit context: Context,
+    s: Session
+  ): Int = {
+    if (insertComment) {
+      IssueComments insert IssueComment(
+        userName = owner,
+        repositoryName = repository,
+        issueId = issueId,
+        action = "delete_label",
+        commentedUserName = context.loginAccount.map(_.userName).getOrElse("Unknown user"),
+        content = "All labels",
+        registeredDate = currentDate,
+        updatedDate = currentDate
+      )
+    }
+    IssueLabels filter (_.byIssue(owner, repository, issueId)) delete
+  }
+
   def createComment(
     owner: String,
     repository: String,
@@ -504,6 +526,15 @@ trait IssuesService {
       .update(title, content, currentDate)
   }
 
+  def changeIssueToPullRequest(owner: String, repository: String, issueId: Int)(implicit s: Session) = {
+    Issues
+      .filter(_.byPrimaryKey(owner, repository, issueId))
+      .map { t =>
+        t.pullRequest
+      }
+      .update(true)
+  }
+
   def updateAssignedUserName(
     owner: String,
     repository: String,
@@ -511,20 +542,24 @@ trait IssuesService {
     assignedUserName: Option[String],
     insertComment: Boolean = false
   )(implicit context: Context, s: Session): Int = {
+    val oldAssigned = getIssue(owner, repository, s"${issueId}").get.assignedUserName
+    val assigned = assignedUserName
+    val assigner = context.loginAccount.map(_.userName)
     if (insertComment) {
-      val oldAssigned = getIssue(owner, repository, s"${issueId}").get.assignedUserName.getOrElse("Not assigned")
-      val assigned = assignedUserName.getOrElse("Not assigned")
       IssueComments insert IssueComment(
         userName = owner,
         repositoryName = repository,
         issueId = issueId,
         action = "assign",
-        commentedUserName = context.loginAccount.map(_.userName).getOrElse("Unknown user"),
-        content = s"${oldAssigned}:${assigned}",
+        commentedUserName = assigner.getOrElse("Unknown user"),
+        content = s"""${oldAssigned.getOrElse("Not assigned")}:${assigned.getOrElse("Not assigned")}""",
         registeredDate = currentDate,
         updatedDate = currentDate
       )
     }
+    for (issue <- getIssue(owner, repository, issueId.toString); repo <- getRepository(owner, repository)) {
+      PluginRegistry().getIssueHooks.foreach(_.assigned(issue, repo, assigner, assigned, oldAssigned))
+    }
     Issues
       .filter(_.byPrimaryKey(owner, repository, issueId))
       .map(t => (t.assignedUserName ?, t.updatedDate))
@@ -625,7 +660,7 @@ trait IssuesService {
    * @param query the keywords separated by whitespace.
    * @return issues with comment count and matched content of issue or comment
    */
-  def searchIssuesByKeyword(owner: String, repository: String, query: String)(
+  def searchIssuesByKeyword(owner: String, repository: String, query: String, pullRequest: Boolean)(
     implicit s: Session
   ): List[(Issue, Int, String)] = {
     //import slick.driver.JdbcDriver.likeEncode
@@ -633,7 +668,9 @@ trait IssuesService {
 
     // Search Issue
     val issues = Issues
-      .filter(_.byRepository(owner, repository))
+      .filter { t =>
+        t.byRepository(owner, repository) && t.pullRequest === pullRequest.bind
+      }
       .join(IssueOutline)
       .on {
         case (t1, t2) =>
@@ -668,11 +705,12 @@ trait IssuesService {
       }
       .filter {
         case ((t1, t2), t3) =>
-          keywords
-            .map { query =>
-              t1.content.toLowerCase like (s"%${likeEncode(query)}%", '^')
-            }
-            .reduceLeft(_ && _)
+          t2.pullRequest === pullRequest.bind &&
+            keywords
+              .map { query =>
+                t1.content.toLowerCase like (s"%${likeEncode(query)}%", '^')
+              }
+              .reduceLeft(_ && _)
       }
       .map {
         case ((t1, t2), t3) =>
@@ -683,7 +721,7 @@ trait IssuesService {
       .union(comments)
       .sortBy {
         case (issue, commentId, _, _) =>
-          issue.issueId -> commentId
+          issue.issueId.desc -> commentId
       }
       .list
       .splitWith {
@@ -700,11 +738,12 @@ trait IssuesService {
 
   def closeIssuesFromMessage(message: String, userName: String, owner: String, repository: String)(
     implicit s: Session
-  ): Unit = {
-    extractCloseId(message).foreach { issueId =>
-      for (issue <- getIssue(owner, repository, issueId) if !issue.closed) {
+  ): Seq[Int] = {
+    extractCloseId(message).flatMap { issueId =>
+      for (issue <- getIssue(owner, repository, issueId) if !issue.closed) yield {
         createComment(owner, repository, userName, issue.issueId, "Close", "close")
         updateClosed(owner, repository, issue.issueId, true)
+        issue.issueId
       }
     }
   }

src/main/scala/gitbucket/core/service/LabelsService.scala

@@ -3,6 +3,7 @@ package gitbucket.core.service
 import gitbucket.core.model.Label
 import gitbucket.core.model.Profile._
 import gitbucket.core.model.Profile.profile.blockingApi._
+import gitbucket.core.util.StringUtil
 
 trait LabelsService {
 
@@ -24,6 +25,11 @@ trait LabelsService {
     )
   }
 
+  def createLabel(owner: String, repository: String, labelName: String)(implicit s: Session): Int = {
+    val color = StringUtil.md5(labelName).substring(0, 6)
+    createLabel(owner, repository, labelName, color)
+  }
+
   def updateLabel(owner: String, repository: String, labelId: Int, labelName: String, color: String)(
     implicit s: Session
   ): Unit =

src/main/scala/gitbucket/core/service/MergeService.scala

@@ -1,8 +1,16 @@
 package gitbucket.core.service
 
-import gitbucket.core.model.Account
+import gitbucket.core.api.JsonFormat
+import gitbucket.core.controller.Context
+import gitbucket.core.model.{Account, PullRequest, WebHook}
+import gitbucket.core.plugin.PluginRegistry
+import gitbucket.core.service.RepositoryService.RepositoryInfo
 import gitbucket.core.util.Directory._
+import gitbucket.core.util.{JGitUtil, LockUtil}
 import gitbucket.core.util.SyntaxSugars._
+import gitbucket.core.model.Profile._
+import gitbucket.core.model.Profile.profile._
+import gitbucket.core.model.Profile.profile.blockingApi._
 import org.eclipse.jgit.merge.{MergeStrategy, Merger, RecursiveMerger}
 import org.eclipse.jgit.api.Git
 import org.eclipse.jgit.transport.RefSpec
@@ -13,6 +21,13 @@ import org.eclipse.jgit.revwalk.{RevCommit, RevWalk}
 import scala.collection.JavaConverters._
 
 trait MergeService {
+  self: AccountService
+    with ActivityService
+    with IssuesService
+    with RepositoryService
+    with PullRequestService
+    with WebHookPullRequestService =>
+
   import MergeService._
 
   /**
@@ -43,7 +58,13 @@ trait MergeService {
   }
 
   /** merge the pull request with a merge commit */
-  def mergePullRequest(git: Git, branch: String, issueId: Int, message: String, committer: PersonIdent): Unit = {
+  def mergePullRequest(
+    git: Git,
+    branch: String,
+    issueId: Int,
+    message: String,
+    committer: PersonIdent
+  ): ObjectId = {
     new MergeCacheInfo(git, branch, issueId).merge(message, committer)
   }
 
@@ -54,12 +75,18 @@ trait MergeService {
     issueId: Int,
     commits: Seq[RevCommit],
     committer: PersonIdent
-  ): Unit = {
+  ): ObjectId = {
     new MergeCacheInfo(git, branch, issueId).rebase(committer, commits)
   }
 
   /** squash commits in the pull request and append it */
-  def squashPullRequest(git: Git, branch: String, issueId: Int, message: String, committer: PersonIdent): Unit = {
+  def squashPullRequest(
+    git: Git,
+    branch: String,
+    issueId: Int,
+    message: String,
+    committer: PersonIdent
+  ): ObjectId = {
     new MergeCacheInfo(git, branch, issueId).squash(message, committer)
   }
 
@@ -136,27 +163,223 @@ trait MergeService {
     tryMergeRemote(userName, repositoryName, branch, requestUserName, requestRepositoryName, requestBranch).left.toOption
 
   def pullRemote(
-    localUserName: String,
-    localRepositoryName: String,
+    localRepository: RepositoryInfo,
     localBranch: String,
-    remoteUserName: String,
-    remoteRepositoryName: String,
+    remoteRepository: RepositoryInfo,
     remoteBranch: String,
     loginAccount: Account,
-    message: String
-  ): Option[ObjectId] = {
+    message: String,
+    pullreq: Option[PullRequest]
+  )(implicit s: Session, c: JsonFormat.Context): Option[ObjectId] = {
+    val localUserName = localRepository.owner
+    val localRepositoryName = localRepository.name
+    val remoteUserName = remoteRepository.owner
+    val remoteRepositoryName = remoteRepository.name
     tryMergeRemote(localUserName, localRepositoryName, localBranch, remoteUserName, remoteRepositoryName, remoteBranch).map {
       case (newTreeId, oldBaseId, oldHeadId) =>
         using(Git.open(getRepositoryDir(localUserName, localRepositoryName))) { git =>
+          val existIds = JGitUtil.getAllCommitIds(git).toSet
+
           val committer = new PersonIdent(loginAccount.fullName, loginAccount.mailAddress)
           val newCommit =
             Util.createMergeCommit(git.getRepository, newTreeId, committer, message, Seq(oldBaseId, oldHeadId))
           Util.updateRefs(git.getRepository, s"refs/heads/${localBranch}", newCommit, false, committer, Some("merge"))
+
+          val commits = git.log
+            .addRange(oldBaseId, newCommit)
+            .call
+            .iterator
+            .asScala
+            .map(c => new JGitUtil.CommitInfo(c))
+            .toList
+
+          commits.foreach { commit =>
+            if (!existIds.contains(commit.id)) {
+              createIssueComment(localUserName, localRepositoryName, commit)
+            }
+          }
+
+          // record activity
+          recordPushActivity(
+            localUserName,
+            localRepositoryName,
+            loginAccount.userName,
+            localBranch,
+            commits
+          )
+
+          // close issue by commit message
+          if (localBranch == localRepository.repository.defaultBranch) {
+            commits.foreach { commit =>
+              closeIssuesFromMessage(commit.fullMessage, loginAccount.userName, localUserName, localRepositoryName)
+                .foreach { issueId =>
+                  getIssue(localRepository.owner, localRepository.name, issueId.toString).foreach { issue =>
+                    callIssuesWebHook("closed", localRepository, issue, loginAccount)
+                    PluginRegistry().getIssueHooks
+                      .foreach(
+                        _.closedByCommitComment(issue, localRepository, commit.fullMessage, loginAccount)
+                      )
+                  }
+                }
+            }
+          }
+
+          pullreq.foreach { pullreq =>
+            callWebHookOf(localRepository.owner, localRepository.name, WebHook.Push) {
+              for {
+                ownerAccount <- getAccountByUserName(localRepository.owner)
+              } yield {
+                WebHookService.WebHookPushPayload(
+                  git,
+                  loginAccount,
+                  pullreq.requestBranch,
+                  localRepository,
+                  commits,
+                  ownerAccount,
+                  oldId = oldBaseId,
+                  newId = newCommit
+                )
+              }
+            }
+          }
         }
         oldBaseId
     }.toOption
   }
 
+  def mergePullRequest(
+    repository: RepositoryInfo,
+    issueId: Int,
+    loginAccount: Account,
+    message: String,
+    strategy: String
+  )(implicit s: Session, c: JsonFormat.Context, context: Context): Either[String, ObjectId] = {
+    if (repository.repository.options.mergeOptions.split(",").contains(strategy)) {
+      LockUtil.lock(s"${repository.owner}/${repository.name}") {
+        getPullRequest(repository.owner, repository.name, issueId)
+          .map {
+            case (issue, pullreq) =>
+              using(Git.open(getRepositoryDir(repository.owner, repository.name))) { git =>
+                // mark issue as merged and close.
+                val commentId =
+                  createComment(repository.owner, repository.name, loginAccount.userName, issueId, message, "merge")
+                createComment(repository.owner, repository.name, loginAccount.userName, issueId, "Close", "close")
+                updateClosed(repository.owner, repository.name, issueId, true)
+
+                // record activity
+                recordMergeActivity(repository.owner, repository.name, loginAccount.userName, issueId, message)
+
+                val (commits, _) = getRequestCompareInfo(
+                  repository.owner,
+                  repository.name,
+                  pullreq.commitIdFrom,
+                  pullreq.requestUserName,
+                  pullreq.requestRepositoryName,
+                  pullreq.commitIdTo
+                )
+
+                val revCommits = using(new RevWalk(git.getRepository)) { revWalk =>
+                  commits.flatten.map { commit =>
+                    revWalk.parseCommit(git.getRepository.resolve(commit.id))
+                  }
+                }.reverse
+
+                // merge git repository
+                (strategy match {
+                  case "merge-commit" =>
+                    Some(
+                      mergePullRequest(
+                        git,
+                        pullreq.branch,
+                        issueId,
+                        s"Merge pull request #${issueId} from ${pullreq.requestUserName}/${pullreq.requestBranch}\n\n" + message,
+                        new PersonIdent(loginAccount.fullName, loginAccount.mailAddress)
+                      )
+                    )
+                  case "rebase" =>
+                    Some(
+                      rebasePullRequest(
+                        git,
+                        pullreq.branch,
+                        issueId,
+                        revCommits,
+                        new PersonIdent(loginAccount.fullName, loginAccount.mailAddress)
+                      )
+                    )
+                  case "squash" =>
+                    Some(
+                      squashPullRequest(
+                        git,
+                        pullreq.branch,
+                        issueId,
+                        s"${issue.title} (#${issueId})\n\n" + message,
+                        new PersonIdent(loginAccount.fullName, loginAccount.mailAddress)
+                      )
+                    )
+                  case _ =>
+                    None
+                }) match {
+                  case Some(newCommitId) =>
+                    // close issue by content of pull request
+                    val defaultBranch = getRepository(repository.owner, repository.name).get.repository.defaultBranch
+                    if (pullreq.branch == defaultBranch) {
+                      commits.flatten.foreach { commit =>
+                        closeIssuesFromMessage(
+                          commit.fullMessage,
+                          loginAccount.userName,
+                          repository.owner,
+                          repository.name
+                        ).foreach { issueId =>
+                          getIssue(repository.owner, repository.name, issueId.toString).foreach { issue =>
+                            callIssuesWebHook("closed", repository, issue, loginAccount)
+                            PluginRegistry().getIssueHooks
+                              .foreach(_.closedByCommitComment(issue, repository, commit.fullMessage, loginAccount))
+                          }
+                        }
+                      }
+                      val issueContent = issue.title + " " + issue.content.getOrElse("")
+                      closeIssuesFromMessage(
+                        issueContent,
+                        loginAccount.userName,
+                        repository.owner,
+                        repository.name
+                      ).foreach { issueId =>
+                        getIssue(repository.owner, repository.name, issueId.toString).foreach { issue =>
+                          callIssuesWebHook("closed", repository, issue, loginAccount)
+                          PluginRegistry().getIssueHooks
+                            .foreach(_.closedByCommitComment(issue, repository, issueContent, loginAccount))
+                        }
+                      }
+                      closeIssuesFromMessage(message, loginAccount.userName, repository.owner, repository.name)
+                        .foreach { issueId =>
+                          getIssue(repository.owner, repository.name, issueId.toString).foreach { issue =>
+                            callIssuesWebHook("closed", repository, issue, loginAccount)
+                            PluginRegistry().getIssueHooks
+                              .foreach(_.closedByCommitComment(issue, repository, issueContent, loginAccount))
+                          }
+                        }
+                    }
+
+                    updatePullRequests(repository.owner, repository.name, pullreq.branch, loginAccount, "closed")
+
+                    // call hooks
+                    PluginRegistry().getPullRequestHooks.foreach { h =>
+                      h.addedComment(commentId, message, issue, repository)
+                      h.merged(issue, repository)
+                    }
+
+                    Right(newCommitId)
+                  case None =>
+                    Left("Unknown strategy")
+                }
+              }
+            case _ => Left("Unknown error")
+          }
+          .getOrElse(Left("Pull request not found"))
+      }
+    } else Left("Strategy not allowed")
+
+  }
 }
 
 object MergeService {
@@ -191,13 +414,15 @@ object MergeService {
       force: Boolean,
       committer: PersonIdent,
       refLogMessage: Option[String] = None
-    ): Unit = {
+    ): ObjectId = {
       val refUpdate = repository.updateRef(ref)
       refUpdate.setNewObjectId(newObjectId)
       refUpdate.setForceUpdate(force)
       refUpdate.setRefLogIdent(committer)
-      refLogMessage.map(refUpdate.setRefLogMessage(_, true))
+      refLogMessage.foreach(refUpdate.setRefLogMessage(_, true))
       refUpdate.update()
+
+      newObjectId
     }
   }
 
@@ -265,7 +490,7 @@ object MergeService {
     }
 
     // update branch from cache
-    def merge(message: String, committer: PersonIdent) = {
+    def merge(message: String, committer: PersonIdent): ObjectId = {
       if (checkConflict().isDefined) {
         throw new RuntimeException("This pull request can't merge automatically.")
       }
@@ -278,7 +503,7 @@ object MergeService {
       Util.updateRefs(repository, s"refs/heads/${branch}", mergeCommitId, false, committer, Some("merged"))
     }
 
-    def rebase(committer: PersonIdent, commits: Seq[RevCommit]): Unit = {
+    def rebase(committer: PersonIdent, commits: Seq[RevCommit]): ObjectId = {
       if (checkConflict().isDefined) {
         throw new RuntimeException("This pull request can't merge automatically.")
       }
@@ -310,7 +535,7 @@ object MergeService {
       Util.updateRefs(repository, s"refs/heads/${branch}", previousId, false, committer, Some("rebased"))
     }
 
-    def squash(message: String, committer: PersonIdent): Unit = {
+    def squash(message: String, committer: PersonIdent): ObjectId = {
       if (checkConflict().isDefined) {
         throw new RuntimeException("This pull request can't merge automatically.")
       }

src/main/scala/gitbucket/core/service/PullRequestService.scala

@@ -1,20 +1,26 @@
 package gitbucket.core.service
 
-import gitbucket.core.model.{Issue, PullRequest, CommitStatus, CommitState, CommitComment}
+import gitbucket.core.model.{CommitComments => _, Session => _, _}
 import gitbucket.core.model.Profile._
 import gitbucket.core.model.Profile.profile.blockingApi._
 import difflib.{Delta, DiffUtils}
+import gitbucket.core.service.RepositoryService.RepositoryInfo
+import gitbucket.core.api.JsonFormat
 import gitbucket.core.util.SyntaxSugars._
 import gitbucket.core.util.Directory._
 import gitbucket.core.util.Implicits._
 import gitbucket.core.util.JGitUtil
+import gitbucket.core.util.StringUtil._
 import gitbucket.core.util.JGitUtil.{CommitInfo, DiffInfo}
 import gitbucket.core.view
 import gitbucket.core.view.helpers
 import org.eclipse.jgit.api.Git
+import org.eclipse.jgit.lib.ObjectId
+
 import scala.collection.JavaConverters._
 
-trait PullRequestService { self: IssuesService with CommitsService =>
+trait PullRequestService {
+  self: IssuesService with CommitsService with WebHookService with WebHookPullRequestService with RepositoryService =>
   import PullRequestService._
 
   def getPullRequest(owner: String, repository: String, issueId: Int)(
@@ -115,6 +121,24 @@ trait PullRequestService { self: IssuesService with CommitsService =>
       .map { case (t1, t2) => t1 }
       .list
 
+  def getPullRequestsByBranch(userName: String, repositoryName: String, branch: String, closed: Option[Boolean])(
+    implicit s: Session
+  ): List[PullRequest] =
+    PullRequests
+      .join(Issues)
+      .on { (t1, t2) =>
+        t1.byPrimaryKey(t2.userName, t2.repositoryName, t2.issueId)
+      }
+      .filter {
+        case (t1, t2) =>
+          (t1.requestUserName === userName.bind) &&
+            (t1.requestRepositoryName === repositoryName.bind) &&
+            (t1.branch === branch.bind) &&
+            (t2.closed === closed.get.bind, closed.isDefined)
+      }
+      .map { case (t1, t2) => t1 }
+      .list
+
   /**
    * for repository viewer.
    * 1. find pull request from `branch` to other branch on same repository
@@ -145,7 +169,10 @@ trait PullRequestService { self: IssuesService with CommitsService =>
   /**
    * Fetch pull request contents into refs/pull/${issueId}/head and update pull request table.
    */
-  def updatePullRequests(owner: String, repository: String, branch: String)(implicit s: Session): Unit =
+  def updatePullRequests(owner: String, repository: String, branch: String, loginAccount: Account, action: String)(
+    implicit s: Session,
+    c: JsonFormat.Context
+  ): Unit = {
     getPullRequestsByRequest(owner, repository, branch, Some(false)).foreach { pullreq =>
       if (Repositories.filter(_.byRepository(pullreq.userName, pullreq.repositoryName)).exists.run) {
         // Update the git repository
@@ -162,9 +189,9 @@ trait PullRequestService { self: IssuesService with CommitsService =>
         // Collect comment positions
         val positions = getCommitComments(pullreq.userName, pullreq.repositoryName, pullreq.commitIdTo, true)
           .collect {
-            case CommitComment(_, _, _, commentId, _, _, Some(file), None, Some(newLine), _, _, _) =>
+            case CommitComment(_, _, _, commentId, _, _, Some(file), None, Some(newLine), _, _, _, _, _, _) =>
               (file, commentId, Right(newLine))
-            case CommitComment(_, _, _, commentId, _, _, Some(file), Some(oldLine), None, _, _, _) =>
+            case CommitComment(_, _, _, commentId, _, _, Some(file), Some(oldLine), None, _, _, _, _, _, _) =>
               (file, commentId, Left(oldLine))
           }
           .groupBy { case (file, _, _) => file }
@@ -185,8 +212,17 @@ trait PullRequestService { self: IssuesService with CommitsService =>
 
         // Update commit id in the PULL_REQUEST table
         updateCommitId(pullreq.userName, pullreq.repositoryName, pullreq.issueId, commitIdTo, commitIdFrom)
+
+        // call web hook
+        callPullRequestWebHookByRequestBranch(
+          action,
+          getRepository(owner, repository).get,
+          pullreq.requestBranch,
+          loginAccount
+        )
       }
     }
+  }
 
   def getPullRequestByRequestCommit(
     userName: String,
@@ -234,8 +270,8 @@ trait PullRequestService { self: IssuesService with CommitsService =>
           .map { diff =>
             (diff.oldContent, diff.newContent) match {
               case (Some(oldContent), Some(newContent)) => {
-                val oldLines = oldContent.replace("\r\n", "\n").split("\n")
-                val newLines = newContent.replace("\r\n", "\n").split("\n")
+                val oldLines = convertLineSeparator(oldContent, "LF").split("\n")
+                val newLines = convertLineSeparator(newContent, "LF").split("\n")
                 file -> Option(DiffUtils.diff(oldLines.toList.asJava, newLines.toList.asJava))
               }
               case _ =>
@@ -314,11 +350,109 @@ trait PullRequestService { self: IssuesService with CommitsService =>
           helpers.date(commit1.commitTime) == view.helpers.date(commit2.commitTime)
         }
 
+      // TODO Isolate to an another method?
       val diffs = JGitUtil.getDiffs(newGit, Some(oldId.getName), newId.getName, true, false)
 
       (commits, diffs)
     }
 
+  def getPullRequestComments(userName: String, repositoryName: String, issueId: Int, commits: Seq[CommitInfo])(
+    implicit s: Session
+  ): Seq[Comment] = {
+    (commits
+      .map(commit => getCommitComments(userName, repositoryName, commit.id, true))
+      .flatten ++ getComments(userName, repositoryName, issueId))
+      .groupBy {
+        case x: IssueComment                        => (Some(x.commentId), None, None, None)
+        case x: CommitComment if x.fileName.isEmpty => (Some(x.commentId), None, None, None)
+        case x: CommitComment                       => (None, x.fileName, x.originalOldLine, x.originalNewLine)
+        case x                                      => throw new MatchError(x)
+      }
+      .toSeq
+      .map {
+        // Normal comment
+        case ((Some(_), _, _, _), comments) =>
+          comments.head
+        // Comment on a specific line of a commit
+        case ((None, Some(fileName), oldLine, newLine), comments) =>
+          gitbucket.core.model.CommitComments(
+            fileName = fileName,
+            commentedUserName = comments.head.commentedUserName,
+            registeredDate = comments.head.registeredDate,
+            comments = comments.map(_.asInstanceOf[CommitComment]),
+            diff = loadCommitCommentDiff(
+              userName,
+              repositoryName,
+              comments.head.asInstanceOf[CommitComment].originalCommitId,
+              fileName,
+              oldLine,
+              newLine
+            )
+          )
+      }
+      .sortWith(_.registeredDate before _.registeredDate)
+  }
+
+  def markMergeAndClosePullRequest(userName: String, owner: String, repository: String, pull: PullRequest)(
+    implicit s: Session
+  ): Unit = {
+    createComment(owner, repository, userName, pull.issueId, "Merged by user", "merge")
+    createComment(owner, repository, userName, pull.issueId, "Close", "close")
+    updateClosed(owner, repository, pull.issueId, true)
+  }
+
+  /**
+   * Parses branch identifier and extracts owner and branch name as tuple.
+   *
+   * - "owner:branch" to ("owner", "branch")
+   * - "branch" to ("defaultOwner", "branch")
+   */
+  def parseCompareIdentifier(value: String, defaultOwner: String): (String, String) =
+    if (value.contains(':')) {
+      val array = value.split(":")
+      (array(0), array(1))
+    } else {
+      (defaultOwner, value)
+    }
+
+  def getPullRequestCommitFromTo(
+    originRepository: RepositoryInfo,
+    forkedRepository: RepositoryInfo,
+    originId: String,
+    forkedId: String
+  ): (Option[ObjectId], Option[ObjectId]) = {
+    using(
+      Git.open(getRepositoryDir(originRepository.owner, originRepository.name)),
+      Git.open(getRepositoryDir(forkedRepository.owner, forkedRepository.name))
+    ) {
+      case (oldGit, newGit) =>
+        if (originRepository.branchList.contains(originId)) {
+          val forkedId2 =
+            forkedRepository.tags.collectFirst { case x if x.name == forkedId => x.id }.getOrElse(forkedId)
+
+          val originId2 = JGitUtil.getForkedCommitId(
+            oldGit,
+            newGit,
+            originRepository.owner,
+            originRepository.name,
+            originId,
+            forkedRepository.owner,
+            forkedRepository.name,
+            forkedId2
+          )
+
+          (Option(oldGit.getRepository.resolve(originId2)), Option(newGit.getRepository.resolve(forkedId2)))
+
+        } else {
+          val originId2 =
+            originRepository.tags.collectFirst { case x if x.name == originId => x.id }.getOrElse(originId)
+          val forkedId2 =
+            forkedRepository.tags.collectFirst { case x if x.name == forkedId => x.id }.getOrElse(forkedId)
+
+          (Option(oldGit.getRepository.resolve(originId2)), Option(newGit.getRepository.resolve(forkedId2)))
+        }
+    }
+  }
 }
 
 object PullRequestService {

src/main/scala/gitbucket/core/service/RepositoryCommitFileService.scala

@@ -0,0 +1,188 @@
+package gitbucket.core.service
+import gitbucket.core.api.JsonFormat
+import gitbucket.core.model.{Account, WebHook}
+import gitbucket.core.model.Profile._
+import gitbucket.core.model.Profile.profile.blockingApi._
+import gitbucket.core.plugin.PluginRegistry
+import gitbucket.core.service.WebHookService.WebHookPushPayload
+import gitbucket.core.util.Directory.getRepositoryDir
+import gitbucket.core.util.JGitUtil.CommitInfo
+import gitbucket.core.util.{JGitUtil, LockUtil}
+import gitbucket.core.util.SyntaxSugars.using
+import org.eclipse.jgit.api.Git
+import org.eclipse.jgit.dircache.{DirCache, DirCacheBuilder}
+import org.eclipse.jgit.lib._
+import org.eclipse.jgit.transport.{ReceiveCommand, ReceivePack}
+
+trait RepositoryCommitFileService {
+  self: AccountService with ActivityService with IssuesService with PullRequestService with WebHookPullRequestService =>
+  import RepositoryCommitFileService._
+
+  def commitFiles(
+    repository: RepositoryService.RepositoryInfo,
+    files: Seq[CommitFile],
+    branch: String,
+    path: String,
+    message: String,
+    loginAccount: Account
+  )(
+    f: (Git, ObjectId, DirCacheBuilder, ObjectInserter) => Unit
+  )(implicit s: Session, c: JsonFormat.Context) = {
+    // prepend path to the filename
+    _commitFile(repository, branch, message, loginAccount)(f)
+  }
+
+  def commitFile(
+    repository: RepositoryService.RepositoryInfo,
+    branch: String,
+    path: String,
+    newFileName: Option[String],
+    oldFileName: Option[String],
+    content: String,
+    charset: String,
+    message: String,
+    commit: String,
+    loginAccount: Account
+  )(implicit s: Session, c: JsonFormat.Context) = {
+
+    val newPath = newFileName.map { newFileName =>
+      if (path.length == 0) newFileName else s"${path}/${newFileName}"
+    }
+    val oldPath = oldFileName.map { oldFileName =>
+      if (path.length == 0) oldFileName else s"${path}/${oldFileName}"
+    }
+
+    _commitFile(repository, branch, message, loginAccount) {
+      case (git, headTip, builder, inserter) =>
+        if (headTip.getName == commit) {
+          val permission = JGitUtil
+            .processTree(git, headTip) { (path, tree) =>
+              // Add all entries except the editing file
+              if (!newPath.contains(path) && !oldPath.contains(path)) {
+                builder.add(JGitUtil.createDirCacheEntry(path, tree.getEntryFileMode, tree.getEntryObjectId))
+              }
+              // Retrieve permission if file exists to keep it
+              oldPath.collect { case x if x == path => tree.getEntryFileMode.getBits }
+            }
+            .flatten
+            .headOption
+
+          newPath.foreach { newPath =>
+            builder.add(JGitUtil.createDirCacheEntry(newPath, permission.map { bits =>
+              FileMode.fromBits(bits)
+            } getOrElse FileMode.REGULAR_FILE, inserter.insert(Constants.OBJ_BLOB, content.getBytes(charset))))
+          }
+          builder.finish()
+        }
+    }
+  }
+
+  private def _commitFile(
+    repository: RepositoryService.RepositoryInfo,
+    branch: String,
+    message: String,
+    loginAccount: Account
+  )(
+    f: (Git, ObjectId, DirCacheBuilder, ObjectInserter) => Unit
+  )(implicit s: Session, c: JsonFormat.Context) = {
+
+    LockUtil.lock(s"${repository.owner}/${repository.name}") {
+      using(Git.open(getRepositoryDir(repository.owner, repository.name))) { git =>
+        val builder = DirCache.newInCore.builder()
+        val inserter = git.getRepository.newObjectInserter()
+        val headName = s"refs/heads/${branch}"
+        val headTip = git.getRepository.resolve(headName)
+
+        f(git, headTip, builder, inserter)
+
+        val commitId = JGitUtil.createNewCommit(
+          git,
+          inserter,
+          headTip,
+          builder.getDirCache.writeTree(inserter),
+          headName,
+          loginAccount.fullName,
+          loginAccount.mailAddress,
+          message
+        )
+
+        inserter.flush()
+        inserter.close()
+
+        val receivePack = new ReceivePack(git.getRepository)
+        val receiveCommand = new ReceiveCommand(headTip, commitId, headName)
+
+        // call post commit hook
+        val error = PluginRegistry().getReceiveHooks.flatMap { hook =>
+          hook.preReceive(repository.owner, repository.name, receivePack, receiveCommand, loginAccount.userName)
+        }.headOption
+
+        error match {
+          case Some(error) =>
+            // commit is rejected
+            // TODO Notify commit failure to edited user
+            val refUpdate = git.getRepository.updateRef(headName)
+            refUpdate.setNewObjectId(headTip)
+            refUpdate.setForceUpdate(true)
+            refUpdate.update()
+
+          case None =>
+            // update refs
+            val refUpdate = git.getRepository.updateRef(headName)
+            refUpdate.setNewObjectId(commitId)
+            refUpdate.setForceUpdate(false)
+            refUpdate.setRefLogIdent(new PersonIdent(loginAccount.fullName, loginAccount.mailAddress))
+            refUpdate.update()
+
+            // update pull request
+            updatePullRequests(repository.owner, repository.name, branch, loginAccount, "synchronize")
+
+            // record activity
+            val commitInfo = new CommitInfo(JGitUtil.getRevCommitFromId(git, commitId))
+            recordPushActivity(repository.owner, repository.name, loginAccount.userName, branch, List(commitInfo))
+
+            // create issue comment by commit message
+            createIssueComment(repository.owner, repository.name, commitInfo)
+
+            // close issue by commit message
+            if (branch == repository.repository.defaultBranch) {
+              closeIssuesFromMessage(message, loginAccount.userName, repository.owner, repository.name).foreach {
+                issueId =>
+                  getIssue(repository.owner, repository.name, issueId.toString).foreach { issue =>
+                    callIssuesWebHook("closed", repository, issue, loginAccount)
+                    PluginRegistry().getIssueHooks
+                      .foreach(_.closedByCommitComment(issue, repository, message, loginAccount))
+                  }
+              }
+            }
+
+            // call post commit hook
+            PluginRegistry().getReceiveHooks.foreach { hook =>
+              hook.postReceive(repository.owner, repository.name, receivePack, receiveCommand, loginAccount.userName)
+            }
+
+            val commit = new JGitUtil.CommitInfo(JGitUtil.getRevCommitFromId(git, commitId))
+            callWebHookOf(repository.owner, repository.name, WebHook.Push) {
+              getAccountByUserName(repository.owner).map { ownerAccount =>
+                WebHookPushPayload(
+                  git,
+                  loginAccount,
+                  headName,
+                  repository,
+                  List(commit),
+                  ownerAccount,
+                  oldId = headTip,
+                  newId = commitId
+                )
+              }
+            }
+        }
+      }
+    }
+  }
+
+}
+
+object RepositoryCommitFileService {
+  case class CommitFile(id: String, name: String)
+}

src/main/scala/gitbucket/core/service/RepositorySearchService.scala

@@ -14,18 +14,21 @@ import gitbucket.core.model.Profile.profile.blockingApi._
 trait RepositorySearchService { self: IssuesService =>
   import RepositorySearchService._
 
-  def countIssues(owner: String, repository: String, query: String)(implicit session: Session): Int =
-    searchIssuesByKeyword(owner, repository, query).length
+  def countIssues(owner: String, repository: String, query: String, pullRequest: Boolean)(
+    implicit session: Session
+  ): Int =
+    searchIssuesByKeyword(owner, repository, query, pullRequest).length
 
-  def searchIssues(owner: String, repository: String, query: String)(
+  def searchIssues(owner: String, repository: String, query: String, pullRequest: Boolean)(
     implicit session: Session
   ): List[IssueSearchResult] =
-    searchIssuesByKeyword(owner, repository, query).map {
+    searchIssuesByKeyword(owner, repository, query, pullRequest).map {
       case (issue, commentCount, content) =>
         IssueSearchResult(
           issue.issueId,
           issue.isPullRequest,
           issue.title,
+          issue.closed,
           issue.openedUserName,
           issue.registeredDate,
           commentCount,
@@ -142,6 +145,7 @@ object RepositorySearchService {
     issueId: Int,
     isPullRequest: Boolean,
     title: String,
+    isClosed: Boolean,
     openedUserName: String,
     registeredDate: java.util.Date,
     commentCount: Int,

src/main/scala/gitbucket/core/service/RepositoryService.scala

@@ -1,16 +1,25 @@
 package gitbucket.core.service
 
+import gitbucket.core.api.JsonFormat
 import gitbucket.core.controller.Context
 import gitbucket.core.util._
 import gitbucket.core.util.SyntaxSugars._
-import gitbucket.core.model.{Account, Collaborator, Repository, RepositoryOptions, Role, ReleaseTag}
+import gitbucket.core.model.{CommitComments => _, Session => _, _}
 import gitbucket.core.model.Profile._
 import gitbucket.core.model.Profile.profile.blockingApi._
 import gitbucket.core.model.Profile.dateColumnType
-import gitbucket.core.util.JGitUtil.FileInfo
+import gitbucket.core.plugin.PluginRegistry
+import gitbucket.core.service.WebHookService.WebHookPushPayload
+import gitbucket.core.util.Directory.{getRepositoryDir, getRepositoryFilesDir, getTemporaryDir, getWikiRepositoryDir}
+import gitbucket.core.util.JGitUtil.{CommitInfo, FileInfo}
+import org.apache.commons.io.FileUtils
 import org.eclipse.jgit.api.Git
+import org.eclipse.jgit.dircache.{DirCache, DirCacheBuilder}
+import org.eclipse.jgit.lib.{Repository => _, _}
+import org.eclipse.jgit.transport.{ReceiveCommand, ReceivePack}
 
-trait RepositoryService { self: AccountService =>
+trait RepositoryService {
+  self: AccountService =>
   import RepositoryService._
 
   /**
@@ -67,182 +76,233 @@ trait RepositoryService { self: AccountService =>
     getAccountByUserName(newUserName).foreach { account =>
       (Repositories filter { t =>
         t.byRepository(oldUserName, oldRepositoryName)
-      } firstOption).map { repository =>
-        Repositories insert repository.copy(userName = newUserName, repositoryName = newRepositoryName)
+      } firstOption).foreach { repository =>
+        LockUtil.lock(s"${repository.userName}/${repository.repositoryName}") {
+          Repositories insert repository.copy(userName = newUserName, repositoryName = newRepositoryName)
 
-        val webHooks = RepositoryWebHooks.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val webHookEvents = RepositoryWebHookEvents.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val milestones = Milestones.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val issueId = IssueId.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val issues = Issues.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val pullRequests = PullRequests.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val labels = Labels.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val priorities = Priorities.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val issueComments = IssueComments.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val issueLabels = IssueLabels.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val commitComments = CommitComments.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val commitStatuses = CommitStatuses.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val collaborators = Collaborators.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val protectedBranches = ProtectedBranches.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val protectedBranchContexts =
-          ProtectedBranchContexts.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val deployKeys = DeployKeys.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val releases = ReleaseTags.filter(_.byRepository(oldUserName, oldRepositoryName)).list
-        val releaseAssets = ReleaseAssets.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val webHooks = RepositoryWebHooks.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val webHookEvents = RepositoryWebHookEvents.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val milestones = Milestones.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val issueId = IssueId.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val issues = Issues.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val pullRequests = PullRequests.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val labels = Labels.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val priorities = Priorities.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val issueComments = IssueComments.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val issueLabels = IssueLabels.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val commitComments = CommitComments.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val commitStatuses = CommitStatuses.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val collaborators = Collaborators.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val protectedBranches = ProtectedBranches.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val protectedBranchContexts =
+            ProtectedBranchContexts.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val deployKeys = DeployKeys.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val releases = ReleaseTags.filter(_.byRepository(oldUserName, oldRepositoryName)).list
+          val releaseAssets = ReleaseAssets.filter(_.byRepository(oldUserName, oldRepositoryName)).list
 
-        Repositories
-          .filter { t =>
-            (t.originUserName === oldUserName.bind) && (t.originRepositoryName === oldRepositoryName.bind)
-          }
-          .map { t =>
-            t.originUserName -> t.originRepositoryName
-          }
-          .update(newUserName, newRepositoryName)
-
-        Repositories
-          .filter { t =>
-            (t.parentUserName === oldUserName.bind) && (t.parentRepositoryName === oldRepositoryName.bind)
-          }
-          .map { t =>
-            t.parentUserName -> t.parentRepositoryName
-          }
-          .update(newUserName, newRepositoryName)
-
-        // Updates activity fk before deleting repository because activity is sorted by activityId
-        // and it can't be changed by deleting-and-inserting record.
-        Activities.filter(_.byRepository(oldUserName, oldRepositoryName)).list.foreach { activity =>
-          Activities
-            .filter(_.activityId === activity.activityId.bind)
-            .map(x => (x.userName, x.repositoryName))
-            .update(newUserName, newRepositoryName)
-        }
-
-        deleteRepository(oldUserName, oldRepositoryName)
-
-        RepositoryWebHooks.insertAll(
-          webHooks.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
-        )
-        RepositoryWebHookEvents.insertAll(
-          webHookEvents.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
-        )
-        Milestones.insertAll(milestones.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*)
-        Priorities.insertAll(priorities.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*)
-        IssueId.insertAll(issueId.map(_.copy(_1 = newUserName, _2 = newRepositoryName)): _*)
-
-        val newMilestones = Milestones.filter(_.byRepository(newUserName, newRepositoryName)).list
-        val newPriorities = Priorities.filter(_.byRepository(newUserName, newRepositoryName)).list
-        Issues.insertAll(issues.map { x =>
-          x.copy(
-            userName = newUserName,
-            repositoryName = newRepositoryName,
-            milestoneId = x.milestoneId.map { id =>
-              newMilestones.find(_.title == milestones.find(_.milestoneId == id).get.title).get.milestoneId
-            },
-            priorityId = x.priorityId.map { id =>
-              newPriorities.find(_.priorityName == priorities.find(_.priorityId == id).get.priorityName).get.priorityId
+          Repositories
+            .filter { t =>
+              (t.originUserName === oldUserName.bind) && (t.originRepositoryName === oldRepositoryName.bind)
             }
+            .map { t =>
+              t.originUserName -> t.originRepositoryName
+            }
+            .update(newUserName, newRepositoryName)
+
+          Repositories
+            .filter { t =>
+              (t.parentUserName === oldUserName.bind) && (t.parentRepositoryName === oldRepositoryName.bind)
+            }
+            .map { t =>
+              t.parentUserName -> t.parentRepositoryName
+            }
+            .update(newUserName, newRepositoryName)
+
+          // Updates activity fk before deleting repository because activity is sorted by activityId
+          // and it can't be changed by deleting-and-inserting record.
+          Activities.filter(_.byRepository(oldUserName, oldRepositoryName)).list.foreach { activity =>
+            Activities
+              .filter(_.activityId === activity.activityId.bind)
+              .map(x => (x.userName, x.repositoryName))
+              .update(newUserName, newRepositoryName)
+          }
+
+          deleteRepositoryOnModel(oldUserName, oldRepositoryName)
+
+          RepositoryWebHooks.insertAll(
+            webHooks.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
           )
-        }: _*)
+          RepositoryWebHookEvents.insertAll(
+            webHookEvents.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
+          )
+          Milestones.insertAll(milestones.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*)
+          Priorities.insertAll(priorities.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*)
+          IssueId.insertAll(issueId.map(_.copy(_1 = newUserName, _2 = newRepositoryName)): _*)
 
-        PullRequests.insertAll(pullRequests.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*)
-        IssueComments.insertAll(
-          issueComments.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
-        )
-        Labels.insertAll(labels.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*)
-        CommitComments.insertAll(
-          commitComments.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
-        )
-        CommitStatuses.insertAll(
-          commitStatuses.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
-        )
-        ProtectedBranches.insertAll(
-          protectedBranches.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
-        )
-        ProtectedBranchContexts.insertAll(
-          protectedBranchContexts.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
-        )
-        DeployKeys.insertAll(deployKeys.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*)
-        ReleaseTags.insertAll(releases.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*)
-        ReleaseAssets.insertAll(
-          releaseAssets.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
-        )
-
-        // Update source repository of pull requests
-        PullRequests
-          .filter { t =>
-            (t.requestUserName === oldUserName.bind) && (t.requestRepositoryName === oldRepositoryName.bind)
-          }
-          .map { t =>
-            t.requestUserName -> t.requestRepositoryName
-          }
-          .update(newUserName, newRepositoryName)
-
-        // Convert labelId
-        val oldLabelMap = labels.map(x => (x.labelId, x.labelName)).toMap
-        val newLabelMap =
-          Labels.filter(_.byRepository(newUserName, newRepositoryName)).map(x => (x.labelName, x.labelId)).list.toMap
-        IssueLabels.insertAll(
-          issueLabels.map(
-            x =>
-              x.copy(
-                labelId = newLabelMap(oldLabelMap(x.labelId)),
-                userName = newUserName,
-                repositoryName = newRepositoryName
+          val newMilestones = Milestones.filter(_.byRepository(newUserName, newRepositoryName)).list
+          val newPriorities = Priorities.filter(_.byRepository(newUserName, newRepositoryName)).list
+          Issues.insertAll(issues.map { x =>
+            x.copy(
+              userName = newUserName,
+              repositoryName = newRepositoryName,
+              milestoneId = x.milestoneId.map { id =>
+                newMilestones.find(_.title == milestones.find(_.milestoneId == id).get.title).get.milestoneId
+              },
+              priorityId = x.priorityId.map { id =>
+                newPriorities
+                  .find(_.priorityName == priorities.find(_.priorityId == id).get.priorityName)
+                  .get
+                  .priorityId
+              }
             )
-          ): _*
-        )
+          }: _*)
 
-        // TODO Drop transferred owner from collaborators?
-        Collaborators.insertAll(
-          collaborators.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
-        )
+          PullRequests.insertAll(
+            pullRequests.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
+          )
+          IssueComments.insertAll(
+            issueComments.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
+          )
+          Labels.insertAll(labels.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*)
+          CommitComments.insertAll(
+            commitComments.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
+          )
+          CommitStatuses.insertAll(
+            commitStatuses.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
+          )
+          ProtectedBranches.insertAll(
+            protectedBranches.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
+          )
+          ProtectedBranchContexts.insertAll(
+            protectedBranchContexts.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
+          )
+          DeployKeys.insertAll(deployKeys.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*)
+          ReleaseTags.insertAll(releases.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*)
+          ReleaseAssets.insertAll(
+            releaseAssets.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
+          )
 
-        // Update activity messages
-        Activities
-          .filter { t =>
-            (t.message like s"%:${oldUserName}/${oldRepositoryName}]%") ||
-            (t.message like s"%:${oldUserName}/${oldRepositoryName}#%") ||
-            (t.message like s"%:${oldUserName}/${oldRepositoryName}@%")
+          // Update source repository of pull requests
+          PullRequests
+            .filter { t =>
+              (t.requestUserName === oldUserName.bind) && (t.requestRepositoryName === oldRepositoryName.bind)
+            }
+            .map { t =>
+              t.requestUserName -> t.requestRepositoryName
+            }
+            .update(newUserName, newRepositoryName)
+
+          // Convert labelId
+          val oldLabelMap = labels.map(x => (x.labelId, x.labelName)).toMap
+          val newLabelMap =
+            Labels.filter(_.byRepository(newUserName, newRepositoryName)).map(x => (x.labelName, x.labelId)).list.toMap
+          IssueLabels.insertAll(
+            issueLabels.map(
+              x =>
+                x.copy(
+                  labelId = newLabelMap(oldLabelMap(x.labelId)),
+                  userName = newUserName,
+                  repositoryName = newRepositoryName
+              )
+            ): _*
+          )
+
+          // TODO Drop transferred owner from collaborators?
+          Collaborators.insertAll(
+            collaborators.map(_.copy(userName = newUserName, repositoryName = newRepositoryName)): _*
+          )
+
+          // Update activity messages
+          Activities
+            .filter { t =>
+              (t.message like s"%:${oldUserName}/${oldRepositoryName}]%") ||
+              (t.message like s"%:${oldUserName}/${oldRepositoryName}#%") ||
+              (t.message like s"%:${oldUserName}/${oldRepositoryName}@%")
+            }
+            .map { t =>
+              t.activityId -> t.message
+            }
+            .list
+            .foreach {
+              case (activityId, message) =>
+                Activities
+                  .filter(_.activityId === activityId.bind)
+                  .map(_.message)
+                  .update(
+                    message
+                      .replace(
+                        s"[repo:${oldUserName}/${oldRepositoryName}]",
+                        s"[repo:${newUserName}/${newRepositoryName}]"
+                      )
+                      .replace(
+                        s"[branch:${oldUserName}/${oldRepositoryName}#",
+                        s"[branch:${newUserName}/${newRepositoryName}#"
+                      )
+                      .replace(
+                        s"[tag:${oldUserName}/${oldRepositoryName}#",
+                        s"[tag:${newUserName}/${newRepositoryName}#"
+                      )
+                      .replace(
+                        s"[pullreq:${oldUserName}/${oldRepositoryName}#",
+                        s"[pullreq:${newUserName}/${newRepositoryName}#"
+                      )
+                      .replace(
+                        s"[issue:${oldUserName}/${oldRepositoryName}#",
+                        s"[issue:${newUserName}/${newRepositoryName}#"
+                      )
+                      .replace(
+                        s"[commit:${oldUserName}/${oldRepositoryName}@",
+                        s"[commit:${newUserName}/${newRepositoryName}@"
+                      )
+                  )
+            }
+          // Move git repository
+          defining(getRepositoryDir(oldUserName, oldRepositoryName)) { dir =>
+            if (dir.isDirectory) {
+              FileUtils.moveDirectory(dir, getRepositoryDir(newUserName, newRepositoryName))
+            }
           }
-          .map { t =>
-            t.activityId -> t.message
+          // Move wiki repository
+          defining(getWikiRepositoryDir(oldUserName, oldRepositoryName)) { dir =>
+            if (dir.isDirectory) {
+              FileUtils.moveDirectory(dir, getWikiRepositoryDir(newUserName, newRepositoryName))
+            }
           }
-          .list
-          .foreach {
-            case (activityId, message) =>
-              Activities
-                .filter(_.activityId === activityId.bind)
-                .map(_.message)
-                .update(
-                  message
-                    .replace(
-                      s"[repo:${oldUserName}/${oldRepositoryName}]",
-                      s"[repo:${newUserName}/${newRepositoryName}]"
-                    )
-                    .replace(
-                      s"[branch:${oldUserName}/${oldRepositoryName}#",
-                      s"[branch:${newUserName}/${newRepositoryName}#"
-                    )
-                    .replace(s"[tag:${oldUserName}/${oldRepositoryName}#", s"[tag:${newUserName}/${newRepositoryName}#")
-                    .replace(
-                      s"[pullreq:${oldUserName}/${oldRepositoryName}#",
-                      s"[pullreq:${newUserName}/${newRepositoryName}#"
-                    )
-                    .replace(
-                      s"[issue:${oldUserName}/${oldRepositoryName}#",
-                      s"[issue:${newUserName}/${newRepositoryName}#"
-                    )
-                    .replace(
-                      s"[commit:${oldUserName}/${oldRepositoryName}@",
-                      s"[commit:${newUserName}/${newRepositoryName}@"
-                    )
-                )
+          // Move files directory
+          defining(getRepositoryFilesDir(oldUserName, oldRepositoryName)) { dir =>
+            if (dir.isDirectory) {
+              FileUtils.moveDirectory(dir, getRepositoryFilesDir(newUserName, newRepositoryName))
+            }
           }
+          // Delete parent directory
+          FileUtil.deleteDirectoryIfEmpty(getRepositoryFilesDir(oldUserName, oldRepositoryName))
+
+          // Call hooks
+          if (oldUserName == newUserName) {
+            PluginRegistry().getRepositoryHooks.foreach(_.renamed(oldUserName, oldRepositoryName, newRepositoryName))
+          } else {
+            PluginRegistry().getRepositoryHooks.foreach(_.transferred(oldUserName, newUserName, newRepositoryName))
+          }
+        }
       }
     }
   }
 
-  def deleteRepository(userName: String, repositoryName: String)(implicit s: Session): Unit = {
+  def deleteRepository(repository: Repository)(implicit s: Session): Unit = {
+    LockUtil.lock(s"${repository.userName}/${repository.repositoryName}") {
+      deleteRepositoryOnModel(repository.userName, repository.repositoryName)
+
+      FileUtils.deleteDirectory(getRepositoryDir(repository.userName, repository.repositoryName))
+      FileUtils.deleteDirectory(getWikiRepositoryDir(repository.userName, repository.repositoryName))
+      FileUtils.deleteDirectory(getTemporaryDir(repository.userName, repository.repositoryName))
+      FileUtils.deleteDirectory(getRepositoryFilesDir(repository.userName, repository.repositoryName))
+
+      // Call hooks
+      PluginRegistry().getRepositoryHooks.foreach(_.deleted(repository.userName, repository.repositoryName))
+    }
+  }
+
+  private def deleteRepositoryOnModel(userName: String, repositoryName: String)(implicit s: Session): Unit = {
     Activities.filter(_.byRepository(userName, repositoryName)).delete
     Collaborators.filter(_.byRepository(userName, repositoryName)).delete
     CommitComments.filter(_.byRepository(userName, repositoryName)).delete
@@ -313,28 +373,33 @@ trait RepositoryService { self: AccountService =>
    * @return the repository information
    */
   def getRepository(userName: String, repositoryName: String)(implicit s: Session): Option[RepositoryInfo] = {
-    (Repositories filter { t =>
-      t.byRepository(userName, repositoryName)
-    } firstOption) map { repository =>
-      // for getting issue count and pull request count
-      val issues = Issues
-        .filter { t =>
-          t.byRepository(repository.userName, repository.repositoryName) && (t.closed === false.bind)
-        }
-        .map(_.pullRequest)
-        .list
+    (Repositories
+      .join(Accounts)
+      .on(_.userName === _.userName)
+      .filter {
+        case (t1, t2) =>
+          t1.byRepository(userName, repositoryName) && t2.removed === false.bind
+    } firstOption) map {
+      case (repository, account) =>
+        // for getting issue count and pull request count
+        val issues = Issues
+          .filter { t =>
+            t.byRepository(repository.userName, repository.repositoryName) && (t.closed === false.bind)
+          }
+          .map(_.pullRequest)
+          .list
 
-      new RepositoryInfo(
-        JGitUtil.getRepositoryInfo(repository.userName, repository.repositoryName),
-        repository,
-        issues.count(_ == false),
-        issues.count(_ == true),
-        getForkedCount(
-          repository.originUserName.getOrElse(repository.userName),
-          repository.originRepositoryName.getOrElse(repository.repositoryName)
-        ),
-        getRepositoryManagers(repository.userName)
-      )
+        new RepositoryInfo(
+          JGitUtil.getRepositoryInfo(repository.userName, repository.repositoryName),
+          repository,
+          issues.count(_ == false),
+          issues.count(_ == true),
+          getForkedCount(
+            repository.originUserName.getOrElse(repository.userName),
+            repository.originRepositoryName.getOrElse(repository.repositoryName)
+          ),
+          getRepositoryManagers(repository.userName, repository.repositoryName)
+        )
     }
   }
 
@@ -366,6 +431,10 @@ trait RepositoryService { self: AccountService =>
       .list
   }
 
+  /**
+   * Returns the list of repositories which are owned by the specified user.
+   * This list includes group repositories if the specified user is a member of the group.
+   */
   def getUserRepositories(userName: String, withoutPhysicalInfo: Boolean = false)(
     implicit s: Session
   ): List[RepositoryInfo] = {
@@ -383,29 +452,7 @@ trait RepositoryService { self: AccountService =>
       }
       .sortBy(_.lastActivityDate desc)
       .list
-      .map { repository =>
-        new RepositoryInfo(
-          if (withoutPhysicalInfo) {
-            new JGitUtil.RepositoryInfo(repository.userName, repository.repositoryName)
-          } else {
-            JGitUtil.getRepositoryInfo(repository.userName, repository.repositoryName)
-          },
-          repository,
-          if (withoutPhysicalInfo) {
-            -1
-          } else {
-            getForkedCount(
-              repository.originUserName.getOrElse(repository.userName),
-              repository.originRepositoryName.getOrElse(repository.repositoryName)
-            )
-          },
-          if (withoutPhysicalInfo) {
-            Nil
-          } else {
-            getRepositoryManagers(repository.userName)
-          }
-        )
-      }
+      .map(createRepositoryInfo(_, withoutPhysicalInfo))
   }
 
   /**
@@ -425,21 +472,35 @@ trait RepositoryService { self: AccountService =>
   )(implicit s: Session): List[RepositoryInfo] = {
     (loginAccount match {
       // for Administrators
-      case Some(x) if (x.isAdmin) => Repositories
+      case Some(x) if (x.isAdmin) =>
+        Repositories
+          .join(Accounts)
+          .on(_.userName === _.userName)
+          .filter { case (t1, t2) => t2.removed === false.bind }
+          .map { case (t1, t2) => t1 }
       // for Normal Users
       case Some(x) if (!x.isAdmin) =>
-        Repositories filter { t =>
-          (t.isPrivate === false.bind) || (t.userName === x.userName) ||
-          (t.userName in GroupMembers.filter(_.userName === x.userName.bind).map(_.groupName)) ||
-          (Collaborators.filter { t2 =>
-            t2.byRepository(t.userName, t.repositoryName) &&
-            ((t2.collaboratorName === x.userName.bind) || (t2.collaboratorName in GroupMembers
-              .filter(_.userName === x.userName.bind)
-              .map(_.groupName)))
-          } exists)
-        }
+        Repositories
+          .join(Accounts)
+          .on(_.userName === _.userName)
+          .filter {
+            case (t1, t2) =>
+              (t2.removed === false.bind) && ((t1.isPrivate === false.bind) || (t1.userName === x.userName) ||
+                (t1.userName in GroupMembers.filter(_.userName === x.userName.bind).map(_.groupName)) ||
+                (Collaborators.filter { t3 =>
+                  t3.byRepository(t1.userName, t1.repositoryName) &&
+                  ((t3.collaboratorName === x.userName.bind) ||
+                  (t3.collaboratorName in GroupMembers.filter(_.userName === x.userName.bind).map(_.groupName)))
+                } exists))
+          }
+          .map { case (t1, t2) => t1 }
       // for Guests
-      case None => Repositories filter (_.isPrivate === false.bind)
+      case None =>
+        Repositories
+          .join(Accounts)
+          .on(_.userName === _.userName)
+          .filter { case (t1, t2) => t1.isPrivate === false.bind && t2.removed === false.bind }
+          .map { case (t1, t2) => t1 }
     }).filter { t =>
         repositoryUserName.map { userName =>
           t.userName === userName.bind
@@ -447,37 +508,45 @@ trait RepositoryService { self: AccountService =>
       }
       .sortBy(_.lastActivityDate desc)
       .list
-      .map { repository =>
-        new RepositoryInfo(
-          if (withoutPhysicalInfo) {
-            new JGitUtil.RepositoryInfo(repository.userName, repository.repositoryName)
-          } else {
-            JGitUtil.getRepositoryInfo(repository.userName, repository.repositoryName)
-          },
-          repository,
-          if (withoutPhysicalInfo) {
-            -1
-          } else {
-            getForkedCount(
-              repository.originUserName.getOrElse(repository.userName),
-              repository.originRepositoryName.getOrElse(repository.repositoryName)
-            )
-          },
-          if (withoutPhysicalInfo) {
-            Nil
-          } else {
-            getRepositoryManagers(repository.userName)
-          }
-        )
-      }
+      .map(createRepositoryInfo(_, withoutPhysicalInfo))
   }
 
-  private def getRepositoryManagers(userName: String)(implicit s: Session): Seq[String] =
-    if (getAccountByUserName(userName).exists(_.isGroupAccount)) {
-      getGroupMembers(userName).collect { case x if (x.isManager) => x.userName }
-    } else {
-      Seq(userName)
-    }
+  private def createRepositoryInfo(repository: Repository, withoutPhysicalInfo: Boolean = false)(
+    implicit s: Session
+  ): RepositoryInfo = {
+    new RepositoryInfo(
+      if (withoutPhysicalInfo) {
+        new JGitUtil.RepositoryInfo(repository.userName, repository.repositoryName)
+      } else {
+        JGitUtil.getRepositoryInfo(repository.userName, repository.repositoryName)
+      },
+      repository,
+      if (withoutPhysicalInfo) {
+        -1
+      } else {
+        getForkedCount(
+          repository.originUserName.getOrElse(repository.userName),
+          repository.originRepositoryName.getOrElse(repository.repositoryName)
+        )
+      },
+      if (withoutPhysicalInfo) {
+        Nil
+      } else {
+        getRepositoryManagers(repository.userName, repository.repositoryName)
+      }
+    )
+  }
+
+  /**
+   * TODO It seems to be able to improve performance. For example, RequestCache can be used for getAccountByUserName call.
+   */
+  private def getRepositoryManagers(userName: String, repositoryName: String)(implicit s: Session): Seq[String] = {
+    (if (getAccountByUserName(userName).exists(_.isGroupAccount)) {
+       getGroupMembers(userName).collect { case x if (x.isManager) => x.userName }
+     } else {
+       Seq(userName)
+     }) ++ getCollaboratorUserNames(userName, repositoryName, Seq(Role.ADMIN))
+  }
 
   /**
    * Updates the last activity date of the repository.
@@ -551,6 +620,14 @@ trait RepositoryService { self: AccountService =>
   ): Unit =
     Collaborators insert Collaborator(userName, repositoryName, collaboratorName, role)
 
+  /**
+   * Remove specified collaborator from the repository.
+   */
+  def removeCollaborator(userName: String, repositoryName: String, collaboratorName: String)(
+    implicit s: Session
+  ): Unit =
+    Collaborators.filter(_.byPrimaryKey(userName, repositoryName, collaboratorName)).delete
+
   /**
    * Remove all collaborators from the repository.
    */
@@ -701,7 +778,6 @@ trait RepositoryService { self: AccountService =>
 }
 
 object RepositoryService {
-
   case class RepositoryInfo(
     owner: String,
     name: String,
@@ -750,7 +826,7 @@ object RepositoryService {
   def httpUrl(owner: String, name: String)(implicit context: Context): String =
     s"${context.baseUrl}/git/${owner}/${name}.git"
   def sshUrl(owner: String, name: String)(implicit context: Context): Option[String] =
-    if (context.settings.ssh) {
+    if (context.settings.ssh.enabled) {
       context.settings.sshAddress.map { x =>
         s"ssh://${x.genericUser}@${x.host}:${x.port}/${owner}/${name}.git"
       }

src/main/scala/gitbucket/core/service/SystemSettingsService.scala

@@ -1,7 +1,6 @@
 package gitbucket.core.service
 
 import javax.servlet.http.HttpServletRequest
-
 import com.nimbusds.jose.JWSAlgorithm
 import com.nimbusds.oauth2.sdk.auth.Secret
 import com.nimbusds.oauth2.sdk.id.{ClientID, Issuer}
@@ -24,9 +23,9 @@ trait SystemSettingsService {
       props.setProperty(Gravatar, settings.gravatar.toString)
       props.setProperty(Notification, settings.notification.toString)
       settings.activityLogLimit.foreach(x => props.setProperty(ActivityLogLimit, x.toString))
-      props.setProperty(Ssh, settings.ssh.toString)
-      settings.sshHost.foreach(x => props.setProperty(SshHost, x.trim))
-      settings.sshPort.foreach(x => props.setProperty(SshPort, x.toString))
+      props.setProperty(SshEnabled, settings.ssh.enabled.toString)
+      settings.ssh.sshHost.foreach(x => props.setProperty(SshHost, x.trim))
+      settings.ssh.sshPort.foreach(x => props.setProperty(SshPort, x.toString))
       props.setProperty(UseSMTP, settings.useSMTP.toString)
       if (settings.useSMTP) {
         settings.smtp.foreach { smtp =>
@@ -42,7 +41,7 @@ trait SystemSettingsService {
       }
       props.setProperty(LdapAuthentication, settings.ldapAuthentication.toString)
       if (settings.ldapAuthentication) {
-        settings.ldap.map { ldap =>
+        settings.ldap.foreach { ldap =>
           props.setProperty(LdapHost, ldap.host)
           ldap.port.foreach(x => props.setProperty(LdapPort, x.toString))
           ldap.bindDN.foreach(x => props.setProperty(LdapBindDN, x))
@@ -59,16 +58,29 @@ trait SystemSettingsService {
       }
       props.setProperty(OidcAuthentication, settings.oidcAuthentication.toString)
       if (settings.oidcAuthentication) {
-        settings.oidc.map { oidc =>
+        settings.oidc.foreach { oidc =>
           props.setProperty(OidcIssuer, oidc.issuer.getValue)
           props.setProperty(OidcClientId, oidc.clientID.getValue)
           props.setProperty(OidcClientSecret, oidc.clientSecret.getValue)
-          oidc.jwsAlgorithm.map { x =>
+          oidc.jwsAlgorithm.foreach { x =>
             props.setProperty(OidcJwsAlgorithm, x.getName)
           }
         }
       }
       props.setProperty(SkinName, settings.skinName.toString)
+      props.setProperty(ShowMailAddress, settings.showMailAddress.toString)
+      props.setProperty(PluginNetworkInstall, settings.pluginNetworkInstall.toString)
+      settings.pluginProxy.foreach { proxy =>
+        props.setProperty(PluginProxyHost, proxy.host)
+        props.setProperty(PluginProxyPort, proxy.port.toString)
+        proxy.user.foreach { user =>
+          props.setProperty(PluginProxyUser, user)
+        }
+        proxy.password.foreach { password =>
+          props.setProperty(PluginProxyPassword, password)
+        }
+      }
+
       using(new java.io.FileOutputStream(GitBucketConf)) { out =>
         props.store(out, null)
       }
@@ -91,9 +103,11 @@ trait SystemSettingsService {
         getValue(props, Gravatar, false),
         getValue(props, Notification, false),
         getOptionValue[Int](props, ActivityLogLimit, None),
-        getValue(props, Ssh, false),
-        getOptionValue[String](props, SshHost, None).map(_.trim),
-        getOptionValue(props, SshPort, Some(DefaultSshPort)),
+        Ssh(
+          getValue(props, SshEnabled, false),
+          getOptionValue[String](props, SshHost, None).map(_.trim),
+          getOptionValue(props, SshPort, Some(DefaultSshPort))
+        ),
         getValue(props, UseSMTP, getValue(props, Notification, false)), // handle migration scenario from only notification to useSMTP
         if (getValue(props, UseSMTP, getValue(props, Notification, false))) {
           Some(
@@ -108,9 +122,7 @@ trait SystemSettingsService {
               getOptionValue(props, SmtpFromName, None)
             )
           )
-        } else {
-          None
-        },
+        } else None,
         getValue(props, LdapAuthentication, false),
         if (getValue(props, LdapAuthentication, false)) {
           Some(
@@ -129,9 +141,7 @@ trait SystemSettingsService {
               getOptionValue(props, LdapKeystore, None)
             )
           )
-        } else {
-          None
-        },
+        } else None,
         getValue(props, OidcAuthentication, false),
         if (getValue(props, OidcAuthentication, false)) {
           Some(
@@ -145,7 +155,19 @@ trait SystemSettingsService {
         } else {
           None
         },
-        getValue(props, SkinName, "skin-blue")
+        getValue(props, SkinName, "skin-blue"),
+        getValue(props, ShowMailAddress, false),
+        getValue(props, PluginNetworkInstall, false),
+        if (getValue(props, PluginProxyHost, "").nonEmpty) {
+          Some(
+            Proxy(
+              getValue(props, PluginProxyHost, ""),
+              getValue(props, PluginProxyPort, 8080),
+              getOptionValue(props, PluginProxyUser, None),
+              getOptionValue(props, PluginProxyPassword, None)
+            )
+          )
+        } else None
       )
     }
   }
@@ -155,6 +177,8 @@ trait SystemSettingsService {
 object SystemSettingsService {
   import scala.reflect.ClassTag
 
+  private val HttpProtocols = Vector("http", "https")
+
   case class SystemSettings(
     baseUrl: Option[String],
     information: Option[String],
@@ -164,31 +188,47 @@ object SystemSettingsService {
     gravatar: Boolean,
     notification: Boolean,
     activityLogLimit: Option[Int],
-    ssh: Boolean,
-    sshHost: Option[String],
-    sshPort: Option[Int],
+    ssh: Ssh,
     useSMTP: Boolean,
     smtp: Option[Smtp],
     ldapAuthentication: Boolean,
     ldap: Option[Ldap],
     oidcAuthentication: Boolean,
     oidc: Option[OIDC],
-    skinName: String
+    skinName: String,
+    showMailAddress: Boolean,
+    pluginNetworkInstall: Boolean,
+    pluginProxy: Option[Proxy]
   ) {
 
     def baseUrl(request: HttpServletRequest): String =
-      baseUrl.fold {
-        val url = request.getRequestURL.toString
-        val len = url.length - (request.getRequestURI.length - request.getContextPath.length)
-        url.substring(0, len).stripSuffix("/")
-      }(_.stripSuffix("/"))
+      baseUrl.getOrElse(parseBaseUrl(request)).stripSuffix("/")
 
-    def sshAddress: Option[SshAddress] = sshHost.collect {
-      case host if ssh =>
-        SshAddress(host, sshPort.getOrElse(DefaultSshPort), "git")
+    def parseBaseUrl(req: HttpServletRequest): String = {
+      val url = req.getRequestURL.toString
+      val path = req.getRequestURI
+      val contextPath = req.getContextPath
+      val len = url.length - path.length + contextPath.length
+
+      val base = url.substring(0, len).stripSuffix("/")
+      Option(req.getHeader("X-Forwarded-Proto"))
+        .map(_.toLowerCase())
+        .filter(HttpProtocols.contains)
+        .fold(base)(_ + base.dropWhile(_ != ':'))
+    }
+
+    def sshAddress: Option[SshAddress] = ssh.sshHost.collect {
+      case host if ssh.enabled =>
+        SshAddress(host, ssh.sshPort.getOrElse(DefaultSshPort), "git")
     }
   }
 
+  case class Ssh(
+    enabled: Boolean,
+    sshHost: Option[String],
+    sshPort: Option[Int]
+  )
+
   case class Ldap(
     host: String,
     port: Option[Int],
@@ -226,6 +266,13 @@ object SystemSettingsService {
     fromName: Option[String]
   )
 
+  case class Proxy(
+    host: String,
+    port: Int,
+    user: Option[String],
+    password: Option[String],
+  )
+
   case class SshAddress(host: String, port: Int, genericUser: String)
 
   case class Lfs(serverUrl: Option[String])
@@ -242,7 +289,7 @@ object SystemSettingsService {
   private val Gravatar = "gravatar"
   private val Notification = "notification"
   private val ActivityLogLimit = "activity_log_limit"
-  private val Ssh = "ssh"
+  private val SshEnabled = "ssh"
   private val SshHost = "ssh.host"
   private val SshPort = "ssh.port"
   private val UseSMTP = "useSMTP"
@@ -273,6 +320,12 @@ object SystemSettingsService {
   private val OidcClientSecret = "oidc.client_secret"
   private val OidcJwsAlgorithm = "oidc.jws_algorithm"
   private val SkinName = "skinName"
+  private val ShowMailAddress = "showMailAddress"
+  private val PluginNetworkInstall = "plugin.networkInstall"
+  private val PluginProxyHost = "plugin.proxy.host"
+  private val PluginProxyPort = "plugin.proxy.port"
+  private val PluginProxyUser = "plugin.proxy.user"
+  private val PluginProxyPassword = "plugin.proxy.password"
 
   private def getValue[A: ClassTag](props: java.util.Properties, key: String, default: A): A = {
     getSystemProperty(key).getOrElse(getEnvironmentVariable(key).getOrElse {

src/main/scala/gitbucket/core/service/WebHookService.scala

@@ -311,7 +311,6 @@ trait WebHookPullRequestService extends WebHookService {
     action: String,
     repository: RepositoryService.RepositoryInfo,
     issue: Issue,
-    baseUrl: String,
     sender: Account
   )(implicit s: Session, context: JsonFormat.Context): Unit = {
     callWebHookOf(repository.owner, repository.name, WebHook.Issues) {
@@ -341,7 +340,6 @@ trait WebHookPullRequestService extends WebHookService {
     action: String,
     repository: RepositoryService.RepositoryInfo,
     issueId: Int,
-    baseUrl: String,
     sender: Account
   )(implicit s: Session, c: JsonFormat.Context): Unit = {
     import WebHookService._
@@ -404,7 +402,6 @@ trait WebHookPullRequestService extends WebHookService {
     action: String,
     requestRepository: RepositoryService.RepositoryInfo,
     requestBranch: String,
-    baseUrl: String,
     sender: Account
   )(implicit s: Session, c: JsonFormat.Context): Unit = {
     import WebHookService._
@@ -450,7 +447,6 @@ trait WebHookPullRequestReviewCommentService extends WebHookService {
     repository: RepositoryService.RepositoryInfo,
     issue: Issue,
     pullRequest: PullRequest,
-    baseUrl: String,
     sender: Account
   )(implicit s: Session, c: JsonFormat.Context): Unit = {
     import WebHookService._

src/main/scala/gitbucket/core/servlet/GitRepositoryServlet.scala

@@ -221,6 +221,7 @@ class CommitLogHook(owner: String, repository: String, pusher: String, baseUrl:
     with PrioritiesService
     with MilestonesService
     with WebHookPullRequestService
+    with WebHookPullRequestReviewCommentService
     with CommitsService {
 
   private val logger = LoggerFactory.getLogger(classOf[CommitLogHook])
@@ -296,13 +297,34 @@ class CommitLogHook(owner: String, repository: String, pusher: String, baseUrl:
                   createIssueComment(owner, repository, commit)
                   // close issues
                   if (refName(1) == "heads" && branchName == defaultBranch && command.getType == ReceiveCommand.Type.UPDATE) {
-                    closeIssuesFromMessage(commit.fullMessage, pusher, owner, repository)
+                    getAccountByUserName(pusher).foreach { pusherAccount =>
+                      closeIssuesFromMessage(commit.fullMessage, pusher, owner, repository).foreach { issueId =>
+                        getIssue(owner, repository, issueId.toString).foreach { issue =>
+                          callIssuesWebHook("closed", repositoryInfo, issue, pusherAccount)
+                          PluginRegistry().getIssueHooks
+                            .foreach(_.closedByCommitComment(issue, repositoryInfo, commit.fullMessage, pusherAccount))
+                        }
+                      }
+                    }
                   }
                 }
                 Some(commit)
               } else None
             }
 
+            // set PR as merged
+            val pulls = getPullRequestsByBranch(owner, repository, branchName, Some(false))
+            pulls.foreach { pull =>
+              if (commits.find { c =>
+                    c.id == pull.commitIdTo
+                  }.isDefined) {
+                markMergeAndClosePullRequest(pusher, owner, repository, pull)
+                getAccountByUserName(pusher).foreach { pusherAccount =>
+                  callPullRequestWebHook("closed", repositoryInfo, pull.issueId, pusherAccount)
+                }
+              }
+            }
+
             // record activity
             if (refName(1) == "heads") {
               command.getType match {
@@ -325,15 +347,8 @@ class CommitLogHook(owner: String, repository: String, pusher: String, baseUrl:
               command.getType match {
                 case ReceiveCommand.Type.CREATE | ReceiveCommand.Type.UPDATE |
                     ReceiveCommand.Type.UPDATE_NONFASTFORWARD =>
-                  updatePullRequests(owner, repository, branchName)
-                  getAccountByUserName(pusher).map { pusherAccount =>
-                    callPullRequestWebHookByRequestBranch(
-                      "synchronize",
-                      repositoryInfo,
-                      branchName,
-                      baseUrl,
-                      pusherAccount
-                    )
+                  getAccountByUserName(pusher).foreach { pusherAccount =>
+                    updatePullRequests(owner, repository, branchName, pusherAccount, "synchronize")
                   }
                 case _ =>
               }
@@ -418,7 +433,7 @@ class WikiCommitHook(owner: String, repository: String, pusher: String, baseUrl:
             }
           }
 
-          commitIds.map {
+          commitIds.foreach {
             case (oldCommitId, newCommitId) =>
               val commits = using(Git.open(Directory.getWikiRepositoryDir(owner, repository))) { git =>
                 JGitUtil.getCommitLog(git, oldCommitId, newCommitId).flatMap { commit =>

src/main/scala/gitbucket/core/servlet/InitializeListener.scala

@@ -5,7 +5,7 @@ import java.io.{File, FileOutputStream}
 import akka.event.Logging
 import com.typesafe.config.ConfigFactory
 import gitbucket.core.GitBucketCoreModule
-import gitbucket.core.plugin.{PluginRegistry, PluginRepository}
+import gitbucket.core.plugin.PluginRegistry
 import gitbucket.core.service.{ActivityService, SystemSettingsService}
 import gitbucket.core.util.DatabaseConfig
 import gitbucket.core.util.Directory._
@@ -20,7 +20,6 @@ import org.apache.commons.io.{FileUtils, IOUtils}
 import org.slf4j.LoggerFactory
 import akka.actor.{Actor, ActorSystem, Props}
 import com.typesafe.akka.extension.quartz.QuartzSchedulerExtension
-import com.github.zafarkhaja.semver.{Version => Semver}
 
 import scala.collection.JavaConverters._
 
@@ -136,40 +135,30 @@ class InitializeListener extends ServletContextListener with SystemSettingsServi
   }
 
   private def extractBundledPlugins(gitbucketVersion: String): Unit = {
-    logger.info("Extract bundled plugins")
+    logger.info("Extract bundled plugins...")
     val cl = Thread.currentThread.getContextClassLoader
     try {
-      using(cl.getResourceAsStream("plugins/plugins.json")) { pluginsFile =>
+      using(cl.getResourceAsStream("bundle-plugins.txt")) { pluginsFile =>
         if (pluginsFile != null) {
-          val pluginsJson = IOUtils.toString(pluginsFile, "UTF-8")
+          val plugins = IOUtils.readLines(pluginsFile, "UTF-8")
+          val gitbucketVersion = GitBucketCoreModule.getVersions.asScala.last.getVersion
 
-          FileUtils.forceMkdir(PluginRepository.LocalRepositoryDir)
-          FileUtils.write(PluginRepository.LocalRepositoryIndexFile, pluginsJson, "UTF-8")
+          plugins.asScala.foreach { plugin =>
+            plugin.trim.split(":") match {
+              case Array(pluginId, pluginVersion) =>
+                val fileName = s"gitbucket-${pluginId}-plugin-gitbucket_${gitbucketVersion}-${pluginVersion}.jar"
+                val in = cl.getResourceAsStream("plugins/" + fileName)
+                if (in != null) {
+                  val file = new File(PluginHome, fileName)
+                  logger.info(s"Extract to ${file.getAbsolutePath}")
 
-          val plugins = PluginRepository.parsePluginJson(pluginsJson)
-          plugins.foreach { plugin =>
-            plugin.versions
-              .sortBy { x =>
-                Semver.valueOf(x.version)
-              }
-              .reverse
-              .zipWithIndex
-              .foreach {
-                case (version, i) =>
-                  val file = new File(PluginRepository.LocalRepositoryDir, version.file)
-                  if (!file.exists) {
-                    logger.info(s"Copy ${plugin} to ${file.getAbsolutePath}")
-                    FileUtils.forceMkdirParent(file)
-                    using(cl.getResourceAsStream("plugins/" + version.file), new FileOutputStream(file)) {
-                      case (in, out) => IOUtils.copy(in, out)
-                    }
-
-                    if (plugin.default && i == 0) {
-                      logger.info(s"Enable ${file.getName} in default")
-                      FileUtils.copyFile(file, new File(PluginHome, version.file))
-                    }
+                  FileUtils.forceMkdirParent(file)
+                  using(in, new FileOutputStream(file)) {
+                    case (in, out) => IOUtils.copy(in, out)
                   }
-              }
+                }
+              case _ => ()
+            }
           }
         }
       }

src/main/scala/gitbucket/core/servlet/PluginAssetsServlet.scala

@@ -26,7 +26,7 @@ class PluginAssetsServlet extends HttpServlet {
         try {
           val bytes = IOUtils.toByteArray(in)
           resp.setContentLength(bytes.length)
-          resp.setContentType(FileUtil.getContentType(path, bytes))
+          resp.setContentType(FileUtil.getMimeType(path, bytes))
           resp.setHeader("Cache-Control", "max-age=3600")
           resp.getOutputStream.write(bytes)
         } finally {

src/main/scala/gitbucket/core/ssh/GitCommand.scala

@@ -5,7 +5,8 @@ import gitbucket.core.plugin.{GitRepositoryRouting, PluginRegistry}
 import gitbucket.core.service.{AccountService, DeployKeyService, RepositoryService, SystemSettingsService}
 import gitbucket.core.servlet.{CommitLogHook, Database}
 import gitbucket.core.util.{SyntaxSugars, Directory}
-import org.apache.sshd.server.{Command, CommandFactory, Environment, ExitCallback, SessionAware}
+import org.apache.sshd.server.{Environment, ExitCallback, SessionAware}
+import org.apache.sshd.server.command.{Command, CommandFactory}
 import org.apache.sshd.server.session.ServerSession
 import org.slf4j.LoggerFactory
 import java.io.{File, InputStream, OutputStream}
@@ -15,7 +16,7 @@ import org.eclipse.jgit.api.Git
 import Directory._
 import gitbucket.core.ssh.PublicKeyAuthenticator.AuthType
 import org.eclipse.jgit.transport.{ReceivePack, UploadPack}
-import org.apache.sshd.server.scp.UnknownCommand
+import org.apache.sshd.server.shell.UnknownCommand
 import org.eclipse.jgit.errors.RepositoryNotFoundException
 
 object GitCommand {

src/main/scala/gitbucket/core/ssh/NoShell.scala

@@ -2,7 +2,8 @@ package gitbucket.core.ssh
 
 import gitbucket.core.service.SystemSettingsService.SshAddress
 import org.apache.sshd.common.Factory
-import org.apache.sshd.server.{Environment, ExitCallback, Command}
+import org.apache.sshd.server.{Environment, ExitCallback}
+import org.apache.sshd.server.command.Command
 import java.io.{OutputStream, InputStream}
 import org.eclipse.jgit.lib.Constants
 

src/main/scala/gitbucket/core/ssh/SshServerListener.scala

@@ -17,7 +17,9 @@ object SshServer {
 
   private def configure(sshAddress: SshAddress, baseUrl: String) = {
     server.setPort(sshAddress.port)
-    val provider = new SimpleGeneratorHostKeyProvider(new File(s"${Directory.GitBucketHome}/gitbucket.ser"))
+    val provider = new SimpleGeneratorHostKeyProvider(
+      java.nio.file.Paths.get(s"${Directory.GitBucketHome}/gitbucket.ser")
+    )
     provider.setAlgorithm("RSA")
     provider.setOverwriteAllowed(false)
     server.setKeyPairProvider(provider)

src/main/scala/gitbucket/core/util/Authenticator.scala

@@ -15,14 +15,10 @@ trait OneselfAuthenticator { self: ControllerBase =>
   protected def oneselfOnly[T](action: T => Any) = (form: T) => { authenticate(action(form)) }
 
   private def authenticate(action: => Any) = {
-    {
-      defining(request.paths) { paths =>
-        context.loginAccount match {
-          case Some(x) if (x.isAdmin)              => action
-          case Some(x) if (paths(0) == x.userName) => action
-          case _                                   => Unauthorized()
-        }
-      }
+    context.loginAccount match {
+      case Some(x) if (x.isAdmin)                      => action
+      case Some(x) if (request.paths(0) == x.userName) => action
+      case _                                           => Unauthorized()
     }
   }
 }
@@ -35,24 +31,22 @@ trait OwnerAuthenticator { self: ControllerBase with RepositoryService with Acco
   protected def ownerOnly[T](action: (T, RepositoryInfo) => Any) = (form: T) => { authenticate(action(form, _)) }
 
   private def authenticate(action: (RepositoryInfo) => Any) = {
-    {
-      defining(request.paths) { paths =>
-        getRepository(paths(0), paths(1)).map { repository =>
-          context.loginAccount match {
-            case Some(x) if (x.isAdmin)                      => action(repository)
-            case Some(x) if (repository.owner == x.userName) => action(repository)
-            // TODO Repository management is allowed for only group managers?
-            case Some(x) if (getGroupMembers(repository.owner).exists { m =>
-                  m.userName == x.userName && m.isManager == true
-                }) =>
-              action(repository)
-            case Some(x) if (getCollaboratorUserNames(paths(0), paths(1), Seq(Role.ADMIN)).contains(x.userName)) =>
-              action(repository)
-            case _ => Unauthorized()
-          }
-        } getOrElse NotFound()
+    val userName = params("owner")
+    val repoName = params("repository")
+    getRepository(userName, repoName).map { repository =>
+      context.loginAccount match {
+        case Some(x) if (x.isAdmin)                      => action(repository)
+        case Some(x) if (repository.owner == x.userName) => action(repository)
+        // TODO Repository management is allowed for only group managers?
+        case Some(x) if (getGroupMembers(repository.owner).exists { m =>
+              m.userName == x.userName && m.isManager == true
+            }) =>
+          action(repository)
+        case Some(x) if (getCollaboratorUserNames(userName, repoName, Seq(Role.ADMIN)).contains(x.userName)) =>
+          action(repository)
+        case _ => Unauthorized()
       }
-    }
+    } getOrElse NotFound()
   }
 }
 
@@ -64,11 +58,9 @@ trait UsersAuthenticator { self: ControllerBase =>
   protected def usersOnly[T](action: T => Any) = (form: T) => { authenticate(action(form)) }
 
   private def authenticate(action: => Any) = {
-    {
-      context.loginAccount match {
-        case Some(x) => action
-        case None    => Unauthorized()
-      }
+    context.loginAccount match {
+      case Some(x) => action
+      case None    => Unauthorized()
     }
   }
 }
@@ -81,11 +73,9 @@ trait AdminAuthenticator { self: ControllerBase =>
   protected def adminOnly[T](action: T => Any) = (form: T) => { authenticate(action(form)) }
 
   private def authenticate(action: => Any) = {
-    {
-      context.loginAccount match {
-        case Some(x) if (x.isAdmin) => action
-        case _                      => Unauthorized()
-      }
+    context.loginAccount match {
+      case Some(x) if (x.isAdmin) => action
+      case _                      => Unauthorized()
     }
   }
 }
@@ -98,17 +88,15 @@ trait ReferrerAuthenticator { self: ControllerBase with RepositoryService with A
   protected def referrersOnly[T](action: (T, RepositoryInfo) => Any) = (form: T) => { authenticate(action(form, _)) }
 
   private def authenticate(action: (RepositoryInfo) => Any) = {
-    {
-      defining(request.paths) { paths =>
-        getRepository(paths(0), paths(1)).map { repository =>
-          if (isReadable(repository.repository, context.loginAccount)) {
-            action(repository)
-          } else {
-            Unauthorized()
-          }
-        } getOrElse NotFound()
+    val userName = params("owner")
+    val repoName = params("repository")
+    getRepository(userName, repoName).map { repository =>
+      if (isReadable(repository.repository, context.loginAccount)) {
+        action(repository)
+      } else {
+        Unauthorized()
       }
-    }
+    } getOrElse NotFound()
   }
 }
 
@@ -122,20 +110,18 @@ trait ReadableUsersAuthenticator { self: ControllerBase with RepositoryService w
   }
 
   private def authenticate(action: (RepositoryInfo) => Any) = {
-    {
-      defining(request.paths) { paths =>
-        getRepository(paths(0), paths(1)).map { repository =>
-          context.loginAccount match {
-            case Some(x) if (x.isAdmin)                                                          => action(repository)
-            case Some(x) if (!repository.repository.isPrivate)                                   => action(repository)
-            case Some(x) if (paths(0) == x.userName)                                             => action(repository)
-            case Some(x) if (getGroupMembers(repository.owner).exists(_.userName == x.userName)) => action(repository)
-            case Some(x) if (getCollaboratorUserNames(paths(0), paths(1)).contains(x.userName))  => action(repository)
-            case _                                                                               => Unauthorized()
-          }
-        } getOrElse NotFound()
+    val userName = params("owner")
+    val repoName = params("repository")
+    getRepository(userName, repoName).map { repository =>
+      context.loginAccount match {
+        case Some(x) if (x.isAdmin)                                                          => action(repository)
+        case Some(x) if (!repository.repository.isPrivate)                                   => action(repository)
+        case Some(x) if (userName == x.userName)                                             => action(repository)
+        case Some(x) if (getGroupMembers(repository.owner).exists(_.userName == x.userName)) => action(repository)
+        case Some(x) if (getCollaboratorUserNames(userName, repoName).contains(x.userName))  => action(repository)
+        case _                                                                               => Unauthorized()
       }
-    }
+    } getOrElse NotFound()
   }
 }
 
@@ -149,22 +135,20 @@ trait WritableUsersAuthenticator { self: ControllerBase with RepositoryService w
   }
 
   private def authenticate(action: (RepositoryInfo) => Any) = {
-    {
-      defining(request.paths) { paths =>
-        getRepository(paths(0), paths(1)).map { repository =>
-          context.loginAccount match {
-            case Some(x) if (x.isAdmin)                                                          => action(repository)
-            case Some(x) if (paths(0) == x.userName)                                             => action(repository)
-            case Some(x) if (getGroupMembers(repository.owner).exists(_.userName == x.userName)) => action(repository)
-            case Some(x)
-                if (getCollaboratorUserNames(paths(0), paths(1), Seq(Role.ADMIN, Role.DEVELOPER))
-                  .contains(x.userName)) =>
-              action(repository)
-            case _ => Unauthorized()
-          }
-        } getOrElse NotFound()
+    val userName = params("owner")
+    val repoName = params("repository")
+    getRepository(userName, repoName).map { repository =>
+      context.loginAccount match {
+        case Some(x) if (x.isAdmin)                                                          => action(repository)
+        case Some(x) if (userName == x.userName)                                             => action(repository)
+        case Some(x) if (getGroupMembers(repository.owner).exists(_.userName == x.userName)) => action(repository)
+        case Some(x)
+            if (getCollaboratorUserNames(userName, repoName, Seq(Role.ADMIN, Role.DEVELOPER))
+              .contains(x.userName)) =>
+          action(repository)
+        case _ => Unauthorized()
       }
-    }
+    } getOrElse NotFound()
   }
 }
 
@@ -176,16 +160,14 @@ trait GroupManagerAuthenticator { self: ControllerBase with AccountService =>
   protected def managersOnly[T](action: T => Any) = (form: T) => { authenticate(action(form)) }
 
   private def authenticate(action: => Any) = {
-    {
-      defining(request.paths) { paths =>
-        context.loginAccount match {
-          case Some(x) if (getGroupMembers(paths(0)).exists { member =>
-                member.userName == x.userName && member.isManager
-              }) =>
-            action
-          case _ => Unauthorized()
-        }
-      }
+    context.loginAccount match {
+      case Some(x) if x.isAdmin                      => action
+      case Some(x) if x.userName == request.paths(0) => action
+      case Some(x) if (getGroupMembers(request.paths(0)).exists { member =>
+            member.userName == x.userName && member.isManager
+          }) =>
+        action
+      case _ => Unauthorized()
     }
   }
 }

src/main/scala/gitbucket/core/util/Directory.scala

@@ -67,6 +67,12 @@ object Directory {
   def getLfsDir(owner: String, repository: String): File =
     new File(getRepositoryFilesDir(owner, repository), "lfs")
 
+  /**
+   * Directory for files which store diff fragment
+   */
+  def getDiffDir(owner: String, repository: String): File =
+    new File(getRepositoryFilesDir(owner, repository), "diff")
+
   /**
    * Directory for uploaded files by the specified user.
    */

src/main/scala/gitbucket/core/util/EditorConfigUtil.scala

@@ -0,0 +1,146 @@
+package gitbucket.core.util
+
+import java.io.{IOException, InputStreamReader, Reader}
+import java.nio.charset.StandardCharsets
+
+import org.ec4j.core.Resource.Resources.StringRandomReader
+import org.ec4j.core.model.PropertyType.{EndOfLineValue, IndentStyleValue}
+import org.ec4j.core.model.{Ec4jPath, PropertyType, Version}
+import org.ec4j.core.parser.ParseException
+import org.ec4j.core._
+import org.eclipse.jgit.api.Git
+import org.eclipse.jgit.lib.{ObjectReader, Repository}
+import org.eclipse.jgit.revwalk.{RevTree, RevWalk}
+import org.eclipse.jgit.treewalk.TreeWalk
+import gitbucket.core.util.SyntaxSugars._
+
+object EditorConfigUtil {
+  private class JGitResource(repo: Repository, revStr: String, path: Ec4jPath) extends Resource {
+    private def removeInitialSlash(path: Ec4jPath) = Ec4jPath.Ec4jPaths.root.relativize(path).toString
+
+    def this(git: Git, revStr: String, path: String) = {
+      this(git.getRepository, revStr, Ec4jPath.Ec4jPaths.of(if (path.startsWith("/")) path else "/" + path))
+    }
+
+    def this(repo: Repository, revStr: String, path: String) = {
+      this(repo, revStr, Ec4jPath.Ec4jPaths.of(if (path.startsWith("/")) path else "/" + path))
+    }
+
+    private def getRevTree: RevTree = {
+      using(repo.newObjectReader()) { reader: ObjectReader =>
+        val revWalk = new RevWalk(reader)
+        val id = repo.resolve(revStr)
+        val commit = revWalk.parseCommit(id)
+        commit.getTree
+      }
+    }
+
+    override def exists(): Boolean = {
+      using(repo.newObjectReader()) { reader: ObjectReader =>
+        try {
+          val treeWalk = Option(TreeWalk.forPath(reader, removeInitialSlash(path), getRevTree))
+          treeWalk.isDefined
+        } catch {
+          case e: IOException => false
+        }
+      }
+    }
+
+    override def getPath: Ec4jPath = {
+      path
+    }
+
+    override def getParent: ResourcePath = {
+      Option(path.getParentPath).map { new JGitResourcePath(repo, revStr, _) }.getOrElse(null)
+    }
+
+    override def openRandomReader(): Resource.RandomReader = {
+      StringRandomReader.ofReader(openReader())
+    }
+
+    override def openReader(): Reader = {
+      using(repo.newObjectReader) { reader: ObjectReader =>
+        val treeWalk = TreeWalk.forPath(reader, removeInitialSlash(path), getRevTree)
+        new InputStreamReader(reader.open(treeWalk.getObjectId(0)).openStream, StandardCharsets.UTF_8)
+      }
+    }
+  }
+
+  private class JGitResourcePath(repo: Repository, revStr: String, path: Ec4jPath) extends ResourcePath {
+
+    override def getParent: ResourcePath = {
+      Option(path.getParentPath).map { new JGitResourcePath(repo, revStr, _) }.getOrElse(null)
+    }
+
+    override def getPath: Ec4jPath = {
+      path
+    }
+
+    override def hasParent: Boolean = {
+      Option(path.getParentPath).isDefined
+    }
+
+    override def relativize(resource: Resource): Resource = {
+      resource match {
+        case r: JGitResource =>
+          new JGitResource(repo, revStr, path.relativize(r.getPath).toString)
+      }
+    }
+
+    override def resolve(name: String): Resource = {
+      Option(path)
+        .map { p =>
+          new JGitResource(repo, revStr, p.resolve(name))
+        }
+        .getOrElse {
+          new JGitResource(repo, revStr, name)
+        }
+    }
+  }
+
+  private object JGitResourcePath {
+    def RootDirectory(git: Git, revStr: String) =
+      new JGitResourcePath(git.getRepository, revStr, Ec4jPath.Ec4jPaths.of("/"))
+  }
+
+  private val TabSizeDefault: Int = 8
+  private val NewLineModeDefault: String = "auto"
+  private val UseSoftTabsDefault = false
+
+  case class EditorConfigInfo(
+    tabSize: Int,
+    newLineMode: String,
+    useSoftTabs: Boolean
+  )
+
+  def getEditorConfigInfo(git: Git, rev: String, path: String): EditorConfigInfo = {
+    try {
+      val resourcePropertiesService = ResourcePropertiesService
+        .builder()
+        .configFileName(EditorConfigConstants.EDITORCONFIG)
+        .rootDirectory(JGitResourcePath.RootDirectory(git, rev))
+        .loader(EditorConfigLoader.of(Version.CURRENT))
+        .keepUnset(true)
+        .build()
+
+      val props = resourcePropertiesService.queryProperties(new JGitResource(git, rev, path))
+      EditorConfigInfo(
+        tabSize = props.getValue[Integer](PropertyType.tab_width, TabSizeDefault, false),
+        newLineMode = props.getValue[EndOfLineValue](PropertyType.end_of_line, null, false) match {
+          case EndOfLineValue.cr   => "cr"
+          case EndOfLineValue.lf   => "lf"
+          case EndOfLineValue.crlf => "crlf"
+          case _                   => "auto"
+        },
+        props.getValue[IndentStyleValue](PropertyType.indent_style, null, false) match {
+          case IndentStyleValue.space => true
+          case IndentStyleValue.tab   => false
+          case _                      => false
+        }
+      )
+    } catch {
+      case e: ParseException => EditorConfigInfo(TabSizeDefault, NewLineModeDefault, UseSoftTabsDefault)
+      case e: IOException    => EditorConfigInfo(TabSizeDefault, NewLineModeDefault, UseSoftTabsDefault)
+    }
+  }
+}

src/main/scala/gitbucket/core/util/FileUtil.scala

@@ -16,7 +16,7 @@ object FileUtil {
       }
     }
 
-  def getContentType(name: String, bytes: Array[Byte]): String = {
+  def getMimeType(name: String, bytes: Array[Byte]): String = {
     defining(getMimeType(name)) { mimeType =>
       if (mimeType == "application/octet-stream" && isText(bytes)) {
         "text/plain"
@@ -26,6 +26,10 @@ object FileUtil {
     }
   }
 
+  def getSafeMimeType(name: String): String = {
+    getMimeType(name).replace("text/html", "text/plain")
+  }
+
   def isImage(name: String): Boolean = getMimeType(name).startsWith("image/")
 
   def isLarge(size: Long): Boolean = (size > 1024 * 1000)
@@ -52,7 +56,7 @@ object FileUtil {
   }
 
   def getLfsFilePath(owner: String, repository: String, oid: String): String =
-    Directory.getLfsDir(owner, repository) + "/" + oid
+    Directory.getLfsDir(owner, repository) + "/" + checkFilename(oid)
 
   def readableSize(size: Long): String = FileUtils.byteCountToDisplaySize(size)
 
@@ -76,6 +80,16 @@ object FileUtil {
     file
   }
 
+  /**
+   * Create an instance of java.io.File safely.
+   */
+  def checkFilename(name: String): String = {
+    if (name.contains("..")) {
+      throw new IllegalArgumentException(s"Invalid file name: ${name}")
+    }
+    name
+  }
+
   lazy val MaxFileSize =
     if (System.getProperty("gitbucket.maxFileSize") != null)
       System.getProperty("gitbucket.maxFileSize").toLong

src/main/scala/gitbucket/core/util/HttpClientUtil.scala

@@ -0,0 +1,35 @@
+package gitbucket.core.util
+
+import gitbucket.core.service.SystemSettingsService
+import org.apache.http.HttpHost
+import org.apache.http.auth.{AuthScope, UsernamePasswordCredentials}
+import org.apache.http.impl.client.{BasicCredentialsProvider, CloseableHttpClient, HttpClientBuilder}
+
+object HttpClientUtil {
+
+  def withHttpClient[T](proxy: Option[SystemSettingsService.Proxy])(f: CloseableHttpClient => T): T = {
+    val builder = HttpClientBuilder.create.useSystemProperties
+
+    proxy.foreach { proxy =>
+      builder.setProxy(new HttpHost(proxy.host, proxy.port))
+
+      for (user <- proxy.user; password <- proxy.password) {
+        val credential = new BasicCredentialsProvider()
+        credential.setCredentials(
+          new AuthScope(proxy.host, proxy.port),
+          new UsernamePasswordCredentials(user, password)
+        )
+        builder.setDefaultCredentialsProvider(credential)
+      }
+    }
+
+    val httpClient = builder.build()
+
+    try {
+      f(httpClient)
+    } finally {
+      httpClient.close()
+    }
+  }
+
+}

src/main/scala/gitbucket/core/util/JDBCUtil.scala

@@ -143,6 +143,7 @@ object JDBCUtil {
                       case Types.BOOLEAN | Types.BIT                                   => rs.getBoolean(columnName)
                       case Types.VARCHAR | Types.CLOB | Types.CHAR | Types.LONGVARCHAR => rs.getString(columnName)
                       case Types.INTEGER                                               => rs.getInt(columnName)
+                      case Types.BIGINT                                                => rs.getLong(columnName)
                       case Types.TIMESTAMP                                             => rs.getTimestamp(columnName)
                     }
                   }
@@ -202,8 +203,7 @@ object JDBCUtil {
 
     private def allTablesOrderByDependencies(meta: DatabaseMetaData): Seq[String] = {
       val tables = allTableNames.map { tableName =>
-        val result = TableDependency(tableName, childTables(meta, tableName))
-        result
+        TableDependency(tableName, childTables(meta, tableName))
       }
 
       val edges = tables.flatMap { table =>
@@ -212,7 +212,10 @@ object JDBCUtil {
         }
       }
 
-      tsort(edges).toSeq
+      val ordered = tsort(edges).toSeq
+      val orphans = tables.collect { case x if !ordered.contains(x.tableName) => x.tableName }
+
+      ordered ++ orphans
     }
 
     def tsort[A](edges: Traversable[(A, A)]): Iterable[A] = {

src/main/scala/gitbucket/core/util/JGitUtil.scala

@@ -1,6 +1,6 @@
 package gitbucket.core.util
 
-import java.io.ByteArrayOutputStream
+import java.io.{ByteArrayOutputStream, File, FileInputStream, InputStream}
 
 import gitbucket.core.service.RepositoryService
 import org.eclipse.jgit.api.Git
@@ -23,12 +23,7 @@ import java.util.concurrent.TimeUnit
 import java.util.function.Consumer
 
 import org.cache2k.Cache2kBuilder
-import org.eclipse.jgit.api.errors.{
-  InvalidRefNameException,
-  JGitInternalException,
-  NoHeadException,
-  RefAlreadyExistsException
-}
+import org.eclipse.jgit.api.errors._
 import org.eclipse.jgit.diff.{DiffEntry, DiffFormatter, RawTextComparator}
 import org.eclipse.jgit.dircache.DirCacheEntry
 import org.eclipse.jgit.util.io.DisabledOutputStream
@@ -390,7 +385,7 @@ object JGitUtil {
             lazy val newParentsMap = newCommit.getParents.map(_ -> newCommit).toMap
             useTreeWalk(newCommit) { walk =>
               while (walk.next) {
-                rest.remove(walk.getNameString -> walk.getObjectId(0)).map {
+                rest.remove(walk.getNameString -> walk.getObjectId(0)).foreach {
                   case (tuple, _) =>
                     if (newParentsMap.isEmpty) {
                       nextResult +:= tupleAdd(tuple, newCommit)
@@ -400,7 +395,7 @@ object JGitUtil {
                 }
               }
             }
-            rest.values.map {
+            rest.values.foreach {
               case (tuple, parentsMap) =>
                 val restParentsMap = parentsMap - newCommit
                 if (restParentsMap.isEmpty) {
@@ -618,8 +613,12 @@ object JGitUtil {
     df.setRepository(git.getRepository)
     df.setDiffComparator(RawTextComparator.DEFAULT)
     df.setDetectRenames(true)
-    df.format(getDiffEntries(git, from, to).head)
-    new String(out.toByteArray, "UTF-8")
+    getDiffEntries(git, from, to)
+      .map { entry =>
+        df.format(entry)
+        new String(out.toByteArray, "UTF-8")
+      }
+      .mkString("\n")
   }
 
   private def getDiffEntries(git: Git, from: Option[String], to: String): Seq[DiffEntry] = {
@@ -745,15 +744,17 @@ object JGitUtil {
   def getBranchesOfCommit(git: Git, commitId: String): List[String] =
     using(new RevWalk(git.getRepository)) { revWalk =>
       defining(revWalk.parseCommit(git.getRepository.resolve(commitId + "^0"))) { commit =>
-        git.getRepository.getAllRefs.entrySet.asScala
+        git.getRepository.getRefDatabase
+          .getRefsByPrefix(Constants.R_HEADS)
+          .asScala
           .filter { e =>
-            (e.getKey.startsWith(Constants.R_HEADS) && revWalk.isMergedInto(
+            (revWalk.isMergedInto(
               commit,
-              revWalk.parseCommit(e.getValue.getObjectId)
+              revWalk.parseCommit(e.getObjectId)
             ))
           }
           .map { e =>
-            e.getValue.getName.substring(org.eclipse.jgit.lib.Constants.R_HEADS.length)
+            e.getName.substring(Constants.R_HEADS.length)
           }
           .toList
           .sorted
@@ -761,20 +762,42 @@ object JGitUtil {
     }
 
   /**
-   * Returns the list of tags of the specified commit.
+   * Returns the list of tags which pointed on the specified commit.
+   */
+  def getTagsOnCommit(git: Git, commitId: String): List[String] = {
+    git.getRepository.getAllRefsByPeeledObjectId.asScala
+      .get(git.getRepository.resolve(commitId + "^0"))
+      .map {
+        _.asScala
+          .collect {
+            case x if x.getName.startsWith(Constants.R_TAGS) =>
+              x.getName.substring(Constants.R_TAGS.length)
+          }
+          .toList
+          .sorted
+      }
+      .getOrElse {
+        List.empty
+      }
+  }
+
+  /**
+   * Returns the list of tags which contains the specified commit.
    */
   def getTagsOfCommit(git: Git, commitId: String): List[String] =
     using(new RevWalk(git.getRepository)) { revWalk =>
       defining(revWalk.parseCommit(git.getRepository.resolve(commitId + "^0"))) { commit =>
-        git.getRepository.getAllRefs.entrySet.asScala
+        git.getRepository.getRefDatabase
+          .getRefsByPrefix(Constants.R_TAGS)
+          .asScala
           .filter { e =>
-            (e.getKey.startsWith(Constants.R_TAGS) && revWalk.isMergedInto(
+            (revWalk.isMergedInto(
               commit,
-              revWalk.parseCommit(e.getValue.getObjectId)
+              revWalk.parseCommit(e.getObjectId)
             ))
           }
           .map { e =>
-            e.getValue.getName.substring(org.eclipse.jgit.lib.Constants.R_TAGS.length)
+            e.getName.substring(Constants.R_TAGS.length)
           }
           .toList
           .sorted
@@ -816,6 +839,25 @@ object JGitUtil {
       .find(_._1 != null)
   }
 
+  def createTag(git: Git, name: String, message: Option[String], commitId: String) = {
+    try {
+      val objectId: ObjectId = git.getRepository.resolve(commitId)
+      using(new RevWalk(git.getRepository)) { walk =>
+        val tagCommand = git.tag().setName(name).setObjectId(walk.parseCommit(objectId))
+        message.foreach { message =>
+          tagCommand.setMessage(message)
+        }
+        tagCommand.call()
+      }
+      Right("Tag added.")
+    } catch {
+      case e: GitAPIException              => Left("Sorry, some Git operation error occurs.")
+      case e: ConcurrentRefUpdateException => Left("Sorry some error occurs.")
+      case e: InvalidTagNameException      => Left("Sorry, that name is invalid.")
+      case e: NoHeadException              => Left("Sorry, this repo doesn't have HEAD reference")
+    }
+  }
+
   def createBranch(git: Git, fromBranch: String, newBranch: String) = {
     try {
       git.branchCreate().setStartPoint(fromBranch).setName(newBranch).call()
@@ -1200,4 +1242,61 @@ object JGitUtil {
       Option(git.getRepository.resolve(revstr)).map(ObjectId.toString(_))
     }
   }
+
+  def getFileSize(git: Git, repository: RepositoryService.RepositoryInfo, treeWalk: TreeWalk): Long = {
+    val attrs = treeWalk.getAttributes
+    val loader = git.getRepository.open(treeWalk.getObjectId(0))
+    if (attrs.containsKey("filter") && attrs.get("filter").getValue == "lfs") {
+      val lfsAttrs = getLfsAttributes(loader)
+      lfsAttrs.get("size").map(_.toLong).get
+    } else {
+      loader.getSize
+    }
+  }
+
+  def getFileSize(git: Git, repository: RepositoryService.RepositoryInfo, tree: RevTree, path: String): Long = {
+    using(TreeWalk.forPath(git.getRepository, path, tree)) { treeWalk =>
+      getFileSize(git, repository, treeWalk)
+    }
+  }
+
+  def openFile[T](git: Git, repository: RepositoryService.RepositoryInfo, treeWalk: TreeWalk)(
+    f: InputStream => T
+  ): T = {
+    val attrs = treeWalk.getAttributes
+    val loader = git.getRepository.open(treeWalk.getObjectId(0))
+    if (attrs.containsKey("filter") && attrs.get("filter").getValue == "lfs") {
+      val lfsAttrs = getLfsAttributes(loader)
+      if (lfsAttrs.nonEmpty) {
+        val oid = lfsAttrs("oid").split(":")(1)
+
+        val file = new File(FileUtil.getLfsFilePath(repository.owner, repository.name, oid))
+        using(new FileInputStream(FileUtil.getLfsFilePath(repository.owner, repository.name, oid))) { in =>
+          f(in)
+        }
+      } else {
+        throw new NoSuchElementException("LFS attribute is empty.")
+      }
+    } else {
+      using(loader.openStream()) { in =>
+        f(in)
+      }
+    }
+  }
+
+  def openFile[T](git: Git, repository: RepositoryService.RepositoryInfo, tree: RevTree, path: String)(
+    f: InputStream => T
+  ): T = {
+    using(TreeWalk.forPath(git.getRepository, path, tree)) { treeWalk =>
+      openFile(git, repository, treeWalk)(f)
+    }
+  }
+
+  private def getLfsAttributes(loader: ObjectLoader): Map[String, String] = {
+    val bytes = loader.getCachedBytes
+    val text = new String(bytes, "UTF-8")
+
+    JGitUtil.getLfsObjects(text)
+  }
+
 }

src/main/scala/gitbucket/core/util/LDAPUtil.scala

@@ -5,8 +5,11 @@ import SyntaxSugars._
 import gitbucket.core.service.SystemSettingsService
 import gitbucket.core.service.SystemSettingsService.Ldap
 import com.novell.ldap._
-import java.security.Security
+import java.security.{Provider, Security}
+import java.util.concurrent.atomic.AtomicReference
+
 import org.slf4j.LoggerFactory
+
 import scala.annotation.tailrec
 
 /**
@@ -15,10 +18,11 @@ import scala.annotation.tailrec
 object LDAPUtil {
 
   private val LDAP_VERSION: Int = LDAPConnection.LDAP_V3
-  private val logger = LoggerFactory.getLogger(getClass().getName())
-
   private val LDAP_DUMMY_MAL = "@ldap-devnull"
 
+  private val logger = LoggerFactory.getLogger(getClass().getName())
+  private val provider = new AtomicReference[Provider](null)
+
   /**
    * Returns true if mail address ends with "@ldap-devnull"
    */
@@ -120,6 +124,21 @@ object LDAPUtil {
     }).replaceAll("[^a-zA-Z0-9\\-_.]", "").replaceAll("^[_\\-]", "")
   }
 
+  private def getSslProvider(): Provider = {
+    val cachedInstance = provider.get()
+    if (cachedInstance == null) {
+      val newInstance = Class
+        .forName("com.sun.net.ssl.internal.ssl.Provider")
+        .getDeclaredConstructor()
+        .newInstance()
+        .asInstanceOf[Provider]
+      provider.compareAndSet(null, newInstance)
+      newInstance
+    } else {
+      cachedInstance
+    }
+  }
+
   private def bind[A](
     host: String,
     port: Int,
@@ -132,7 +151,7 @@ object LDAPUtil {
   )(f: LDAPConnection => Either[String, A]): Either[String, A] = {
     if (tls) {
       // Dynamically set Sun as the security provider
-      Security.addProvider(new com.sun.net.ssl.internal.ssl.Provider())
+      Security.addProvider(getSslProvider())
 
       if (keystore.compareTo("") != 0) {
         // Dynamically set the property that JSSE uses to identify

src/main/scala/gitbucket/core/util/StringUtil.scala

@@ -1,10 +1,13 @@
 package gitbucket.core.util
 
 import java.net.{URLDecoder, URLEncoder}
-import java.util.Base64
+import java.security.SecureRandom
+import java.util.{Base64, UUID}
 
 import org.mozilla.universalchardet.UniversalDetector
 import SyntaxSugars._
+import javax.crypto.SecretKeyFactory
+import javax.crypto.spec.PBEKeySpec
 import org.apache.commons.io.input.BOMInputStream
 import org.apache.commons.io.IOUtils
 
@@ -13,9 +16,33 @@ import scala.util.control.Exception._
 object StringUtil {
 
   private lazy val BlowfishKey = {
-    // last 4 numbers in current timestamp
-    val time = System.currentTimeMillis.toString
-    time.substring(time.length - 4)
+    UUID.randomUUID().toString.substring(0, 16)
+  }
+
+  def base64Encode(value: Array[Byte]): String = {
+    Base64.getEncoder.encodeToString(value)
+  }
+
+  def base64Decode(value: String): Array[Byte] = {
+    Base64.getDecoder.decode(value)
+  }
+
+  def pbkdf2_sha256(iter: Int, salt: String, value: String): String = {
+    val keyFactory = SecretKeyFactory.getInstance("PBKDF2WithHmacSHA256")
+    val ks = new PBEKeySpec(value.toCharArray, base64Decode(salt), iter, 256)
+    val s = keyFactory.generateSecret(ks)
+    base64Encode(s.getEncoded)
+  }
+
+  def pbkdf2_sha256(value: String) = {
+    val keyFactory = SecretKeyFactory.getInstance("PBKDF2WithHmacSHA256")
+    val secureRandom = new SecureRandom
+    val salt: Array[Byte] = new Array(32)
+    secureRandom.nextBytes(salt)
+    val iter = 100000
+    val ks = new PBEKeySpec(value.toCharArray, salt, iter, 256)
+    val s = keyFactory.generateSecret(ks)
+    s"""$$pbkdf2-sha256$$${iter}$$${base64Encode(salt)}$$${base64Encode(s.getEncoded)}"""
   }
 
   def sha1(value: String): String =

src/main/scala/gitbucket/core/util/SyntaxSugars.scala

@@ -65,7 +65,7 @@ object SyntaxSugars {
   implicit class HeadValueAccessibleMap(map: Map[String, Seq[String]]) {
     def value(key: String): String = map(key).head
     def optionValue(key: String): Option[String] = map.get(key).flatMap(_.headOption)
-    def values(key: String): Seq[String] = map.get(key).getOrElse(Seq.empty)
+    def values(key: String): Seq[String] = map.getOrElse(key, Seq.empty)
   }
 
 }

src/main/scala/gitbucket/core/view/LinkConverter.scala

@@ -3,23 +3,23 @@ package gitbucket.core.view
 import gitbucket.core.controller.Context
 import gitbucket.core.service.{RepositoryService, RequestCache}
 import gitbucket.core.util.Implicits.RichString
+import gitbucket.core.util.StringUtil
 
 trait LinkConverter { self: RequestCache =>
 
   /**
    * Creates a link to the issue or the pull request from the issue id.
    */
-  protected def createIssueLink(repository: RepositoryService.RepositoryInfo, issueId: Int)(
+  protected def createIssueLink(repository: RepositoryService.RepositoryInfo, issueId: Int, title: String)(
     implicit context: Context
   ): String = {
     val userName = repository.repository.userName
     val repositoryName = repository.repository.repositoryName
 
     getIssue(userName, repositoryName, issueId.toString) match {
-      case Some(issue) if (issue.isPullRequest) =>
-        s"""<a href="${context.path}/${userName}/${repositoryName}/pull/${issueId}">Pull #${issueId}</a>"""
-      case Some(_) =>
-        s"""<a href="${context.path}/${userName}/${repositoryName}/issues/${issueId}">Issue #${issueId}</a>"""
+      case Some(issue) =>
+        s"""<a href="${context.path}/${userName}/${repositoryName}/${if (issue.isPullRequest) "pull" else "issues"}/${issueId}"><strong>${StringUtil
+          .escapeHtml(title)}</strong> #${issueId}</a>"""
       case None =>
         s"Unknown #${issueId}"
     }

src/main/scala/gitbucket/core/view/Markdown.scala

@@ -16,6 +16,7 @@ object Markdown {
    * Converts Markdown of Wiki pages to HTML.
    *
    * @param repository the repository which contains the markdown
+   * @param branch the target branch
    * @param enableWikiLink if true then wiki style link is available in markdown
    * @param enableRefsLink if true then issue reference (e.g. #123) is rendered as link
    * @param enableAnchor if true then anchor for headline is generated
@@ -27,6 +28,7 @@ object Markdown {
   def toHtml(
     markdown: String,
     repository: RepositoryService.RepositoryInfo,
+    branch: String,
     enableWikiLink: Boolean,
     enableRefsLink: Boolean,
     enableAnchor: Boolean,
@@ -45,6 +47,7 @@ object Markdown {
     val renderer = new GitBucketMarkedRenderer(
       options,
       repository,
+      branch,
       enableWikiLink,
       enableRefsLink,
       enableAnchor,
@@ -62,6 +65,7 @@ object Markdown {
   class GitBucketMarkedRenderer(
     options: Options,
     repository: RepositoryService.RepositoryInfo,
+    branch: String,
     enableWikiLink: Boolean,
     enableRefsLink: Boolean,
     enableAnchor: Boolean,
@@ -131,11 +135,11 @@ object Markdown {
     }
 
     override def link(href: String, title: String, text: String): String = {
-      super.link(fixUrl(href, false), title, text)
+      super.link(fixUrl(href, branch, false), title, text)
     }
 
     override def image(href: String, title: String, text: String): String = {
-      super.image(fixUrl(href, true), title, text)
+      super.image(fixUrl(href, branch, true), title, text)
     }
 
     override def nolink(text: String): String = {
@@ -162,7 +166,7 @@ object Markdown {
       }
     }
 
-    private def fixUrl(url: String, isImage: Boolean = false): String = {
+    private def fixUrl(url: String, branch: String, isImage: Boolean = false): String = {
       lazy val urlWithRawParam: String = url + (if (isImage && !url.endsWith("?raw=true")) "?raw=true" else "")
 
       if (url.startsWith("http://") || url.startsWith("https://") || url.startsWith("mailto:") || url.startsWith("/")) {
@@ -172,13 +176,7 @@ object Markdown {
       } else if (!enableWikiLink) {
         if (context.currentPath.contains("/blob/")) {
           urlWithRawParam
-        } else if (context.currentPath.contains("/tree/")) {
-          val paths = context.currentPath.split("/")
-          val branch = if (paths.length > 3) paths.drop(4).mkString("/") else repository.repository.defaultBranch
-          repository.httpUrl.replaceFirst("/git/", "/").stripSuffix(".git") + "/blob/" + branch + "/" + urlWithRawParam
         } else {
-          val paths = context.currentPath.split("/")
-          val branch = if (paths.length > 3) paths.last else repository.repository.defaultBranch
           repository.httpUrl.replaceFirst("/git/", "/").stripSuffix(".git") + "/blob/" + branch + "/" + urlWithRawParam
         }
       } else {

src/main/scala/gitbucket/core/view/helpers.scala

@@ -3,6 +3,7 @@ package gitbucket.core.view
 import java.text.SimpleDateFormat
 import java.util.{Date, Locale, TimeZone}
 
+import com.nimbusds.jose.util.JSONObjectUtils
 import gitbucket.core.controller.Context
 import gitbucket.core.model.CommitState
 import gitbucket.core.plugin.{PluginRegistry, RenderRequest}
@@ -101,6 +102,7 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
   def markdown(
     markdown: String,
     repository: RepositoryService.RepositoryInfo,
+    branch: String,
     enableWikiLink: Boolean,
     enableRefsLink: Boolean,
     enableLineBreaks: Boolean,
@@ -113,6 +115,7 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
       Markdown.toHtml(
         markdown = markdown,
         repository = repository,
+        branch = branch,
         enableWikiLink = enableWikiLink,
         enableRefsLink = enableRefsLink,
         enableAnchor = enableAnchor,
@@ -155,8 +158,10 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
   /**
    * Creates a link to the issue or the pull request from the issue id.
    */
-  def issueLink(repository: RepositoryService.RepositoryInfo, issueId: Int)(implicit context: Context): Html = {
-    Html(createIssueLink(repository, issueId))
+  def issueLink(repository: RepositoryService.RepositoryInfo, issueId: Int, title: String)(
+    implicit context: Context
+  ): Html = {
+    Html(createIssueLink(repository, issueId, title))
   }
 
   /**
@@ -229,6 +234,12 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
             s"""<a href="${context.path}/${m.group(1)}/${m.group(2)}/commit/${m.group(3)}">${m.group(1)}/${m
               .group(2)}@${m.group(3).substring(0, 7)}</a>"""
         )
+        .replaceAll(
+          "\\[release:([^\\s]+?)/([^\\s]+?)/([^\\s]+?)\\]",
+          (m: Match) =>
+            s"""<a href="${context.path}/${m.group(1)}/${m.group(2)}/releases/${encodeRefName(m.group(3))}">${m
+              .group(3)}</a>"""
+        )
     )
 
   /**
@@ -249,12 +260,12 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
    * Generates the url to the repository.
    */
   def url(repository: RepositoryService.RepositoryInfo)(implicit context: Context): String =
-    s"${context.path}/${repository.owner}/${repository.name}"
+    s"${context.path}/${encodeRefName(repository.owner)}/${encodeRefName(repository.name)}"
 
   /**
    * Generates the url to the account page.
    */
-  def url(userName: String)(implicit context: Context): String = s"${context.path}/${userName}"
+  def url(userName: String)(implicit context: Context): String = s"${context.path}/${encodeRefName(userName)}"
 
   /**
    * Returns the url to the root of assets.
@@ -272,7 +283,7 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
    * If user does not exist or disabled, this method returns user name as text without link.
    */
   def user(userName: String, mailAddress: String = "", styleClass: String = "")(implicit context: Context): Html =
-    userWithContent(userName, mailAddress, styleClass)(Html(userName))
+    userWithContent(userName, mailAddress, styleClass)(Html(StringUtil.escapeHtml(userName)))
 
   /**
    * Generates the avatar link to the account page.
@@ -315,44 +326,6 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
    */
   def isPast(date: Date): Boolean = System.currentTimeMillis > date.getTime
 
-  /**
-   * Returns file type for AceEditor.
-   */
-  def editorType(fileName: String): String = {
-    fileName.toLowerCase match {
-      case x if (x.endsWith(".bat"))     => "batchfile"
-      case x if (x.endsWith(".java"))    => "java"
-      case x if (x.endsWith(".scala"))   => "scala"
-      case x if (x.endsWith(".js"))      => "javascript"
-      case x if (x.endsWith(".css"))     => "css"
-      case x if (x.endsWith(".md"))      => "markdown"
-      case x if (x.endsWith(".html"))    => "html"
-      case x if (x.endsWith(".xml"))     => "xml"
-      case x if (x.endsWith(".c"))       => "c_cpp"
-      case x if (x.endsWith(".cpp"))     => "c_cpp"
-      case x if (x.endsWith(".coffee"))  => "coffee"
-      case x if (x.endsWith(".ejs"))     => "ejs"
-      case x if (x.endsWith(".hs"))      => "haskell"
-      case x if (x.endsWith(".json"))    => "json"
-      case x if (x.endsWith(".jsp"))     => "jsp"
-      case x if (x.endsWith(".jsx"))     => "jsx"
-      case x if (x.endsWith(".cl"))      => "lisp"
-      case x if (x.endsWith(".clojure")) => "lisp"
-      case x if (x.endsWith(".lua"))     => "lua"
-      case x if (x.endsWith(".php"))     => "php"
-      case x if (x.endsWith(".py"))      => "python"
-      case x if (x.endsWith(".rdoc"))    => "rdoc"
-      case x if (x.endsWith(".rhtml"))   => "rhtml"
-      case x if (x.endsWith(".ruby"))    => "ruby"
-      case x if (x.endsWith(".sh"))      => "sh"
-      case x if (x.endsWith(".sql"))     => "sql"
-      case x if (x.endsWith(".tcl"))     => "tcl"
-      case x if (x.endsWith(".vbs"))     => "vbscript"
-      case x if (x.endsWith(".yml"))     => "yaml"
-      case _                             => "plain_text"
-    }
-  }
-
   def pre(value: Html): Html = Html(s"<pre>${value.body.trim.split("\n").map(_.trim).mkString("\n")}</pre>")
 
   /**
@@ -462,4 +435,44 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
    */
   def readableSize(size: Option[Long]): String = FileUtil.readableSize(size.getOrElse(0))
 
+  /**
+   * Make HTML fragment of the partial diff for a comment on a line of diff.
+   *
+   * @param jsonString JSON string which is stored in COMMIT_COMMENT table.
+   * @return HTML fragment of diff
+   */
+  def diff(jsonString: String): Html = {
+    import org.json4s._
+    import org.json4s.jackson.JsonMethods._
+    implicit val formats = DefaultFormats
+
+    val diff = parse(jsonString).extract[Seq[CommentDiffLine]]
+
+    val sb = new StringBuilder()
+    sb.append("<table class=\"diff inlinediff\">")
+    diff.foreach { line =>
+      sb.append("<tr>")
+      sb.append(s"""<th class="line-num oldline ${line.`type`}">""")
+      line.oldLine.foreach { oldLine =>
+        sb.append(oldLine)
+      }
+      sb.append("</th>")
+      sb.append(s"""<th class="line-num newline ${line.`type`}">""")
+      line.newLine.foreach { newLine =>
+        sb.append(newLine)
+      }
+      sb.append("</th>")
+
+      sb.append(s"""<td class="body ${line.`type`}">""")
+      sb.append(StringUtil.escapeHtml(line.text))
+      sb.append("</td>")
+      sb.append("</tr>")
+    }
+    sb.append("</table>")
+
+    Html(sb.toString())
+  }
+
+  case class CommentDiffLine(newLine: Option[String], oldLine: Option[String], `type`: String, text: String)
+
 }

src/main/twirl/gitbucket/core/account/activity.scala.html

@@ -1,8 +1,9 @@
 @(account: gitbucket.core.model.Account,
   groupNames: List[String],
-  activities: List[gitbucket.core.model.Activity])(implicit context: gitbucket.core.controller.Context)
+  activities: List[gitbucket.core.model.Activity],
+  extraMailAddresses: List[String])(implicit context: gitbucket.core.controller.Context)
 @import gitbucket.core.view.helpers
-@gitbucket.core.account.html.main(account, groupNames, "activity"){
+@gitbucket.core.account.html.main(account, groupNames, "activity", extraMailAddresses){
   <div class="pull-right">
     <a href="@context.path/@{account.userName}.atom"><img src="@helpers.assets("/common/images/feed.png")" alt="activities"></a>
   </div>

src/main/twirl/gitbucket/core/account/edit.scala.html

@@ -1,4 +1,4 @@
-@(account: gitbucket.core.model.Account, info: Option[Any], error: Option[Any])(implicit context: gitbucket.core.controller.Context)
+@(account: gitbucket.core.model.Account, extraMailAddresses: List[String], info: Option[Any], error: Option[Any])(implicit context: gitbucket.core.controller.Context)
 @import gitbucket.core.util.LDAPUtil
 @import gitbucket.core.view.helpers
 @gitbucket.core.html.main("Edit your profile"){
@@ -31,6 +31,13 @@
                 <input type="text" name="mailAddress" id="mailAddress" class="form-control" value="@if(!LDAPUtil.isDummyMailAddress(account)){@account.mailAddress}"/>
                 <span id="error-mailAddress" class="error"></span>
               </fieldset>
+              <fieldset class="form-group" id="extraMailAddresses">
+                <span class="strong">Additional Mail Address:</span>
+                @extraMailAddresses.zipWithIndex.map { case (mail, idx) =>
+                  <input type="text" name="extraMailAddresses[@idx]" id="extraMailAddresses[@idx]" class="form-control extraMailAddress" value="@mail"/>
+                  <span id="error-extraMailAddresses_@idx" class="error"></span>
+                }
+              </fieldset>
               <fieldset class="form-group">
                 <label for="url" class="strong">URL (optional):</label>
                 <input type="text" name="url" id="url" class="form-control" value="@account.url"/>
@@ -62,6 +69,8 @@
 }
 <script>
 $(function(){
+  addExtraMailAddress();
+  $('#extraMailAddresses').on('change', '.extraMailAddress', checkExtraMailAddress);
   $('#save').click(function(){
     if($('#password').val() != ''){
       return confirm('Are you sure you want to change password?');