Add Version 3.0 to versions

Conflicts:
	src/main/twirl/issues/list.scala.html
	src/main/twirl/issues/listparts.scala.html

README.md

@@ -1,7 +1,7 @@
 GitBucket [![Gitter chat](https://badges.gitter.im/takezoe/gitbucket.png)](https://gitter.im/takezoe/gitbucket) [![Build Status](https://travis-ci.org/takezoe/gitbucket.svg?branch=master)](https://travis-ci.org/takezoe/gitbucket)
 =========
 
-GitBucket is the easily installable Github clone written with Scala.
+GitBucket is the easily installable GitHub clone powered by Scala.
 
 
 Features
@@ -79,6 +79,19 @@ Run the following commands in `Terminal` to
 
 Release Notes
 --------
+### 3.0 - 3 Mar 2015
+- New plug-in system is available
+- Connection pooling by c3p0
+- New branch UI
+- Compare between specified commit ids
+
+### 2.8 - 1 Feb 2015
+- New logo and icons
+- New system setting options to control visibility
+- Comment on side-by-side diff
+- Information message on sign-in page
+- Fork repository by group account
+
 ### 2.7 - 29 Dec 2014
 - Comment for commit and diff
 - Fix security issue in markdown rendering

build.xml

@@ -5,7 +5,7 @@
   <property name="embed.classes.dir" value="${target.dir}/embed-classes"/>
   <property name="jetty.dir" value="embed-jetty"/>
   <property name="scala.version" value="2.11"/>
-  <property name="gitbucket.version" value="0.0.1"/>
+  <property name="gitbucket.version" value="3.0.0"/>
   <property name="jetty.version" value="8.1.8.v20121106"/>
   <property name="servlet.version" value="3.0.0.v201112011016"/>
 

contrib/README.md

@@ -8,6 +8,6 @@ Common scripts are in this directory.
 This version of scripts has so far only been tested on Ubuntu and Mac. Someone else will have to test on RedHat.
 
 To run:
-1. Edit `gitbucket.conf` to suit.
-2. Type: `install`
 
+  1. Edit `gitbucket.conf` to suit.
+  2. Type: `install`

etc/deploy-assemby-jar.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+mvn deploy:deploy-file \
+  -DgroupId=gitbucket\
+  -DartifactId=gitbucket-assembly\
+  -Dversion=3.0.0\
+  -Dpackaging=jar\
+  -Dfile=../target/scala-2.11/gitbucket-assembly-3.0.0.jar\
+  -DrepositoryId=sourceforge.jp\
+  -Durl=scp://shell.sourceforge.jp/home/groups/a/am/amateras/htdocs/mvn/

etc/pom.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <groupId>jp.sf.amateras</groupId>
+    <artifactId>gitbucket-assembly</artifactId>
+    <version>0.0.1</version>
+    <build>
+        <extensions>
+            <extension>
+                <groupId>org.apache.maven.wagon</groupId>
+                <artifactId>wagon-ssh</artifactId>
+                <version>1.0-beta-6</version>
+            </extension>
+        </extensions>
+    </build>
+</project>

project/build.scala

@@ -4,11 +4,13 @@ import org.scalatra.sbt._
 import com.typesafe.sbteclipse.plugin.EclipsePlugin.EclipseKeys
 import play.twirl.sbt.SbtTwirl
 import play.twirl.sbt.Import.TwirlKeys._
+import sbtassembly._
+import sbtassembly.AssemblyKeys._
 
 object MyBuild extends Build {
-  val Organization = "jp.sf.amateras"
+  val Organization = "gitbucket"
   val Name = "gitbucket"
-  val Version = "0.0.1"
+  val Version = "3.0.0"
   val ScalaVersion = "2.11.2"
   val ScalatraVersion = "2.3.0"
 
@@ -17,6 +19,17 @@ object MyBuild extends Build {
     file(".")
   )
   .settings(ScalatraPlugin.scalatraWithJRebel: _*)
+  .settings(
+    test in assembly := {},
+    assemblyMergeStrategy in assembly := {
+      case PathList("META-INF", xs @ _*) =>
+        (xs map {_.toLowerCase}) match {
+          case ("manifest.mf" :: Nil) => MergeStrategy.discard
+          case _ => MergeStrategy.discard
+      }
+      case x => MergeStrategy.first
+    }
+  )
   .settings(
     sourcesInBase := false,
     organization := Organization,
@@ -44,14 +57,16 @@ object MyBuild extends Build {
       "org.apache.sshd" % "apache-sshd" % "0.11.0",
       "com.typesafe.slick" %% "slick" % "2.1.0",
       "com.novell.ldap" % "jldap" % "2009-10-07",
-      "org.quartz-scheduler" % "quartz" % "2.2.1",
       "com.h2database" % "h2" % "1.4.180",
-      "ch.qos.logback" % "logback-classic" % "1.0.13" % "runtime",
+//      "ch.qos.logback" % "logback-classic" % "1.0.13" % "runtime",
       "org.eclipse.jetty" % "jetty-webapp" % "8.1.8.v20121106" % "container;provided",
       "org.eclipse.jetty.orbit" % "javax.servlet" % "3.0.0.v201112011016" % "container;provided;test" artifacts Artifact("javax.servlet", "jar", "jar"),
       "junit" % "junit" % "4.11" % "test",
+      "com.mchange" % "c3p0" % "0.9.5",
+      "com.typesafe" % "config" % "1.2.1",
       "com.typesafe.play" %% "twirl-compiler" % "1.0.2"
     ),
+    play.twirl.sbt.Import.TwirlKeys.templateImports += "gitbucket.core._",
     EclipseKeys.withSource := true,
     javacOptions in compile ++= Seq("-target", "7", "-source", "7"),
     testOptions in Test += Tests.Argument(TestFrameworks.Specs2, "junitxml", "console"),

project/plugins.sbt

@@ -7,3 +7,5 @@ addSbtPlugin("org.scalatra.sbt" % "scalatra-sbt" % "0.3.5")
 addSbtPlugin("com.typesafe.sbt" % "sbt-twirl" % "1.0.2")
 
 addSbtPlugin("com.timushev.sbt" % "sbt-updates" % "0.1.4")
+
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.12.0")

src/main/java/gitbucket/core/util/PatchUtil.java

@@ -1,4 +1,4 @@
-package util;
+package gitbucket.core.util;
 
 import org.eclipse.jgit.api.errors.PatchApplyException;
 import org.eclipse.jgit.diff.RawText;

src/main/resources/database.conf

@@ -0,0 +1,6 @@
+db {
+  driver = "org.h2.Driver"
+  url = "jdbc:h2:${DatabaseHome};MVCC=true"
+  user = "sa"
+  password = "sa"
+}

src/main/resources/update/2_8.sql

@@ -0,0 +1 @@
+ALTER TABLE COMMIT_COMMENT ALTER COLUMN FILE_NAME NVARCHAR(260);

src/main/scala/ScalatraBootstrap.scala

@@ -1,5 +1,9 @@
-import _root_.servlet.{PluginActionInvokeFilter, BasicAuthenticationFilter, TransactionFilter}
-import app._
+
+import gitbucket.core.controller._
+import gitbucket.core.plugin.PluginRegistry
+import gitbucket.core.servlet.{TransactionFilter, BasicAuthenticationFilter}
+import gitbucket.core.util.Directory
+
 //import jp.sf.amateras.scalatra.forms.ValidationJavaScriptProvider
 import org.scalatra._
 import javax.servlet._
@@ -10,12 +14,16 @@ class ScalatraBootstrap extends LifeCycle {
     // Register TransactionFilter and BasicAuthenticationFilter at first
     context.addFilter("transactionFilter", new TransactionFilter)
     context.getFilterRegistration("transactionFilter").addMappingForUrlPatterns(EnumSet.allOf(classOf[DispatcherType]), true, "/*")
-    context.addFilter("pluginActionInvokeFilter", new PluginActionInvokeFilter)
-    context.getFilterRegistration("pluginActionInvokeFilter").addMappingForUrlPatterns(EnumSet.allOf(classOf[DispatcherType]), true, "/*")
     context.addFilter("basicAuthenticationFilter", new BasicAuthenticationFilter)
     context.getFilterRegistration("basicAuthenticationFilter").addMappingForUrlPatterns(EnumSet.allOf(classOf[DispatcherType]), true, "/git/*")
 
     // Register controllers
+    context.mount(new AnonymousAccessController, "/*")
+
+    PluginRegistry().getControllers.foreach { case (controller, path) =>
+      context.mount(controller, path)
+    }
+
     context.mount(new IndexController, "/")
     context.mount(new SearchController, "/")
     context.mount(new FileUploadController, "/upload")
@@ -32,7 +40,7 @@ class ScalatraBootstrap extends LifeCycle {
     context.mount(new RepositorySettingsController, "/*")
 
     // Create GITBUCKET_HOME directory if it does not exist
-    val dir = new java.io.File(_root_.util.Directory.GitBucketHome)
+    val dir = new java.io.File(Directory.GitBucketHome)
     if(!dir.exists){
       dir.mkdirs()
     }

src/main/scala/app/SystemSettingsController.scala

@@ -1,202 +0,0 @@
-package app
-
-import service.{AccountService, SystemSettingsService}
-import SystemSettingsService._
-import util.AdminAuthenticator
-import util.Directory._
-import util.ControlUtil._
-import jp.sf.amateras.scalatra.forms._
-import ssh.SshServer
-import org.apache.commons.io.FileUtils
-import java.io.FileInputStream
-import plugin.{Plugin, PluginSystem}
-import org.scalatra.Ok
-import util.Implicits._
-
-class SystemSettingsController extends SystemSettingsControllerBase
-  with AccountService with AdminAuthenticator
-
-trait SystemSettingsControllerBase extends ControllerBase {
-  self: AccountService with AdminAuthenticator =>
-
-  private val form = mapping(
-    "baseUrl"                  -> trim(label("Base URL", optional(text()))),
-    "information"              -> trim(label("Information", optional(text()))),
-    "allowAccountRegistration" -> trim(label("Account registration", boolean())),
-    "gravatar"                 -> trim(label("Gravatar", boolean())),
-    "notification"             -> trim(label("Notification", boolean())),
-    "ssh"                      -> trim(label("SSH access", boolean())),
-    "sshPort"                  -> trim(label("SSH port", optional(number()))),
-    "smtp"                     -> optionalIfNotChecked("notification", mapping(
-        "host"                     -> trim(label("SMTP Host", text(required))),
-        "port"                     -> trim(label("SMTP Port", optional(number()))),
-        "user"                     -> trim(label("SMTP User", optional(text()))),
-        "password"                 -> trim(label("SMTP Password", optional(text()))),
-        "ssl"                      -> trim(label("Enable SSL", optional(boolean()))),
-        "fromAddress"              -> trim(label("FROM Address", optional(text()))),
-        "fromName"                 -> trim(label("FROM Name", optional(text())))
-    )(Smtp.apply)),
-    "ldapAuthentication"       -> trim(label("LDAP", boolean())),
-    "ldap"                     -> optionalIfNotChecked("ldapAuthentication", mapping(
-        "host"                     -> trim(label("LDAP host", text(required))),
-        "port"                     -> trim(label("LDAP port", optional(number()))),
-        "bindDN"                   -> trim(label("Bind DN", optional(text()))),
-        "bindPassword"             -> trim(label("Bind Password", optional(text()))),
-        "baseDN"                   -> trim(label("Base DN", text(required))),
-        "userNameAttribute"        -> trim(label("User name attribute", text(required))),
-        "additionalFilterCondition"-> trim(label("Additional filter condition", optional(text()))),
-        "fullNameAttribute"        -> trim(label("Full name attribute", optional(text()))),
-        "mailAttribute"            -> trim(label("Mail address attribute", optional(text()))),
-        "tls"                      -> trim(label("Enable TLS", optional(boolean()))),
-        "keystore"                 -> trim(label("Keystore", optional(text())))
-    )(Ldap.apply))
-  )(SystemSettings.apply).verifying { settings =>
-    if(settings.ssh && settings.baseUrl.isEmpty){
-      Seq("baseUrl" -> "Base URL is required if SSH access is enabled.")
-    } else Nil
-  }
-
-  private val pluginForm = mapping(
-    "pluginId" -> list(trim(label("", text())))
-  )(PluginForm.apply)
-
-  case class PluginForm(pluginIds: List[String])
-
-  get("/admin/system")(adminOnly {
-    admin.html.system(flash.get("info"))
-  })
-
-  post("/admin/system", form)(adminOnly { form =>
-    saveSystemSettings(form)
-
-    if(form.ssh && SshServer.isActive && context.settings.sshPort != form.sshPort){
-      SshServer.stop()
-    }
-
-    if(form.ssh && !SshServer.isActive && form.baseUrl.isDefined){
-      SshServer.start(request.getServletContext,
-        form.sshPort.getOrElse(SystemSettingsService.DefaultSshPort),
-        form.baseUrl.get)
-    } else if(!form.ssh && SshServer.isActive){
-      SshServer.stop()
-    }
-
-    flash += "info" -> "System settings has been updated."
-    redirect("/admin/system")
-  })
-
-  get("/admin/plugins")(adminOnly {
-    if(enablePluginSystem){
-      val installedPlugins = plugin.PluginSystem.plugins
-      val updatablePlugins = getAvailablePlugins(installedPlugins).filter(_.status == "updatable")
-      admin.plugins.html.installed(installedPlugins, updatablePlugins)
-    } else NotFound
-  })
-
-  post("/admin/plugins/_update", pluginForm)(adminOnly { form =>
-    if(enablePluginSystem){
-      deletePlugins(form.pluginIds)
-      installPlugins(form.pluginIds)
-      redirect("/admin/plugins")
-    } else NotFound
-  })
-
-  post("/admin/plugins/_delete", pluginForm)(adminOnly { form =>
-    if(enablePluginSystem){
-      deletePlugins(form.pluginIds)
-      redirect("/admin/plugins")
-    } else NotFound
-  })
-
-  get("/admin/plugins/available")(adminOnly {
-    if(enablePluginSystem){
-      val installedPlugins = plugin.PluginSystem.plugins
-      val availablePlugins = getAvailablePlugins(installedPlugins).filter(_.status == "available")
-      admin.plugins.html.available(availablePlugins)
-    } else NotFound
-  })
-
-  post("/admin/plugins/_install", pluginForm)(adminOnly { form =>
-    if(enablePluginSystem){
-      installPlugins(form.pluginIds)
-      redirect("/admin/plugins")
-    } else NotFound
-  })
-
-  get("/admin/plugins/console")(adminOnly {
-    if(enablePluginSystem){
-      admin.plugins.html.console()
-    } else NotFound
-  })
-
-  post("/admin/plugins/console")(adminOnly {
-    if(enablePluginSystem){
-      val script = request.getParameter("script")
-      val result = plugin.ScalaPlugin.eval(script)
-      Ok()
-    } else NotFound
-  })
-
-  // TODO Move these methods to PluginSystem or Service?
-  private def deletePlugins(pluginIds: List[String]): Unit = {
-    pluginIds.foreach { pluginId =>
-      plugin.PluginSystem.uninstall(pluginId)
-      val dir = new java.io.File(PluginHome, pluginId)
-      if(dir.exists && dir.isDirectory){
-        FileUtils.deleteQuietly(dir)
-        PluginSystem.uninstall(pluginId)
-      }
-    }
-  }
-
-  private def installPlugins(pluginIds: List[String]): Unit = {
-    val dir = getPluginCacheDir()
-    val installedPlugins = plugin.PluginSystem.plugins
-    getAvailablePlugins(installedPlugins).filter(x => pluginIds.contains(x.id)).foreach { plugin =>
-      val pluginDir = new java.io.File(PluginHome, plugin.id)
-      if(pluginDir.exists){
-        FileUtils.deleteDirectory(pluginDir)
-      }
-      FileUtils.copyDirectory(new java.io.File(dir, plugin.repository + "/" + plugin.id), pluginDir)
-      PluginSystem.installPlugin(plugin.id)
-    }
-  }
-
-  private def getAvailablePlugins(installedPlugins: List[Plugin]): List[SystemSettingsControllerBase.AvailablePlugin] = {
-    val repositoryRoot = getPluginCacheDir()
-
-    if(repositoryRoot.exists && repositoryRoot.isDirectory){
-      PluginSystem.repositories.flatMap { repo =>
-        val repoDir = new java.io.File(repositoryRoot, repo.id)
-        if(repoDir.exists && repoDir.isDirectory){
-          repoDir.listFiles.filter(d => d.isDirectory && !d.getName.startsWith(".")).map { plugin =>
-            val propertyFile = new java.io.File(plugin, "plugin.properties")
-            val properties = new java.util.Properties()
-            if(propertyFile.exists && propertyFile.isFile){
-              using(new FileInputStream(propertyFile)){ in =>
-                properties.load(in)
-              }
-            }
-            SystemSettingsControllerBase.AvailablePlugin(
-              repository  = repo.id,
-              id          = properties.getProperty("id"),
-              version     = properties.getProperty("version"),
-              author      = properties.getProperty("author"),
-              url         = properties.getProperty("url"),
-              description = properties.getProperty("description"),
-              status      = installedPlugins.find(_.id == properties.getProperty("id")) match {
-                case Some(x) if(PluginSystem.isUpdatable(x.version, properties.getProperty("version")))=> "updatable"
-                case Some(x) => "installed"
-                case None    => "available"
-              })
-          }
-        } else Nil
-      }
-    } else Nil
-  }
-}
-
-object SystemSettingsControllerBase {
-  case class AvailablePlugin(repository: String, id: String, version: String,
-                             author: String, url: String, description: String, status: String)
-}

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

@@ -1,19 +1,22 @@
-package app
+package gitbucket.core.controller
 
-import service._
-import util._
-import util.StringUtil._
-import util.Directory._
-import util.ControlUtil._
-import util.Implicits._
-import ssh.SshUtil
+import gitbucket.core.account.html
+import gitbucket.core.helper
+import gitbucket.core.model.GroupMember
+import gitbucket.core.util._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.Directory._
+import gitbucket.core.util.ControlUtil._
+import gitbucket.core.util.StringUtil._
+import gitbucket.core.ssh.SshUtil
+import gitbucket.core.service._
 import jp.sf.amateras.scalatra.forms._
 import org.apache.commons.io.FileUtils
 import org.scalatra.i18n.Messages
 import org.eclipse.jgit.api.Git
 import org.eclipse.jgit.lib.{FileMode, Constants}
 import org.eclipse.jgit.dircache.DirCache
-import model.GroupMember
+
 
 class AccountController extends AccountControllerBase
   with AccountService with RepositoryService with ActivityService with WikiService with LabelsService with SshKeyService
@@ -88,6 +91,12 @@ trait AccountControllerBase extends AccountManagementControllerBase {
     "name"  -> trim(label("Repository name",  text(required)))
   )(ForkRepositoryForm.apply)
 
+  case class AccountForm(accountName: String)
+
+  val accountForm = mapping(
+    "account" -> trim(label("Group/User name", text(required, validAccountName)))
+  )(AccountForm.apply)
+
   /**
    * Displays user information.
    */
@@ -97,21 +106,21 @@ trait AccountControllerBase extends AccountManagementControllerBase {
       params.getOrElse("tab", "repositories") match {
         // Public Activity
         case "activity" =>
-          _root_.account.html.activity(account,
+          gitbucket.core.account.html.activity(account,
             if(account.isGroupAccount) Nil else getGroupsByUserName(userName),
             getActivitiesByUser(userName, true))
 
         // Members
         case "members" if(account.isGroupAccount) => {
           val members = getGroupMembers(account.userName)
-          _root_.account.html.members(account, members.map(_.userName),
+          gitbucket.core.account.html.members(account, members.map(_.userName),
             context.loginAccount.exists(x => members.exists { member => member.userName == x.userName && member.isManager }))
         }
 
         // Repositories
         case _ => {
           val members = getGroupMembers(account.userName)
-          _root_.account.html.repositories(account,
+          gitbucket.core.account.html.repositories(account,
             if(account.isGroupAccount) Nil else getGroupsByUserName(userName),
             getVisibleRepositories(context.loginAccount, context.baseUrl, Some(userName)),
             context.loginAccount.exists(x => members.exists { member => member.userName == x.userName && member.isManager }))
@@ -129,8 +138,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   get("/:userName/_avatar"){
     val userName = params("userName")
     getAccountByUserName(userName).flatMap(_.image).map { image =>
-      contentType = FileUtil.getMimeType(image)
-      new java.io.File(getUserUploadDir(userName), image)
+      RawData(FileUtil.getMimeType(image), new java.io.File(getUserUploadDir(userName), image))
     } getOrElse {
       contentType = "image/png"
       Thread.currentThread.getContextClassLoader.getResourceAsStream("noimage.png")
@@ -140,7 +148,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   get("/:userName/_edit")(oneselfOnly {
     val userName = params("userName")
     getAccountByUserName(userName).map { x =>
-      account.html.edit(x, flash.get("info"))
+      html.edit(x, flash.get("info"))
     } getOrElse NotFound
   })
 
@@ -184,7 +192,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   get("/:userName/_ssh")(oneselfOnly {
     val userName = params("userName")
     getAccountByUserName(userName).map { x =>
-      account.html.ssh(x, getPublicKeys(x.userName))
+      html.ssh(x, getPublicKeys(x.userName))
     } getOrElse NotFound
   })
 
@@ -206,7 +214,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
       if(context.loginAccount.isDefined){
         redirect("/")
       } else {
-        account.html.register()
+        html.register()
       }
     } else NotFound
   }
@@ -220,7 +228,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   }
 
   get("/groups/new")(usersOnly {
-    account.html.group(None, List(GroupMember("", context.loginAccount.get.userName, true)))
+    html.group(None, List(GroupMember("", context.loginAccount.get.userName, true)))
   })
 
   post("/groups/new", newGroupForm)(usersOnly { form =>
@@ -236,7 +244,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
 
   get("/:groupName/_editgroup")(managersOnly {
     defining(params("groupName")){ groupName =>
-      account.html.group(getAccountByUserName(groupName, true), getGroupMembers(groupName))
+      html.group(getAccountByUserName(groupName, true), getGroupMembers(groupName))
     }
   })
 
@@ -285,7 +293,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
    * Show the new repository form.
    */
   get("/new")(usersOnly {
-    account.html.newrepo(getGroupsByUserName(context.loginAccount.get.userName))
+    html.newrepo(getGroupsByUserName(context.loginAccount.get.userName), context.settings.isCreateRepoOptionPublic)
   })
 
   /**
@@ -354,11 +362,31 @@ trait AccountControllerBase extends AccountManagementControllerBase {
   get("/:owner/:repository/fork")(readableUsersOnly { repository =>
     val loginAccount   = context.loginAccount.get
     val loginUserName  = loginAccount.userName
+    val groups         = getGroupsByUserName(loginUserName)
+    groups match {
+      case _: List[String] =>
+        val managerPermissions = groups.map { group =>
+          val members = getGroupMembers(group)
+          context.loginAccount.exists(x => members.exists { member => member.userName == x.userName && member.isManager })
+        }
+        helper.html.forkrepository(
+          repository,
+          (groups zip managerPermissions).toMap
+        )
+      case _ => redirect(s"/${loginUserName}")
+    }
+  })
 
-    LockUtil.lock(s"${loginUserName}/${repository.name}"){
-      if(repository.owner == loginUserName || getRepository(loginAccount.userName, repository.name, baseUrl).isDefined){
+  post("/:owner/:repository/fork", accountForm)(readableUsersOnly { (form, repository) =>
+    val loginAccount  = context.loginAccount.get
+    val loginUserName = loginAccount.userName
+    val accountName   = form.accountName
+
+    LockUtil.lock(s"${accountName}/${repository.name}"){
+      if(getRepository(accountName, repository.name, baseUrl).isDefined ||
+          (accountName != loginUserName && !getGroupsByUserName(loginUserName).contains(accountName))){
         // redirect to the repository if repository already exists
-        redirect(s"/${loginUserName}/${repository.name}")
+        redirect(s"/${accountName}/${repository.name}")
       } else {
         // Insert to the database at first
         val originUserName = repository.repository.originUserName.getOrElse(repository.owner)
@@ -366,7 +394,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
 
         createRepository(
           repositoryName       = repository.name,
-          userName             = loginUserName,
+          userName             = accountName,
           description          = repository.repository.description,
           isPrivate            = repository.repository.isPrivate,
           originRepositoryName = Some(originRepositoryName),
@@ -376,22 +404,22 @@ trait AccountControllerBase extends AccountManagementControllerBase {
         )
 
         // Insert default labels
-        insertDefaultLabels(loginUserName, repository.name)
+        insertDefaultLabels(accountName, repository.name)
 
         // clone repository actually
         JGitUtil.cloneRepository(
           getRepositoryDir(repository.owner, repository.name),
-          getRepositoryDir(loginUserName, repository.name))
+          getRepositoryDir(accountName, repository.name))
 
         // Create Wiki repository
         JGitUtil.cloneRepository(
           getWikiRepositoryDir(repository.owner, repository.name),
-          getWikiRepositoryDir(loginUserName, repository.name))
+          getWikiRepositoryDir(accountName, repository.name))
 
         // Record activity
-        recordForkActivity(repository.owner, repository.name, loginUserName)
+        recordForkActivity(repository.owner, repository.name, loginUserName, accountName)
         // redirect to the repository
-        redirect(s"/${loginUserName}/${repository.name}")
+        redirect(s"/${accountName}/${repository.name}")
       }
     }
   })
@@ -431,4 +459,13 @@ trait AccountControllerBase extends AccountManagementControllerBase {
      case None => Some("Key is invalid.")
     }
   }
+
+  private def validAccountName: Constraint = new Constraint(){
+    override def validate(name: String, value: String, messages: Messages): Option[String] = {
+      getAccountByUserName(value) match {
+        case Some(_) => None
+        case None => Some("Invalid Group/User Account.")
+      }
+    }
+  }
 }

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

@@ -0,0 +1,14 @@
+package gitbucket.core.controller
+
+class AnonymousAccessController extends AnonymousAccessControllerBase
+
+trait AnonymousAccessControllerBase extends ControllerBase {
+  get(!context.settings.allowAnonymousAccess, context.loginAccount.isEmpty) {
+    if(!context.currentPath.startsWith("/assets") && !context.currentPath.startsWith("/signin") &&
+      !context.currentPath.startsWith("/register")) {
+      Unauthorized()
+    } else {
+      pass()
+    }
+  }
+}

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

@@ -1,16 +1,16 @@
-package app
+package gitbucket.core.controller
 
-import _root_.util.Directory._
-import _root_.util.Implicits._
-import _root_.util.ControlUtil._
-import _root_.util.{StringUtil, FileUtil, Validations, Keys}
+import gitbucket.core.service.{AccountService, SystemSettingsService}
+import gitbucket.core.util._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.ControlUtil._
+import gitbucket.core.util.Directory._
+import gitbucket.core.model.Account
 import org.scalatra._
 import org.scalatra.json._
 import org.json4s._
 import jp.sf.amateras.scalatra.forms._
 import org.apache.commons.io.FileUtils
-import model._
-import service.{SystemSettingsService, AccountService}
 import javax.servlet.http.{HttpServletResponse, HttpServletRequest}
 import javax.servlet.{FilterChain, ServletResponse, ServletRequest}
 import org.scalatra.i18n._
@@ -104,10 +104,10 @@ abstract class ControllerBase extends ScalatraFilter
     if(request.hasAttribute(Keys.Request.Ajax)){
       org.scalatra.NotFound()
     } else {
-      org.scalatra.NotFound(html.error("Not Found"))
+      org.scalatra.NotFound(gitbucket.core.html.error("Not Found"))
     }
 
-  protected def Unauthorized()(implicit context: app.Context) =
+  protected def Unauthorized()(implicit context: Context) =
     if(request.hasAttribute(Keys.Request.Ajax)){
       org.scalatra.Unauthorized()
     } else {
@@ -134,6 +134,18 @@ abstract class ControllerBase extends ScalatraFilter
     if (path.startsWith("http")) path
     else baseUrl + super.url(path, params, false, false, false)
 
+  /**
+   * Use this method to response the raw data against XSS.
+   */
+  protected def RawData[T](contentType: String, rawData: T): T = {
+    if(contentType.split(";").head.trim.toLowerCase.startsWith("text/html")){
+      this.contentType = "text/plain"
+    } else {
+      this.contentType = contentType
+    }
+    response.addHeader("X-Content-Type-Options", "nosniff")
+    rawData
+  }
 }
 
 /**

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

@@ -1,9 +1,10 @@
-package app
+package gitbucket.core.controller
 
-import service._
-import util.{StringUtil, UsersAuthenticator, Keys}
-import util.Implicits._
-import service.IssuesService.IssueSearchCondition
+import gitbucket.core.dashboard.html
+import gitbucket.core.service.{RepositoryService, PullRequestService, AccountService, IssuesService}
+import gitbucket.core.util.{StringUtil, Keys, UsersAuthenticator}
+import gitbucket.core.util.Implicits._
+import gitbucket.core.service.IssuesService._
 
 class DashboardController extends DashboardControllerBase
   with IssuesService with PullRequestService with RepositoryService with AccountService
@@ -96,7 +97,7 @@ trait DashboardControllerBase extends ControllerBase {
     val userRepos = getUserRepositories(userName, context.baseUrl, true).map(repo => repo.owner -> repo.name)
     val page      = IssueSearchCondition.page(request)
 
-    dashboard.html.issues(
+    html.issues(
       searchIssue(condition, false, (page - 1) * IssueLimit, IssueLimit, userRepos: _*),
       page,
       countIssue(condition.copy(state = "open"  ), false, userRepos: _*),
@@ -119,7 +120,7 @@ trait DashboardControllerBase extends ControllerBase {
     val allRepos  = getAllRepositories(userName)
     val page      = IssueSearchCondition.page(request)
 
-    dashboard.html.pulls(
+    html.pulls(
       searchIssue(condition, true, (page - 1) * PullRequestLimit, PullRequestLimit, allRepos: _*),
       page,
       countIssue(condition.copy(state = "open"  ), true, allRepos: _*),

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

@@ -1,8 +1,8 @@
-package app
+package gitbucket.core.controller
 
-import util.{Keys, FileUtil}
-import util.ControlUtil._
-import util.Directory._
+import gitbucket.core.util.{Keys, FileUtil}
+import gitbucket.core.util.ControlUtil._
+import gitbucket.core.util.Directory._
 import org.scalatra._
 import org.scalatra.servlet.{MultipartConfig, FileUploadSupport, FileItem}
 import org.apache.commons.io.FileUtils

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

@@ -1,8 +1,11 @@
-package app
+package gitbucket.core.controller
 
-import util._
-import util.Implicits._
-import service._
+import gitbucket.core.html
+import gitbucket.core.helper.xml
+import gitbucket.core.model.Account
+import gitbucket.core.service.{RepositoryService, ActivityService, AccountService}
+import gitbucket.core.util.{LDAPUtil, Keys, UsersAuthenticator}
+import gitbucket.core.util.Implicits._
 import jp.sf.amateras.scalatra.forms._
 
 class IndexController extends IndexControllerBase 
@@ -61,13 +64,13 @@ trait IndexControllerBase extends ControllerBase {
 
   get("/activities.atom"){
     contentType = "application/atom+xml; type=feed"
-    helper.xml.feed(getRecentActivities())
+    xml.feed(getRecentActivities())
   }
 
   /**
    * Set account information into HttpSession and redirect.
    */
-  private def signin(account: model.Account) = {
+  private def signin(account: Account) = {
     session.setAttribute(Keys.Session.LoginAccount, account)
     updateLastLoginDate(account.userName)
 

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

@@ -1,14 +1,17 @@
-package app
+package gitbucket.core.controller
 
+import gitbucket.core.issues.html
+import gitbucket.core.model.Issue
+import gitbucket.core.service._
+import gitbucket.core.util._
+import gitbucket.core.util.ControlUtil._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.view
+import gitbucket.core.view.Markdown
 import jp.sf.amateras.scalatra.forms._
 
-import service._
 import IssuesService._
-import util._
-import util.Implicits._
-import util.ControlUtil._
 import org.scalatra.Ok
-import model.Issue
 
 class IssuesController extends IssuesControllerBase
   with IssuesService with RepositoryService with AccountService with LabelsService with MilestonesService with ActivityService
@@ -60,7 +63,7 @@ trait IssuesControllerBase extends ControllerBase {
   get("/:owner/:repository/issues/:id")(referrersOnly { repository =>
     defining(repository.owner, repository.name, params("id")){ case (owner, name, issueId) =>
       getIssue(owner, name, issueId) map {
-        issues.html.issue(
+        html.issue(
           _,
           getComments(owner, name, issueId.toInt),
           getIssueLabels(owner, name, issueId.toInt),
@@ -75,7 +78,7 @@ trait IssuesControllerBase extends ControllerBase {
 
   get("/:owner/:repository/issues/new")(readableUsersOnly { repository =>
     defining(repository.owner, repository.name){ case (owner, name) =>
-      issues.html.create(
+      html.create(
         (getCollaborators(owner, name) ::: (if(getAccountByUserName(owner).get.isGroupAccount) Nil else List(owner))).sorted,
           getMilestones(owner, name),
           getLabels(owner, name),
@@ -192,13 +195,13 @@ trait IssuesControllerBase extends ControllerBase {
     getIssue(repository.owner, repository.name, params("id")) map { x =>
       if(isEditable(x.userName, x.repositoryName, x.openedUserName)){
         params.get("dataType") collect {
-          case t if t == "html" => issues.html.editissue(
+          case t if t == "html" => html.editissue(
               x.content, x.issueId, x.userName, x.repositoryName)
         } getOrElse {
           contentType = formats("json")
           org.json4s.jackson.Serialization.write(
               Map("title"   -> x.title,
-                  "content" -> view.Markdown.toHtml(x.content getOrElse "No description given.",
+                  "content" -> Markdown.toHtml(x.content getOrElse "No description given.",
                       repository, false, true, true, isEditable(x.userName, x.repositoryName, x.openedUserName))
               ))
         }
@@ -210,7 +213,7 @@ trait IssuesControllerBase extends ControllerBase {
     getComment(repository.owner, repository.name, params("id")) map { x =>
       if(isEditable(x.userName, x.repositoryName, x.commentedUserName)){
         params.get("dataType") collect {
-          case t if t == "html" => issues.html.editcomment(
+          case t if t == "html" => html.editcomment(
               x.content, x.commentId, x.userName, x.repositoryName)
         } getOrElse {
           contentType = formats("json")
@@ -226,14 +229,14 @@ trait IssuesControllerBase extends ControllerBase {
   ajaxPost("/:owner/:repository/issues/:id/label/new")(collaboratorsOnly { repository =>
     defining(params("id").toInt){ issueId =>
       registerIssueLabel(repository.owner, repository.name, issueId, params("labelId").toInt)
-      issues.html.labellist(getIssueLabels(repository.owner, repository.name, issueId))
+      html.labellist(getIssueLabels(repository.owner, repository.name, issueId))
     }
   })
 
   ajaxPost("/:owner/:repository/issues/:id/label/delete")(collaboratorsOnly { repository =>
     defining(params("id").toInt){ issueId =>
       deleteIssueLabel(repository.owner, repository.name, issueId, params("labelId").toInt)
-      issues.html.labellist(getIssueLabels(repository.owner, repository.name, issueId))
+      html.labellist(getIssueLabels(repository.owner, repository.name, issueId))
     }
   })
 
@@ -247,7 +250,7 @@ trait IssuesControllerBase extends ControllerBase {
     milestoneId("milestoneId").map { milestoneId =>
       getMilestonesWithIssueCount(repository.owner, repository.name)
           .find(_._1.milestoneId == milestoneId).map { case (_, openCount, closeCount) =>
-        issues.milestones.html.progress(openCount + closeCount, closeCount)
+        gitbucket.core.issues.milestones.html.progress(openCount + closeCount, closeCount)
       } getOrElse NotFound
     } getOrElse Ok()
   })
@@ -292,8 +295,7 @@ trait IssuesControllerBase extends ControllerBase {
     (Directory.getAttachedDir(repository.owner, repository.name) match {
       case dir if(dir.exists && dir.isDirectory) =>
         dir.listFiles.find(_.getName.startsWith(params("file") + ".")).map { file =>
-          contentType = FileUtil.getMimeType(file.getName)
-          file
+          RawData(FileUtil.getMimeType(file.getName), file)
         }
       case _ => None
     }) getOrElse NotFound
@@ -302,7 +304,7 @@ trait IssuesControllerBase extends ControllerBase {
   val assignedUserName = (key: String) => params.get(key) filter (_.trim != "")
   val milestoneId: String => Option[Int] = (key: String) => params.get(key).flatMap(_.toIntOpt)
 
-  private def isEditable(owner: String, repository: String, author: String)(implicit context: app.Context): Boolean =
+  private def isEditable(owner: String, repository: String, author: String)(implicit context: Context): Boolean =
     hasWritePermission(owner, repository, context.loginAccount) || author == context.loginAccount.get.userName
 
   private def executeBatch(repository: RepositoryService.RepositoryInfo)(execute: Int => Unit) = {
@@ -326,13 +328,13 @@ trait IssuesControllerBase extends ControllerBase {
    * @see [[https://github.com/takezoe/gitbucket/wiki/CommentAction]]
    */
   private def handleComment(issueId: Int, content: Option[String], repository: RepositoryService.RepositoryInfo)
-      (getAction: model.Issue => Option[String] =
+      (getAction: Issue => Option[String] =
            p1 => params.get("action").filter(_ => isEditable(p1.userName, p1.repositoryName, p1.openedUserName))) = {
 
     defining(repository.owner, repository.name){ case (owner, name) =>
       val userName = context.loginAccount.get.userName
 
-      getIssue(owner, name, issueId.toString) map { issue =>
+      getIssue(owner, name, issueId.toString) flatMap { issue =>
         val (action, recordActivity) =
           getAction(issue)
             .collect {
@@ -347,11 +349,10 @@ trait IssuesControllerBase extends ControllerBase {
             }
             .getOrElse(None -> None)
 
-        val commentId = content
-          .map       ( _ -> action.map( _ + "_comment" ).getOrElse("comment") )
-          .getOrElse ( action.get.capitalize -> action.get )
-        match {
-          case (content, action) => createComment(owner, name, userName, issueId, content, action)
+        val commentId = (content, action) match {
+          case (None, None) => None
+          case (None, Some(action)) => Some(createComment(owner, name, userName, issueId, action.capitalize, action))
+          case (Some(content), _) => Some(createComment(owner, name, userName, issueId, content, action.map(_+ "_comment").getOrElse("comment")))
         }
 
         // record comment activity if comment is entered
@@ -372,7 +373,7 @@ trait IssuesControllerBase extends ControllerBase {
             content foreach {
               f.toNotify(repository, issueId, _){
                 Notifier.msgComment(s"${context.baseUrl}/${owner}/${name}/${
-                  if(issue.isPullRequest) "pull" else "issues"}/${issueId}#comment-${commentId}")
+                  if(issue.isPullRequest) "pull" else "issues"}/${issueId}#comment-${commentId.get}")
               }
             }
             action foreach {
@@ -382,7 +383,7 @@ trait IssuesControllerBase extends ControllerBase {
             }
         }
 
-        issue -> commentId
+        commentId.map( issue -> _ )
       }
     }
   }
@@ -396,7 +397,7 @@ trait IssuesControllerBase extends ControllerBase {
       val condition = session.putAndGet(sessionKey,
         if(request.hasQueryString){
           val q = request.getParameter("q")
-          if(q == null){
+          if(q == null || q.trim.isEmpty){
             IssueSearchCondition(request)
           } else {
             IssueSearchCondition(q, getMilestones(owner, repoName).map(x => (x.title, x.milestoneId)).toMap)
@@ -404,7 +405,7 @@ trait IssuesControllerBase extends ControllerBase {
         } else session.getAs[IssueSearchCondition](sessionKey).getOrElse(IssueSearchCondition())
       )
 
-      issues.html.list(
+      html.list(
           "issues",
           searchIssue(condition, false, (page - 1) * IssueLimit, IssueLimit, owner -> repoName),
           page,

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

@@ -1,9 +1,10 @@
-package app
+package gitbucket.core.controller
 
+import gitbucket.core.issues.labels.html
+import gitbucket.core.service.{RepositoryService, AccountService, IssuesService, LabelsService}
+import gitbucket.core.util.{ReferrerAuthenticator, CollaboratorsAuthenticator}
+import gitbucket.core.util.Implicits._
 import jp.sf.amateras.scalatra.forms._
-import service._
-import util.{ReferrerAuthenticator, CollaboratorsAuthenticator}
-import util.Implicits._
 import org.scalatra.i18n.Messages
 import org.scalatra.Ok
 
@@ -23,7 +24,7 @@ trait LabelsControllerBase extends ControllerBase {
   )(LabelForm.apply)
 
   get("/:owner/:repository/issues/labels")(referrersOnly { repository =>
-    issues.labels.html.list(
+    html.list(
       getLabels(repository.owner, repository.name),
       countIssueGroupByLabels(repository.owner, repository.name, IssuesService.IssueSearchCondition(), Map.empty),
       repository,
@@ -31,12 +32,12 @@ trait LabelsControllerBase extends ControllerBase {
   })
 
   ajaxGet("/:owner/:repository/issues/labels/new")(collaboratorsOnly { repository =>
-    issues.labels.html.edit(None, repository)
+    html.edit(None, repository)
   })
 
   ajaxPost("/:owner/:repository/issues/labels/new", labelForm)(collaboratorsOnly { (form, repository) =>
     val labelId = createLabel(repository.owner, repository.name, form.labelName, form.color.substring(1))
-    issues.labels.html.label(
+    html.label(
       getLabel(repository.owner, repository.name, labelId).get,
       // TODO futility
       countIssueGroupByLabels(repository.owner, repository.name, IssuesService.IssueSearchCondition(), Map.empty),
@@ -46,13 +47,13 @@ trait LabelsControllerBase extends ControllerBase {
 
   ajaxGet("/:owner/:repository/issues/labels/:labelId/edit")(collaboratorsOnly { repository =>
     getLabel(repository.owner, repository.name, params("labelId").toInt).map { label =>
-      issues.labels.html.edit(Some(label), repository)
+      html.edit(Some(label), repository)
     } getOrElse NotFound()
   })
 
   ajaxPost("/:owner/:repository/issues/labels/:labelId/edit", labelForm)(collaboratorsOnly { (form, repository) =>
     updateLabel(repository.owner, repository.name, params("labelId").toInt, form.labelName, form.color.substring(1))
-    issues.labels.html.label(
+    html.label(
       getLabel(repository.owner, repository.name, params("labelId").toInt).get,
       // TODO futility
       countIssueGroupByLabels(repository.owner, repository.name, IssuesService.IssueSearchCondition(), Map.empty),

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

@@ -1,11 +1,11 @@
-package app
+package gitbucket.core.controller
 
+import gitbucket.core.issues.milestones.html
+import gitbucket.core.service.{RepositoryService, MilestonesService, AccountService}
+import gitbucket.core.util.{ReferrerAuthenticator, CollaboratorsAuthenticator}
+import gitbucket.core.util.Implicits._
 import jp.sf.amateras.scalatra.forms._
 
-import service._
-import util.{CollaboratorsAuthenticator, ReferrerAuthenticator}
-import util.Implicits._
-
 class MilestonesController extends MilestonesControllerBase
   with MilestonesService with RepositoryService with AccountService
   with ReferrerAuthenticator with CollaboratorsAuthenticator
@@ -23,7 +23,7 @@ trait MilestonesControllerBase extends ControllerBase {
   )(MilestoneForm.apply)
 
   get("/:owner/:repository/issues/milestones")(referrersOnly { repository =>
-    issues.milestones.html.list(
+    html.list(
       params.getOrElse("state", "open"),
       getMilestonesWithIssueCount(repository.owner, repository.name),
       repository,
@@ -31,7 +31,7 @@ trait MilestonesControllerBase extends ControllerBase {
   })
 
   get("/:owner/:repository/issues/milestones/new")(collaboratorsOnly {
-    issues.milestones.html.edit(None, _)
+    html.edit(None, _)
   })
 
   post("/:owner/:repository/issues/milestones/new", milestoneForm)(collaboratorsOnly { (form, repository) =>
@@ -41,7 +41,7 @@ trait MilestonesControllerBase extends ControllerBase {
 
   get("/:owner/:repository/issues/milestones/:milestoneId/edit")(collaboratorsOnly { repository =>
     params("milestoneId").toIntOpt.map{ milestoneId =>
-      issues.milestones.html.edit(getMilestone(repository.owner, repository.name, milestoneId), repository)
+      html.edit(getMilestone(repository.owner, repository.name, milestoneId), repository)
     } getOrElse NotFound
   })
 

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

@@ -1,23 +1,25 @@
-package app
+package gitbucket.core.controller
 
-import util._
-import util.Directory._
-import util.Implicits._
-import util.ControlUtil._
-import service._
+import gitbucket.core.pulls.html
+import gitbucket.core.util._
+import gitbucket.core.util.JGitUtil._
+import gitbucket.core.util.ControlUtil._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.Directory._
+import gitbucket.core.view
+import gitbucket.core.view.helpers
 import org.eclipse.jgit.api.Git
 import jp.sf.amateras.scalatra.forms._
 import org.eclipse.jgit.transport.RefSpec
 import scala.collection.JavaConverters._
 import org.eclipse.jgit.lib.{ObjectId, CommitBuilder, PersonIdent}
-import service.IssuesService._
-import service.PullRequestService._
+import gitbucket.core.service._
+import gitbucket.core.service.IssuesService._
+import gitbucket.core.service.PullRequestService._
+import gitbucket.core.service.WebHookService.WebHookPayload
 import org.slf4j.LoggerFactory
 import org.eclipse.jgit.merge.MergeStrategy
 import org.eclipse.jgit.errors.NoMergeBaseException
-import service.WebHookService.WebHookPayload
-import util.JGitUtil.DiffInfo
-import util.JGitUtil.CommitInfo
 
 
 class PullRequestsController extends PullRequestsControllerBase
@@ -77,7 +79,7 @@ trait PullRequestsControllerBase extends ControllerBase {
           val (commits, diffs) =
             getRequestCompareInfo(owner, name, pullreq.commitIdFrom, owner, name, pullreq.commitIdTo)
 
-          pulls.html.pullreq(
+          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),
@@ -99,7 +101,7 @@ trait PullRequestsControllerBase extends ControllerBase {
       val owner = repository.owner
       val name  = repository.name
       getPullRequest(owner, name, issueId) map { case(issue, pullreq) =>
-        pulls.html.mergeguide(
+        html.mergeguide(
           checkConflictInPullRequest(owner, name, pullreq.branch, pullreq.requestUserName, name, pullreq.requestBranch, issueId),
           pullreq,
           s"${context.baseUrl}/git/${pullreq.requestUserName}/${pullreq.requestRepositoryName}.git")
@@ -242,8 +244,8 @@ trait PullRequestsControllerBase extends ControllerBase {
 
   get("/:owner/:repository/compare/*...*")(referrersOnly { forkedRepository =>
     val Seq(origin, forked) = multiParams("splat")
-    val (originOwner, tmpOriginBranch) = parseCompareIdentifie(origin, forkedRepository.owner)
-    val (forkedOwner, tmpForkedBranch) = parseCompareIdentifie(forked, forkedRepository.owner)
+    val (originOwner, originId) = parseCompareIdentifie(origin, forkedRepository.owner)
+    val (forkedOwner, forkedId) = parseCompareIdentifie(forked, forkedRepository.owner)
 
     (for(
       originRepositoryName <- if(originOwner == forkedOwner){
@@ -259,21 +261,24 @@ trait PullRequestsControllerBase extends ControllerBase {
         Git.open(getRepositoryDir(originRepository.owner, originRepository.name)),
         Git.open(getRepositoryDir(forkedRepository.owner, forkedRepository.name))
       ){ case (oldGit, newGit) =>
-        val originBranch = JGitUtil.getDefaultBranch(oldGit, originRepository, tmpOriginBranch).get._2
-        val forkedBranch = JGitUtil.getDefaultBranch(newGit, forkedRepository, tmpForkedBranch).get._2
+        val (oldId, newId) =
+          if(originRepository.branchList.contains(originId) && forkedRepository.branchList.contains(forkedId)){
+            // Branch name
+            val rootId = JGitUtil.getForkedCommitId(oldGit, newGit,
+              originRepository.owner, originRepository.name, originId,
+              forkedRepository.owner, forkedRepository.name, forkedId)
 
-        val forkedId = JGitUtil.getForkedCommitId(oldGit, newGit,
-          originRepository.owner, originRepository.name, originBranch,
-          forkedRepository.owner, forkedRepository.name, forkedBranch)
-
-        val oldId = oldGit.getRepository.resolve(forkedId)
-        val newId = newGit.getRepository.resolve(forkedBranch)
+            (oldGit.getRepository.resolve(rootId),  newGit.getRepository.resolve(forkedId))
+          } else {
+            // Commit id
+            (oldGit.getRepository.resolve(originId), newGit.getRepository.resolve(forkedId))
+          }
 
         val (commits, diffs) = getRequestCompareInfo(
           originRepository.owner, originRepository.name, oldId.getName,
           forkedRepository.owner, forkedRepository.name, newId.getName)
 
-        pulls.html.compare(
+        html.compare(
           commits,
           diffs,
           (forkedRepository.repository.originUserName, forkedRepository.repository.originRepositoryName) match {
@@ -281,8 +286,8 @@ trait PullRequestsControllerBase extends ControllerBase {
             case _ => (forkedRepository.owner, forkedRepository.name) :: getForkedRepositories(forkedRepository.owner, forkedRepository.name)
           },
           commits.flatten.map(commit => getCommitComments(forkedRepository.owner, forkedRepository.name, commit.id, false)).flatten.toList,
-          originBranch,
-          forkedBranch,
+          originId,
+          forkedId,
           oldId.getName,
           newId.getName,
           forkedRepository,
@@ -315,7 +320,7 @@ trait PullRequestsControllerBase extends ControllerBase {
         val originBranch = JGitUtil.getDefaultBranch(oldGit, originRepository, tmpOriginBranch).get._2
         val forkedBranch = JGitUtil.getDefaultBranch(newGit, forkedRepository, tmpForkedBranch).get._2
 
-        pulls.html.mergecheck(
+        html.mergecheck(
           checkConflict(originRepository.owner, originRepository.name, originBranch,
                         forkedRepository.owner, forkedRepository.name, forkedBranch))
       }
@@ -447,7 +452,7 @@ trait PullRequestsControllerBase extends ControllerBase {
       val commits = newGit.log.addRange(oldId, newId).call.iterator.asScala.map { revCommit =>
         new CommitInfo(revCommit)
       }.toList.splitWith { (commit1, commit2) =>
-        view.helpers.date(commit1.commitTime) == view.helpers.date(commit2.commitTime)
+        helpers.date(commit1.commitTime) == view.helpers.date(commit2.commitTime)
       }
 
       val diffs = JGitUtil.getDiffs(newGit, oldId.getName, newId.getName, true)
@@ -466,7 +471,7 @@ trait PullRequestsControllerBase extends ControllerBase {
         else session.getAs[IssueSearchCondition](sessionKey).getOrElse(IssueSearchCondition())
       )
 
-      issues.html.list(
+      gitbucket.core.issues.html.list(
         "pulls",
         searchIssue(condition, true, (page - 1) * PullRequestLimit, PullRequestLimit, owner -> repoName),
         page,

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

@@ -1,15 +1,17 @@
-package app
+package gitbucket.core.controller
 
-import service._
-import util.Directory._
-import util.Implicits._
-import util.{LockUtil, UsersAuthenticator, OwnerAuthenticator}
+import gitbucket.core.settings.html
+import gitbucket.core.model.WebHook
+import gitbucket.core.service.{RepositoryService, AccountService, WebHookService}
+import gitbucket.core.service.WebHookService.WebHookPayload
+import gitbucket.core.util._
+import gitbucket.core.util.JGitUtil._
+import gitbucket.core.util.ControlUtil._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.Directory._
 import jp.sf.amateras.scalatra.forms._
 import org.apache.commons.io.FileUtils
 import org.scalatra.i18n.Messages
-import service.WebHookService.WebHookPayload
-import util.JGitUtil.CommitInfo
-import util.ControlUtil._
 import org.eclipse.jgit.api.Git
 import org.eclipse.jgit.lib.Constants
 
@@ -63,7 +65,7 @@ trait RepositorySettingsControllerBase extends ControllerBase {
    * Display the Options page.
    */
   get("/:owner/:repository/settings/options")(ownerOnly {
-    settings.html.options(_, flash.get("info"))
+    html.options(_, flash.get("info"))
   })
   
   /**
@@ -105,7 +107,7 @@ trait RepositorySettingsControllerBase extends ControllerBase {
    * Display the Collaborators page.
    */
   get("/:owner/:repository/settings/collaborators")(ownerOnly { repository =>
-    settings.html.collaborators(
+    html.collaborators(
       getCollaborators(repository.owner, repository.name),
       getAccountByUserName(repository.owner).get.isGroupAccount,
       repository)
@@ -135,7 +137,7 @@ trait RepositorySettingsControllerBase extends ControllerBase {
    * Display the web hook page.
    */
   get("/:owner/:repository/settings/hooks")(ownerOnly { repository =>
-    settings.html.hooks(getWebHookURLs(repository.owner, repository.name), flash.get("url"), repository, flash.get("info"))
+    html.hooks(getWebHookURLs(repository.owner, repository.name), flash.get("url"), repository, flash.get("info"))
   })
 
   /**
@@ -167,7 +169,7 @@ trait RepositorySettingsControllerBase extends ControllerBase {
 
       getAccountByUserName(repository.owner).foreach { ownerAccount =>
         callWebHook(repository.owner, repository.name,
-          List(model.WebHook(repository.owner, repository.name, form.url)),
+          List(WebHook(repository.owner, repository.name, form.url)),
           WebHookPayload(git, ownerAccount, "refs/heads/" + repository.repository.defaultBranch, repository, commits.toList, ownerAccount)
         )
       }
@@ -181,7 +183,7 @@ trait RepositorySettingsControllerBase extends ControllerBase {
    * Display the danger zone.
    */
   get("/:owner/:repository/settings/danger")(ownerOnly {
-    settings.html.danger(_)
+    html.danger(_)
   })
 
   /**

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

@@ -1,13 +1,18 @@
-package app
+package gitbucket.core.controller
 
-import _root_.util.JGitUtil.CommitInfo
-import util.Directory._
-import util.Implicits._
-import _root_.util.ControlUtil._
-import _root_.util._
-import service._
+import gitbucket.core.repo.html
+import gitbucket.core.helper
+import gitbucket.core.service._
+import gitbucket.core.util._
+import gitbucket.core.util.JGitUtil._
+import gitbucket.core.util.ControlUtil._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.Directory._
+import gitbucket.core.model.Account
+import gitbucket.core.service.WebHookService.WebHookPayload
+import gitbucket.core.view
+import gitbucket.core.view.helpers
 import org.scalatra._
-import java.io.File
 
 import org.eclipse.jgit.api.{ArchiveCommand, Git}
 import org.eclipse.jgit.archive.{TgzFormat, ZipFormat}
@@ -17,11 +22,10 @@ import org.eclipse.jgit.treewalk._
 import jp.sf.amateras.scalatra.forms._
 import org.eclipse.jgit.dircache.DirCache
 import org.eclipse.jgit.revwalk.RevCommit
-import service.WebHookService.WebHookPayload
 
 class RepositoryViewerController extends RepositoryViewerControllerBase
   with RepositoryService with AccountService with ActivityService with IssuesService with WebHookService with CommitsService
-  with ReadableUsersAuthenticator with ReferrerAuthenticator with CollaboratorsAuthenticator
+  with ReadableUsersAuthenticator with ReferrerAuthenticator with CollaboratorsAuthenticator with PullRequestService
 
 
 /**
@@ -29,7 +33,7 @@ class RepositoryViewerController extends RepositoryViewerControllerBase
  */
 trait RepositoryViewerControllerBase extends ControllerBase {
   self: RepositoryService with AccountService with ActivityService with IssuesService with WebHookService with CommitsService
-    with ReadableUsersAuthenticator with ReferrerAuthenticator with CollaboratorsAuthenticator =>
+    with ReadableUsersAuthenticator with ReferrerAuthenticator with CollaboratorsAuthenticator with PullRequestService =>
 
   ArchiveCommand.registerFormat("zip", new ZipFormat)
   ArchiveCommand.registerFormat("tar.gz", new TgzFormat)
@@ -57,7 +61,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     oldLineNumber: Option[Int],
     newLineNumber: Option[Int],
     content: String,
-    pullRequest: Boolean
+    issueId: Option[Int]
   )
 
   val editorForm = mapping(
@@ -83,7 +87,7 @@ 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))),
-    "pullRequest"   -> trim(label("In pull request", boolean()))
+    "issueId"       -> trim(label("Issue Id", optional(number())))
   )(CommentForm.apply)
 
   /**
@@ -91,7 +95,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
    */
   post("/:owner/:repository/_preview")(referrersOnly { repository =>
     contentType = "text/html"
-    view.helpers.markdown(params("content"), repository,
+    helpers.markdown(params("content"), repository,
       params("enableWikiLink").toBoolean,
       params("enableRefsLink").toBoolean,
       params("enableTaskList").toBoolean,
@@ -127,7 +131,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     using(Git.open(getRepositoryDir(repository.owner, repository.name))){ git =>
       JGitUtil.getCommitLog(git, branchName, page, 30, path) match {
         case Right((logs, hasNext)) =>
-          repo.html.commits(if(path.isEmpty) Nil else path.split("/").toList, branchName, repository,
+          html.commits(if(path.isEmpty) Nil else path.split("/").toList, branchName, repository,
             logs.splitWith{ (commit1, commit2) =>
               view.helpers.date(commit1.commitTime) == view.helpers.date(commit2.commitTime)
             }, page, hasNext, hasWritePermission(repository.owner, repository.name, context.loginAccount))
@@ -138,7 +142,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
 
   get("/:owner/:repository/new/*")(collaboratorsOnly { repository =>
     val (branch, path) = splitPath(repository, multiParams("splat").head)
-    repo.html.editor(branch, repository, if(path.length == 0) Nil else path.split("/").toList,
+    html.editor(branch, repository, if(path.length == 0) Nil else path.split("/").toList,
       None, JGitUtil.ContentInfo("text", None, Some("UTF-8")))
   })
 
@@ -150,7 +154,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
 
       getPathObjectId(git, path, revCommit).map { objectId =>
         val paths = path.split("/")
-        repo.html.editor(branch, repository, paths.take(paths.size - 1).toList, Some(paths.last),
+        html.editor(branch, repository, paths.take(paths.size - 1).toList, Some(paths.last),
           JGitUtil.getContentInfo(git, path, objectId))
       } getOrElse NotFound
     }
@@ -163,7 +167,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
 
       getPathObjectId(git, path, revCommit).map { objectId =>
         val paths = path.split("/")
-        repo.html.delete(branch, repository, paths.take(paths.size - 1).toList, paths.last,
+        html.delete(branch, repository, paths.take(paths.size - 1).toList, paths.last,
           JGitUtil.getContentInfo(git, path, objectId))
       } getOrElse NotFound
     }
@@ -214,11 +218,10 @@ trait RepositoryViewerControllerBase extends ControllerBase {
         if(raw){
           // Download
           defining(JGitUtil.getContentFromId(git, objectId, false).get){ bytes =>
-            contentType = FileUtil.getContentType(path, bytes)
-            bytes
+            RawData(FileUtil.getContentType(path, bytes), bytes)
           }
         } else {
-          repo.html.blob(id, repository, path.split("/").toList, JGitUtil.getContentInfo(git, path, objectId),
+          html.blob(id, repository, path.split("/").toList, JGitUtil.getContentInfo(git, path, objectId),
             new JGitUtil.CommitInfo(lastModifiedCommit), hasWritePermission(repository.owner, repository.name, context.loginAccount))
         }
       } getOrElse NotFound
@@ -234,7 +237,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     using(Git.open(getRepositoryDir(repository.owner, repository.name))){ git =>
       defining(JGitUtil.getRevCommitFromId(git, git.getRepository.resolve(id))){ revCommit =>
         JGitUtil.getDiffs(git, id) match { case (diffs, oldCommitId) =>
-          repo.html.commit(id, new JGitUtil.CommitInfo(revCommit),
+          html.commit(id, new JGitUtil.CommitInfo(revCommit),
             JGitUtil.getBranchesOfCommit(git, revCommit.getName),
             JGitUtil.getTagsOfCommit(git, revCommit.getName),
             getCommitComments(repository.owner, repository.name, id, false),
@@ -247,20 +250,23 @@ trait RepositoryViewerControllerBase extends ControllerBase {
   post("/:owner/:repository/commit/:id/comment/new", commentForm)(readableUsersOnly { (form, repository) =>
     val id = params("id")
     createCommitComment(repository.owner, repository.name, id, context.loginAccount.get.userName, form.content,
-      form.fileName, form.oldLineNumber, form.newLineNumber, form.pullRequest)
-    recordCommentCommitActivity(repository.owner, repository.name, context.loginAccount.get.userName, id, form.content)
+      form.fileName, form.oldLineNumber, form.newLineNumber, form.issueId.isDefined)
+    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}")
   })
 
   ajaxGet("/:owner/:repository/commit/:id/comment/_form")(readableUsersOnly { repository =>
     val id            = params("id")
     val fileName      = params.get("fileName")
-    val oldLineNumber = params.get("oldLineNumber") flatMap {b => Some(b.toInt)}
-    val newLineNumber = params.get("newLineNumber") flatMap {b => Some(b.toInt)}
-    val pullRequest   = params.get("pullRequest")
-    repo.html.commentform(
+    val oldLineNumber = params.get("oldLineNumber") map (_.toInt)
+    val newLineNumber = params.get("newLineNumber") map (_.toInt)
+    val issueId   = params.get("issueId") map (_.toInt)
+    html.commentform(
       commitId = id,
-      fileName, oldLineNumber, newLineNumber, pullRequest.map(_.toBoolean).getOrElse(false),
+      fileName, oldLineNumber, newLineNumber, issueId,
       hasWritePermission = hasWritePermission(repository.owner, repository.name, context.loginAccount),
       repository = repository
     )
@@ -269,8 +275,11 @@ trait RepositoryViewerControllerBase extends ControllerBase {
   ajaxPost("/:owner/:repository/commit/:id/comment/_data/new", commentForm)(readableUsersOnly { (form, repository) =>
     val id = params("id")
     val commentId = createCommitComment(repository.owner, repository.name, id, context.loginAccount.get.userName,
-      form.content, form.fileName, form.oldLineNumber, form.newLineNumber, form.pullRequest)
-    recordCommentCommitActivity(repository.owner, repository.name, context.loginAccount.get.userName, id, form.content)
+      form.content, form.fileName, form.oldLineNumber, form.newLineNumber, form.issueId.isDefined)
+    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)
+    }
     helper.html.commitcomment(getCommitComment(repository.owner, repository.name, commentId.toString).get,
       hasWritePermission(repository.owner, repository.name, context.loginAccount), repository)
   })
@@ -279,7 +288,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     getCommitComment(repository.owner, repository.name, params("id")) map { x =>
       if(isEditable(x.userName, x.repositoryName, x.commentedUserName)){
         params.get("dataType") collect {
-          case t if t == "html" => repo.html.editcomment(
+          case t if t == "html" => html.editcomment(
             x.content, x.commentId, x.userName, x.repositoryName)
         } getOrElse {
           contentType = formats("json")
@@ -317,14 +326,11 @@ trait RepositoryViewerControllerBase extends ControllerBase {
    * Displays branches.
    */
   get("/:owner/:repository/branches")(referrersOnly { repository =>
-    using(Git.open(getRepositoryDir(repository.owner, repository.name))){ git =>
-      // retrieve latest update date of each branch
-      val branchInfo = repository.branchList.map { branchName =>
-        val revCommit = git.log.add(git.getRepository.resolve(branchName)).setMaxCount(1).call.iterator.next
-        (branchName, revCommit.getCommitterIdent.getWhen)
-      }
-      repo.html.branches(branchInfo, hasWritePermission(repository.owner, repository.name, context.loginAccount), repository)
-    }
+    val branches = JGitUtil.getBranches(repository.owner, repository.name, repository.repository.defaultBranch)
+      .sortBy(br => (br.mergeInfo.isEmpty, br.commitTime))
+      .map(br => br -> getPullRequestByRequestCommit(repository.owner, repository.name, repository.repository.defaultBranch, br.name, br.commitId))
+      .reverse
+    html.branches(branches, hasWritePermission(repository.owner, repository.name, context.loginAccount), repository)
   })
 
   /**
@@ -364,7 +370,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
    * Displays tags.
    */
   get("/:owner/:repository/tags")(referrersOnly {
-    repo.html.tags(_)
+    html.tags(_)
   })
 
   /**
@@ -381,7 +387,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
   })
 
   get("/:owner/:repository/network/members")(referrersOnly { repository =>
-    repo.html.forked(
+    html.forked(
       getRepository(
         repository.repository.originUserName.getOrElse(repository.owner),
         repository.repository.originRepositoryName.getOrElse(repository.name),
@@ -392,7 +398,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
       repository)
   })
 
-  private def splitPath(repository: service.RepositoryService.RepositoryInfo, path: String): (String, String) = {
+  private def splitPath(repository: RepositoryService.RepositoryInfo, path: String): (String, String) = {
     val id = repository.branchList.collectFirst {
       case branch if(path == branch || path.startsWith(branch + "/")) => branch
     } orElse repository.tags.collectFirst {
@@ -415,7 +421,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
    */
   private def fileList(repository: RepositoryService.RepositoryInfo, revstr: String = "", path: String = ".") = {
     if(repository.commitCount == 0){
-      repo.html.guide(repository, hasWritePermission(repository.owner, repository.name, context.loginAccount))
+      html.guide(repository, hasWritePermission(repository.owner, repository.name, context.loginAccount))
     } else {
       using(Git.open(getRepositoryDir(repository.owner, repository.name))){ git =>
         // get specified commit
@@ -434,8 +440,12 @@ trait RepositoryViewerControllerBase extends ControllerBase {
                 Git.open(getRepositoryDir(repository.owner, repository.name)), file.id, true).get)
             }
 
-            repo.html.files(revision, repository,
+            html.files(revision, repository,
               if(path == ".") Nil else path.split("/").toList, // current path
+              context.loginAccount match {
+                case None => List()
+                case account: Option[Account] => getGroupsByUserName(account.get.userName)
+              }, // groups of current user
               new JGitUtil.CommitInfo(lastModifiedCommit), // last modified commit
               files, readme, hasWritePermission(repository.owner, repository.name, context.loginAccount),
               flash.get("info"), flash.get("error"))
@@ -445,7 +455,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     }
   }
 
-  private def commitFile(repository: service.RepositoryService.RepositoryInfo,
+  private def commitFile(repository: RepositoryService.RepositoryInfo,
                          branch: String, path: String, newFileName: Option[String], oldFileName: Option[String],
                          content: String, charset: String, message: String) = {
 
@@ -486,6 +496,9 @@ trait RepositoryViewerControllerBase extends ControllerBase {
         //refUpdate.setRefLogMessage("merged", true)
         refUpdate.update()
 
+        // update pull request
+        updatePullRequests(repository.owner, repository.name, branch)
+
         // record activity
         recordPushActivity(repository.owner, repository.name, loginAccount.userName, branch,
           List(new CommitInfo(JGitUtil.getRevCommitFromId(git, commitId))))
@@ -522,7 +535,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     }
   }
 
-  private def archiveRepository(name: String, suffix: String, repository: RepositoryService.RepositoryInfo): File = {
+  private def archiveRepository(name: String, suffix: String, repository: RepositoryService.RepositoryInfo): Unit = {
     val revision = name.stripSuffix(suffix)
     val workDir = getDownloadWorkDir(repository.owner, repository.name, session.getId)
     if(workDir.exists) {
@@ -530,24 +543,26 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     }
     workDir.mkdirs
 
-    val file = new File(workDir, repository.name + "-" +
-      (if(revision.length == 40) revision.substring(0, 10) else revision).replace('/', '_') + suffix)
+    val filename = repository.name + "-" +
+      (if(revision.length == 40) revision.substring(0, 10) else revision).replace('/', '_') + suffix
 
     using(Git.open(getRepositoryDir(repository.owner, repository.name))){ git =>
       val revCommit = JGitUtil.getRevCommitFromId(git, git.getRepository.resolve(revision))
-      using(new java.io.FileOutputStream(file))  { out =>
-        git.archive
-           .setFormat(suffix.tail)
-           .setTree(revCommit.getTree)
-           .setOutputStream(out)
-           .call()
-      }
+
       contentType = "application/octet-stream"
-      response.setHeader("Content-Disposition", s"attachment; filename=${file.getName}")
-      file
+      response.setHeader("Content-Disposition", s"attachment; filename=${filename}")
+      response.setBufferSize(1024 * 1024);
+
+      git.archive
+         .setFormat(suffix.tail)
+         .setTree(revCommit.getTree)
+         .setOutputStream(response.getOutputStream)
+         .call()
+
+      Unit
     }
   }
 
-  private def isEditable(owner: String, repository: String, author: String)(implicit context: app.Context): Boolean =
+  private def isEditable(owner: String, repository: String, author: String)(implicit context: Context): Boolean =
     hasWritePermission(owner, repository, context.loginAccount) || author == context.loginAccount.get.userName
 }

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

@@ -1,9 +1,10 @@
-package app
+package gitbucket.core.controller
 
-import util._
+import gitbucket.core.search.html
+import gitbucket.core.service._
+import gitbucket.core.util.{StringUtil, ControlUtil, ReferrerAuthenticator, Implicits}
 import ControlUtil._
 import Implicits._
-import service._
 import jp.sf.amateras.scalatra.forms._
 
 class SearchController extends SearchControllerBase
@@ -34,12 +35,12 @@ trait SearchControllerBase extends ControllerBase { self: RepositoryService
       }
 
       target.toLowerCase match {
-        case "issue" => search.html.issues(
+        case "issue" => html.issues(
           searchIssues(repository.owner, repository.name, query),
           countFiles(repository.owner, repository.name, query),
           query, page, repository)
 
-        case _ => search.html.code(
+        case _ => html.code(
           searchFiles(repository.owner, repository.name, query),
           countIssues(repository.owner, repository.name, query),
           query, page, repository)

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

@@ -0,0 +1,85 @@
+package gitbucket.core.controller
+
+import gitbucket.core.admin.html
+import gitbucket.core.service.{AccountService, SystemSettingsService}
+import gitbucket.core.util.AdminAuthenticator
+import gitbucket.core.ssh.SshServer
+import SystemSettingsService._
+import jp.sf.amateras.scalatra.forms._
+
+class SystemSettingsController extends SystemSettingsControllerBase
+  with AccountService with AdminAuthenticator
+
+trait SystemSettingsControllerBase extends ControllerBase {
+  self: AccountService with AdminAuthenticator =>
+
+  private val form = mapping(
+    "baseUrl"                  -> trim(label("Base URL", optional(text()))),
+    "information"              -> trim(label("Information", optional(text()))),
+    "allowAccountRegistration" -> trim(label("Account registration", boolean())),
+    "allowAnonymousAccess"     -> trim(label("Anonymous access", boolean())),
+    "isCreateRepoOptionPublic" -> trim(label("Default option to create a new repository", boolean())),
+    "gravatar"                 -> trim(label("Gravatar", boolean())),
+    "notification"             -> trim(label("Notification", boolean())),
+    "ssh"                      -> trim(label("SSH access", boolean())),
+    "sshPort"                  -> trim(label("SSH port", optional(number()))),
+    "smtp"                     -> optionalIfNotChecked("notification", mapping(
+        "host"                     -> trim(label("SMTP Host", text(required))),
+        "port"                     -> trim(label("SMTP Port", optional(number()))),
+        "user"                     -> trim(label("SMTP User", optional(text()))),
+        "password"                 -> trim(label("SMTP Password", optional(text()))),
+        "ssl"                      -> trim(label("Enable SSL", optional(boolean()))),
+        "fromAddress"              -> trim(label("FROM Address", optional(text()))),
+        "fromName"                 -> trim(label("FROM Name", optional(text())))
+    )(Smtp.apply)),
+    "ldapAuthentication"       -> trim(label("LDAP", boolean())),
+    "ldap"                     -> optionalIfNotChecked("ldapAuthentication", mapping(
+        "host"                     -> trim(label("LDAP host", text(required))),
+        "port"                     -> trim(label("LDAP port", optional(number()))),
+        "bindDN"                   -> trim(label("Bind DN", optional(text()))),
+        "bindPassword"             -> trim(label("Bind Password", optional(text()))),
+        "baseDN"                   -> trim(label("Base DN", text(required))),
+        "userNameAttribute"        -> trim(label("User name attribute", text(required))),
+        "additionalFilterCondition"-> trim(label("Additional filter condition", optional(text()))),
+        "fullNameAttribute"        -> trim(label("Full name attribute", optional(text()))),
+        "mailAttribute"            -> trim(label("Mail address attribute", optional(text()))),
+        "tls"                      -> trim(label("Enable TLS", optional(boolean()))),
+        "ssl"                      -> trim(label("Enable SSL", optional(boolean()))),
+        "keystore"                 -> trim(label("Keystore", optional(text())))
+    )(Ldap.apply))
+  )(SystemSettings.apply).verifying { settings =>
+    if(settings.ssh && settings.baseUrl.isEmpty){
+      Seq("baseUrl" -> "Base URL is required if SSH access is enabled.")
+    } else Nil
+  }
+
+  private val pluginForm = mapping(
+    "pluginId" -> list(trim(label("", text())))
+  )(PluginForm.apply)
+
+  case class PluginForm(pluginIds: List[String])
+
+  get("/admin/system")(adminOnly {
+    html.system(flash.get("info"))
+  })
+
+  post("/admin/system", form)(adminOnly { form =>
+    saveSystemSettings(form)
+
+    if(form.ssh && SshServer.isActive && context.settings.sshPort != form.sshPort){
+      SshServer.stop()
+    }
+
+    if(form.ssh && !SshServer.isActive && form.baseUrl.isDefined){
+      SshServer.start(
+        form.sshPort.getOrElse(SystemSettingsService.DefaultSshPort),
+        form.baseUrl.get)
+    } else if(!form.ssh && SshServer.isActive){
+      SshServer.stop()
+    }
+
+    flash += "info" -> "System settings has been updated."
+    redirect("/admin/system")
+  })
+
+}

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

@@ -1,11 +1,12 @@
-package app
+package gitbucket.core.controller
 
-import service._
-import util.AdminAuthenticator
-import util.StringUtil._
-import util.ControlUtil._
-import util.Directory._
-import util.Implicits._
+import gitbucket.core.service.{RepositoryService, AccountService}
+import gitbucket.core.admin.users.html
+import gitbucket.core.util._
+import gitbucket.core.util.ControlUtil._
+import gitbucket.core.util.StringUtil._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.Directory._
 import jp.sf.amateras.scalatra.forms._
 import org.scalatra.i18n.Messages
 import org.apache.commons.io.FileUtils
@@ -75,11 +76,11 @@ trait UserManagementControllerBase extends AccountManagementControllerBase {
       account.userName -> getGroupMembers(account.userName).map(_.userName)
     }.toMap
 
-    admin.users.html.list(users, members, includeRemoved)
+    html.list(users, members, includeRemoved)
   })
   
   get("/admin/users/_newuser")(adminOnly {
-    admin.users.html.user(None)
+    html.user(None)
   })
   
   post("/admin/users/_newuser", newUserForm)(adminOnly { form =>
@@ -90,7 +91,7 @@ trait UserManagementControllerBase extends AccountManagementControllerBase {
   
   get("/admin/users/:userName/_edituser")(adminOnly {
     val userName = params("userName")
-    admin.users.html.user(getAccountByUserName(userName, true))
+    html.user(getAccountByUserName(userName, true))
   })
   
   post("/admin/users/:name/_edituser", editUserForm)(adminOnly { form =>
@@ -124,7 +125,7 @@ trait UserManagementControllerBase extends AccountManagementControllerBase {
   })
 
   get("/admin/users/_newgroup")(adminOnly {
-    admin.users.html.group(None, Nil)
+    html.group(None, Nil)
   })
 
   post("/admin/users/_newgroup", newGroupForm)(adminOnly { form =>
@@ -140,7 +141,7 @@ trait UserManagementControllerBase extends AccountManagementControllerBase {
 
   get("/admin/users/:groupName/_editgroup")(adminOnly {
     defining(params("groupName")){ groupName =>
-      admin.users.html.group(getAccountByUserName(groupName, true), getGroupMembers(groupName))
+      html.group(getAccountByUserName(groupName, true), getGroupMembers(groupName))
     }
   })
 

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

@@ -1,14 +1,14 @@
-package app
+package gitbucket.core.controller
 
-import service._
-import util._
-import util.Directory._
-import util.ControlUtil._
-import util.Implicits._
+import gitbucket.core.wiki.html
+import gitbucket.core.service.{RepositoryService, WikiService, ActivityService, AccountService}
+import gitbucket.core.util._
+import gitbucket.core.util.ControlUtil._
+import gitbucket.core.util.Implicits._
+import gitbucket.core.util.Directory._
 import jp.sf.amateras.scalatra.forms._
 import org.eclipse.jgit.api.Git
 import org.scalatra.i18n.Messages
-import java.util.ResourceBundle
 
 class WikiController extends WikiControllerBase 
   with WikiService with RepositoryService with AccountService with ActivityService with CollaboratorsAuthenticator with ReferrerAuthenticator
@@ -36,7 +36,7 @@ trait WikiControllerBase extends ControllerBase {
   
   get("/:owner/:repository/wiki")(referrersOnly { repository =>
     getWikiPage(repository.owner, repository.name, "Home").map { page =>
-      wiki.html.page("Home", page, getWikiPageList(repository.owner, repository.name),
+      html.page("Home", page, getWikiPageList(repository.owner, repository.name),
         repository, hasWritePermission(repository.owner, repository.name, context.loginAccount))
     } getOrElse redirect(s"/${repository.owner}/${repository.name}/wiki/Home/_edit")
   })
@@ -45,7 +45,7 @@ trait WikiControllerBase extends ControllerBase {
     val pageName = StringUtil.urlDecode(params("page"))
 
     getWikiPage(repository.owner, repository.name, pageName).map { page =>
-      wiki.html.page(pageName, page, getWikiPageList(repository.owner, repository.name),
+      html.page(pageName, page, getWikiPageList(repository.owner, repository.name),
         repository, hasWritePermission(repository.owner, repository.name, context.loginAccount))
     } getOrElse redirect(s"/${repository.owner}/${repository.name}/wiki/${StringUtil.urlEncode(pageName)}/_edit")
   })
@@ -55,7 +55,7 @@ trait WikiControllerBase extends ControllerBase {
 
     using(Git.open(getWikiRepositoryDir(repository.owner, repository.name))){ git =>
       JGitUtil.getCommitLog(git, "master", path = pageName + ".md") match {
-        case Right((logs, hasNext)) => wiki.html.history(Some(pageName), logs, repository)
+        case Right((logs, hasNext)) => html.history(Some(pageName), logs, repository)
         case Left(_) => NotFound
       }
     }
@@ -66,7 +66,7 @@ trait WikiControllerBase extends ControllerBase {
     val Array(from, to) = params("commitId").split("\\.\\.\\.")
 
     using(Git.open(getWikiRepositoryDir(repository.owner, repository.name))){ git =>
-      wiki.html.compare(Some(pageName), from, to, JGitUtil.getDiffs(git, from, to, true).filter(_.newPath == pageName + ".md"), repository,
+      html.compare(Some(pageName), from, to, JGitUtil.getDiffs(git, from, to, true).filter(_.newPath == pageName + ".md"), repository,
         hasWritePermission(repository.owner, repository.name, context.loginAccount), flash.get("info"))
     }
   })
@@ -75,7 +75,7 @@ trait WikiControllerBase extends ControllerBase {
     val Array(from, to) = params("commitId").split("\\.\\.\\.")
 
     using(Git.open(getWikiRepositoryDir(repository.owner, repository.name))){ git =>
-      wiki.html.compare(None, from, to, JGitUtil.getDiffs(git, from, to, true), repository,
+      html.compare(None, from, to, JGitUtil.getDiffs(git, from, to, true), repository,
         hasWritePermission(repository.owner, repository.name, context.loginAccount), flash.get("info"))
     }
   })
@@ -105,7 +105,7 @@ trait WikiControllerBase extends ControllerBase {
 
   get("/:owner/:repository/wiki/:page/_edit")(collaboratorsOnly { repository =>
     val pageName = StringUtil.urlDecode(params("page"))
-    wiki.html.edit(pageName, getWikiPage(repository.owner, repository.name, pageName), repository)
+    html.edit(pageName, getWikiPage(repository.owner, repository.name, pageName), repository)
   })
   
   post("/:owner/:repository/wiki/_edit", editForm)(collaboratorsOnly { (form, repository) =>
@@ -120,7 +120,7 @@ trait WikiControllerBase extends ControllerBase {
   })
   
   get("/:owner/:repository/wiki/_new")(collaboratorsOnly {
-    wiki.html.edit("", None, _)
+    html.edit("", None, _)
   })
   
   post("/:owner/:repository/wiki/_new", newForm)(collaboratorsOnly { (form, repository) =>
@@ -147,14 +147,14 @@ trait WikiControllerBase extends ControllerBase {
   })
   
   get("/:owner/:repository/wiki/_pages")(referrersOnly { repository =>
-    wiki.html.pages(getWikiPageList(repository.owner, repository.name), repository,
+    html.pages(getWikiPageList(repository.owner, repository.name), repository,
       hasWritePermission(repository.owner, repository.name, context.loginAccount))
   })
   
   get("/:owner/:repository/wiki/_history")(referrersOnly { repository =>
     using(Git.open(getWikiRepositoryDir(repository.owner, repository.name))){ git =>
       JGitUtil.getCommitLog(git, "master") match {
-        case Right((logs, hasNext)) => wiki.html.history(None, logs, repository)
+        case Right((logs, hasNext)) => html.history(None, logs, repository)
         case Left(_) => NotFound
       }
     }
@@ -164,8 +164,7 @@ trait WikiControllerBase extends ControllerBase {
     val path = multiParams("splat").head
 
     getFileContent(repository.owner, repository.name, path).map { bytes =>
-      contentType = FileUtil.getContentType(path, bytes)
-      bytes
+      RawData(FileUtil.getContentType(path, bytes), bytes)
     } getOrElse NotFound
   })
 

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait AccountComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait ActivityComponent extends TemplateComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 protected[model] trait TemplateComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait CollaboratorComponent extends TemplateComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait Comment {
   val commentedUserName: String

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait GroupMemberComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait IssueComponent extends TemplateComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait IssueLabelComponent extends TemplateComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait LabelComponent extends TemplateComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait MilestoneComponent extends TemplateComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait PluginComponent extends TemplateComponent { self: Profile =>
   import profile.simple._

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

@@ -1,25 +1,37 @@
-package model
+package gitbucket.core.model
 
 trait Profile {
   val profile: slick.driver.JdbcProfile
   import profile.simple._
 
-  // java.util.Date Mapped Column Types
+  /**
+   * java.util.Date Mapped Column Types
+   */
   implicit val dateColumnType = MappedColumnType.base[java.util.Date, java.sql.Timestamp](
-      d => new java.sql.Timestamp(d.getTime),
-      t => new java.util.Date(t.getTime)
+    d => new java.sql.Timestamp(d.getTime),
+    t => new java.util.Date(t.getTime)
   )
 
+  /**
+   * Extends Column to add conditional condition
+   */
   implicit class RichColumn(c1: Column[Boolean]){
     def &&(c2: => Column[Boolean], guard: => Boolean): Column[Boolean] = if(guard) c1 && c2 else c1
   }
 
+  /**
+   * Returns system date.
+   */
+  def currentDate = new java.util.Date()
+
 }
 
-object Profile extends {
+trait ProfileProvider { self: Profile =>
   val profile = slick.driver.H2Driver
+}
 
-} with AccountComponent
+trait CoreProfile extends ProfileProvider with Profile
+  with AccountComponent
   with ActivityComponent
   with CollaboratorComponent
   with CommitCommentComponent
@@ -33,11 +45,6 @@ object Profile extends {
   with RepositoryComponent
   with SshKeyComponent
   with WebHookComponent
-  with PluginComponent with Profile {
+  with PluginComponent
 
-  /**
-   * Returns system date.
-   */
-  def currentDate = new java.util.Date()
-
-}
+object Profile extends CoreProfile

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait PullRequestComponent extends TemplateComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait RepositoryComponent extends TemplateComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait SshKeyComponent { self: Profile =>
   import profile.simple._

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

@@ -1,4 +1,4 @@
-package model
+package gitbucket.core.model
 
 trait WebHookComponent extends TemplateComponent { self: Profile =>
   import profile.simple._

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

@@ -1,3 +1,5 @@
+package gitbucket.core
+
 package object model {
   type Session = slick.jdbc.JdbcBackend#Session
 }

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

@@ -0,0 +1,10 @@
+package gitbucket.core.plugin
+
+/**
+ * Provides a helper method to generate data URI of images registered by plug-in.
+ */
+object Images {
+
+  def dataURI(id: String) = s"data:image/png;base64,${PluginRegistry().getImage(id)}"
+
+}

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

@@ -0,0 +1,28 @@
+package gitbucket.core.plugin
+
+import gitbucket.core.util.Version
+
+/**
+ * Trait for define plugin interface.
+ * To provide plugin, put Plugin class which mixed in this trait into the package root.
+ */
+trait Plugin {
+
+  val pluginId: String
+  val pluginName: String
+  val description: String
+  val versions: Seq[Version]
+
+  /**
+   * This method is invoked in initialization of plugin system.
+   * Register plugin functionality to PluginRegistry.
+   */
+  def initialize(registry: PluginRegistry): Unit
+
+  /**
+   * This method is invoked in shutdown of plugin system.
+   * If the plugin has any resources, release them in this method.
+   */
+  def shutdown(registry: PluginRegistry): Unit
+
+}

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

@@ -0,0 +1,161 @@
+package gitbucket.core.plugin
+
+import java.io.{File, FilenameFilter, InputStream}
+import java.net.URLClassLoader
+import javax.servlet.ServletContext
+import javax.servlet.http.{HttpServletRequest, HttpServletResponse}
+
+import gitbucket.core.controller.{Context, ControllerBase}
+import gitbucket.core.service.RepositoryService.RepositoryInfo
+import gitbucket.core.util.ControlUtil._
+import gitbucket.core.util.Directory._
+import gitbucket.core.util.JDBCUtil._
+import gitbucket.core.util.{Version, Versions}
+import org.apache.commons.codec.binary.{Base64, StringUtils}
+import org.slf4j.LoggerFactory
+
+import scala.collection.mutable
+import scala.collection.mutable.ListBuffer
+
+class PluginRegistry {
+
+  private val plugins = new ListBuffer[PluginInfo]
+  private val javaScripts = new ListBuffer[(String, String)]
+  private val controllers = new ListBuffer[(ControllerBase, String)]
+  private val images = mutable.Map[String, String]()
+
+  def addPlugin(pluginInfo: PluginInfo): Unit = {
+    plugins += pluginInfo
+  }
+
+  def getPlugins(): List[PluginInfo] = plugins.toList
+
+  def addImage(id: String, in: InputStream): Unit = {
+    val bytes = using(in){ in =>
+      val bytes = new Array[Byte](in.available)
+      in.read(bytes)
+      bytes
+    }
+    val encoded = StringUtils.newStringUtf8(Base64.encodeBase64(bytes, false))
+    images += ((id, encoded))
+  }
+
+  def getImage(id: String): String = images(id)
+
+  def addController(controller: ControllerBase, path: String): Unit = {
+    controllers += ((controller, path))
+  }
+
+  def getControllers(): List[(ControllerBase, String)] = controllers.toList
+
+  def addJavaScript(path: String, script: String): Unit = {
+    javaScripts += Tuple2(path, script)
+  }
+
+  //def getJavaScripts(): List[(String, String)] = javaScripts.toList
+
+  def getJavaScript(currentPath: String): Option[String] = {
+    javaScripts.find(x => currentPath.matches(x._1)).map(_._2)
+  }
+
+  private case class GlobalAction(
+    method: String,
+    path: String,
+    function: (HttpServletRequest, HttpServletResponse, Context) => Any
+  )
+
+  private case class RepositoryAction(
+    method: String,
+    path: String,
+    function: (HttpServletRequest, HttpServletResponse, Context, RepositoryInfo) => Any
+  )
+
+}
+
+/**
+ * Provides entry point to PluginRegistry.
+ */
+object PluginRegistry {
+
+  private val logger = LoggerFactory.getLogger(classOf[PluginRegistry])
+
+  private val instance = new PluginRegistry()
+
+  /**
+   * Returns the PluginRegistry singleton instance.
+   */
+  def apply(): PluginRegistry = instance
+
+  /**
+   * Initializes all installed plugins.
+   */
+  def initialize(context: ServletContext, conn: java.sql.Connection): Unit = {
+    val pluginDir = new File(PluginHome)
+    if(pluginDir.exists && pluginDir.isDirectory){
+      pluginDir.listFiles(new FilenameFilter {
+        override def accept(dir: File, name: String): Boolean = name.endsWith(".jar")
+      }).foreach { pluginJar =>
+        val classLoader = new URLClassLoader(Array(pluginJar.toURI.toURL), Thread.currentThread.getContextClassLoader)
+        try {
+          val plugin = classLoader.loadClass("Plugin").newInstance().asInstanceOf[Plugin]
+
+          // Migration
+          val headVersion = plugin.versions.head
+          val currentVersion = conn.find("SELECT * FROM PLUGIN WHERE PLUGIN_ID = ?", plugin.pluginId)(_.getString("VERSION")) match {
+            case Some(x) => {
+              val dim = x.split("\\.")
+              Version(dim(0).toInt, dim(1).toInt)
+            }
+            case None => Version(0, 0)
+          }
+
+          Versions.update(conn, headVersion, currentVersion, plugin.versions, new URLClassLoader(Array(pluginJar.toURI.toURL))){ conn =>
+            currentVersion.versionString match {
+              case "0.0" =>
+                conn.update("INSERT INTO PLUGIN (PLUGIN_ID, VERSION) VALUES (?, ?)", plugin.pluginId, headVersion.versionString)
+              case _ =>
+                conn.update("UPDATE PLUGIN SET VERSION = ? WHERE PLUGIN_ID = ?", headVersion.versionString, plugin.pluginId)
+            }
+          }
+
+          // Initialize
+          plugin.initialize(instance)
+          instance.addPlugin(PluginInfo(
+            pluginId    = plugin.pluginId,
+            pluginName  = plugin.pluginName,
+            version     = plugin.versions.head.versionString,
+            description = plugin.description,
+            pluginClass = plugin
+          ))
+
+        } catch {
+          case e: Exception => {
+            logger.error(s"Error during plugin initialization", e)
+          }
+        }
+      }
+    }
+  }
+
+  def shutdown(context: ServletContext): Unit = {
+    instance.getPlugins().foreach { pluginInfo =>
+      try {
+        pluginInfo.pluginClass.shutdown(instance)
+      } catch {
+        case e: Exception => {
+          logger.error(s"Error during plugin shutdown", e)
+        }
+      }
+    }
+  }
+
+
+}
+
+case class PluginInfo(
+  pluginId: String,
+  pluginName: String,
+  version: String,
+  description: String,
+  pluginClass: Plugin
+)

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

@@ -0,0 +1,11 @@
+package gitbucket.core.plugin
+
+import play.twirl.api.Html
+
+/**
+ * Defines result case classes returned by plugin controller.
+ */
+object Results {
+  case class Redirect(path: String)
+  case class Fragment(html: Html)
+}

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

@@ -0,0 +1,11 @@
+package gitbucket.core.plugin
+
+import scala.slick.jdbc.JdbcBackend.Session
+
+/**
+ * Provides Slick Session to Plug-ins.
+ */
+object Sessions {
+  val sessions = new ThreadLocal[Session]
+  implicit def session: Session = sessions.get()
+}

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

@@ -1,14 +1,14 @@
-package service
+package gitbucket.core.service
 
-import model.Profile._
+import gitbucket.core.model.{GroupMember, Account}
+import gitbucket.core.model.Profile._
+import gitbucket.core.util.{StringUtil, LDAPUtil}
+import gitbucket.core.service.SystemSettingsService.SystemSettings
 import profile.simple._
-import model.{Account, GroupMember}
-// TODO [Slick 2.0]NOT import directly?
-import model.Profile.dateColumnType
-import service.SystemSettingsService.SystemSettings
-import util.StringUtil._
-import util.LDAPUtil
+import StringUtil._
 import org.slf4j.LoggerFactory
+// TODO Why is direct import required?
+import gitbucket.core.model.Profile.dateColumnType
 
 trait AccountService {
 

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

@@ -1,8 +1,9 @@
-package service
+package gitbucket.core.service
 
-import model.Profile._
+import gitbucket.core.model.Activity
+import gitbucket.core.model.Profile._
+import gitbucket.core.util.JGitUtil
 import profile.simple._
-import model.Activity
 
 trait ActivityService {
 
@@ -121,7 +122,7 @@ trait ActivityService {
       currentDate)
 
   def recordPushActivity(userName: String, repositoryName: String, activityUserName: String,
-      branchName: String, commits: List[util.JGitUtil.CommitInfo])(implicit s: Session): Unit =
+      branchName: String, commits: List[JGitUtil.CommitInfo])(implicit s: Session): Unit =
     Activities insert Activity(userName, repositoryName, activityUserName,
       "push",
       s"[user:${activityUserName}] pushed to [branch:${userName}/${repositoryName}#${branchName}] at [repo:${userName}/${repositoryName}]",
@@ -129,7 +130,7 @@ trait ActivityService {
       currentDate)
 
   def recordCreateTagActivity(userName: String, repositoryName: String, activityUserName: String, 
-      tagName: String, commits: List[util.JGitUtil.CommitInfo])(implicit s: Session): Unit =
+      tagName: String, commits: List[JGitUtil.CommitInfo])(implicit s: Session): Unit =
     Activities insert Activity(userName, repositoryName, activityUserName,
       "create_tag",
       s"[user:${activityUserName}] created tag [tag:${userName}/${repositoryName}#${tagName}] at [repo:${userName}/${repositoryName}]",
@@ -137,7 +138,7 @@ trait ActivityService {
       currentDate)
 
   def recordDeleteTagActivity(userName: String, repositoryName: String, activityUserName: String,
-                              tagName: String, commits: List[util.JGitUtil.CommitInfo])(implicit s: Session): Unit =
+                              tagName: String, commits: List[JGitUtil.CommitInfo])(implicit s: Session): Unit =
     Activities insert Activity(userName, repositoryName, activityUserName,
       "delete_tag",
       s"[user:${activityUserName}] deleted tag ${tagName} at [repo:${userName}/${repositoryName}]",
@@ -160,10 +161,10 @@ trait ActivityService {
       None,
       currentDate)
 
-  def recordForkActivity(userName: String, repositoryName: String, activityUserName: String)(implicit s: Session): Unit =
+  def recordForkActivity(userName: String, repositoryName: String, activityUserName: String, forkedUserName: String)(implicit s: Session): Unit = 
     Activities insert Activity(userName, repositoryName, activityUserName,
       "fork",
-      s"[user:${activityUserName}] forked [repo:${userName}/${repositoryName}] to [repo:${activityUserName}/${repositoryName}]",
+      s"[user:${activityUserName}] forked [repo:${userName}/${repositoryName}] to [repo:${forkedUserName}/${repositoryName}]",
       None,
       currentDate)
 

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

@@ -1,13 +1,14 @@
-package service
+package gitbucket.core.service
+
+import gitbucket.core.model.CommitComment
+import gitbucket.core.util.{StringUtil, Implicits}
 
 import scala.slick.jdbc.{StaticQuery => Q}
 import Q.interpolation
-
-import model.Profile._
+import gitbucket.core.model.Profile._
 import profile.simple._
-import model.CommitComment
-import util.Implicits._
-import util.StringUtil._
+import Implicits._
+import StringUtil._
 
 
 trait CommitsService {

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

@@ -1,13 +1,13 @@
-package service
+package gitbucket.core.service
 
+import gitbucket.core.model._
+import gitbucket.core.util.StringUtil._
+import gitbucket.core.util.Implicits._
 import scala.slick.jdbc.{StaticQuery => Q}
 import Q.interpolation
 
-import model.Profile._
+import gitbucket.core.model.Profile._
 import profile.simple._
-import model.{Issue, IssueComment, IssueLabel, Label}
-import util.Implicits._
-import util.StringUtil._
 
 trait IssuesService {
   import IssuesService._
@@ -139,11 +139,16 @@ trait IssuesService {
         .map { case (owner, repository) => t1.byRepository(owner, repository) }
         .foldLeft[Column[Boolean]](false) ( _ || _ ) &&
       (t1.closed           === (condition.state == "closed").bind) &&
-      (t1.milestoneId      === condition.milestoneId.get.get.bind, condition.milestoneId.flatten.isDefined) &&
-      (t1.milestoneId.?    isEmpty, condition.milestoneId == Some(None)) &&
+      //(t1.milestoneId      === condition.milestoneId.get.get.bind, condition.milestoneId.flatten.isDefined) &&
+      (t1.milestoneId.?    isEmpty, condition.milestone == Some(None)) &&
       (t1.assignedUserName === condition.assigned.get.bind, condition.assigned.isDefined) &&
       (t1.openedUserName   === condition.author.get.bind, condition.author.isDefined) &&
       (t1.pullRequest      === pullRequest.bind) &&
+      // Milestone filter
+      (Milestones filter { t2 =>
+        (t2.byPrimaryKey(t1.userName, t1.repositoryName, t1.milestoneId)) &&
+        (t2.title === condition.milestone.get.get.bind)
+      } exists, condition.milestone.flatten.isDefined) &&
       // Label filter
       (IssueLabels filter { t2 =>
         (t2.byIssue(t1.userName, t1.repositoryName, t1.issueId)) &&
@@ -322,7 +327,7 @@ object IssuesService {
 
   case class IssueSearchCondition(
       labels: Set[String] = Set.empty,
-      milestoneId: Option[Option[Int]] = None,
+      milestone: Option[Option[String]] = None,
       author: Option[String] = None,
       assigned: Option[String] = None,
       mentioned: Option[String] = None,
@@ -333,7 +338,7 @@ object IssuesService {
       groups: Set[String] = Set.empty){
 
     def isEmpty: Boolean = {
-      labels.isEmpty && milestoneId.isEmpty && author.isEmpty && assigned.isEmpty &&
+      labels.isEmpty && milestone.isEmpty && author.isEmpty && assigned.isEmpty &&
         state == "open" && sort == "created" && direction == "desc" && visibility.isEmpty
     }
 
@@ -348,8 +353,8 @@ object IssuesService {
       ).flatten ++
       labels.map(label => s"label:${label}") ++
       List(
-        milestoneId.map { _ match {
-          case Some(x) => s"milestone:${milestoneId}"
+        milestone.map { _ match {
+          case Some(x) => s"milestone:${x}"
           case None    => "no:milestone"
         }},
         (sort, direction) match {
@@ -368,8 +373,8 @@ object IssuesService {
     def toURL: String =
       "?" + List(
         if(labels.isEmpty) None else Some("labels=" + urlEncode(labels.mkString(","))),
-        milestoneId.map { _ match {
-          case Some(x) => "milestone=" + x
+        milestone.map { _ match {
+          case Some(x) => "milestone=" + urlEncode(x)
           case None    => "milestone=none"
         }},
         author   .map(x => "author="    + urlEncode(x)),
@@ -416,7 +421,7 @@ object IssuesService {
         conditions.get("milestone").flatMap(_.headOption) match {
           case None         => None
           case Some("none") => Some(None)
-          case Some(x)      => milestones.get(x).map(x => Some(x))
+          case Some(x)      => Some(Some(x)) //milestones.get(x).map(x => Some(x))
         },
         conditions.get("author").flatMap(_.headOption),
         conditions.get("assignee").flatMap(_.headOption),
@@ -437,7 +442,7 @@ object IssuesService {
         param(request, "labels").map(_.split(",").toSet).getOrElse(Set.empty),
         param(request, "milestone").map {
           case "none" => None
-          case x      => x.toIntOpt
+          case x      => Some(x)
         },
         param(request, "author"),
         param(request, "assigned"),

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

@@ -1,8 +1,8 @@
-package service
+package gitbucket.core.service
 
-import model.Profile._
+import gitbucket.core.model.Label
+import gitbucket.core.model.Profile._
 import profile.simple._
-import model.Label
 
 trait LabelsService {
 

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

@@ -1,10 +1,10 @@
-package service
+package gitbucket.core.service
 
-import model.Profile._
+import gitbucket.core.model.Milestone
+import gitbucket.core.model.Profile._
 import profile.simple._
-import model.Milestone
-// TODO [Slick 2.0]NOT import directly?
-import model.Profile.dateColumnType
+// TODO Why is direct import required?
+import gitbucket.core.model.Profile.dateColumnType
 
 trait MilestonesService {
 

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

@@ -1,8 +1,8 @@
-package service
+package gitbucket.core.service
 
-import model.Profile._
+import gitbucket.core.model.Plugin
+import gitbucket.core.model.Profile._
 import profile.simple._
-import model.Plugin
 
 trait PluginService {
 

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

@@ -1,8 +1,9 @@
-package service
+package gitbucket.core.service
 
-import model.Profile._
+import gitbucket.core.model.{Issue, PullRequest}
+import gitbucket.core.model.Profile._
+import gitbucket.core.util.JGitUtil
 import profile.simple._
-import model.{PullRequest, Issue}
 
 trait PullRequestService { self: IssuesService =>
   import PullRequestService._
@@ -81,6 +82,38 @@ trait PullRequestService { self: IssuesService =>
       .map { case (t1, t2) => t1 }
       .list
 
+  /**
+   * 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 =
+    getPullRequestsByRequest(owner, repository, branch, false).foreach { pullreq =>
+      if(Repositories.filter(_.byRepository(pullreq.userName, pullreq.repositoryName)).exists.run){
+        val (commitIdTo, commitIdFrom) = JGitUtil.updatePullRequest(
+          pullreq.userName, pullreq.repositoryName, pullreq.branch, pullreq.issueId,
+          pullreq.requestUserName, pullreq.requestRepositoryName, pullreq.requestBranch)
+        updateCommitId(pullreq.userName, pullreq.repositoryName, pullreq.issueId, commitIdTo, commitIdFrom)
+      }
+    }
+
+  def getPullRequestByRequestCommit(userName: String, repositoryName: String, toBranch:String, fromBranch: String, commitId: String)
+                              (implicit s: Session): Option[(PullRequest, Issue)] = {
+    if(toBranch == fromBranch){
+      None
+    } else {
+      PullRequests
+        .innerJoin(Issues).on { (t1, t2) => t1.byPrimaryKey(t2.userName, t2.repositoryName, t2.issueId) }
+        .filter { case (t1, t2) =>
+          (t1.userName              === userName.bind) &&
+          (t1.repositoryName        === repositoryName.bind) &&
+          (t1.branch                === toBranch.bind) &&
+          (t1.requestUserName       === userName.bind) &&
+          (t1.requestRepositoryName === repositoryName.bind) &&
+          (t1.requestBranch         === fromBranch.bind) &&
+          (t1.commitIdTo            === commitId.bind)
+        }
+        .firstOption
+    }
+  }
 }
 
 object PullRequestService {

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

@@ -1,13 +1,15 @@
-package service
+package gitbucket.core.service
 
-import util.{FileUtil, StringUtil, JGitUtil}
-import util.Directory._
-import util.ControlUtil._
+import gitbucket.core.model.Issue
+import gitbucket.core.util._
+import gitbucket.core.util.StringUtil
+import Directory._
+import ControlUtil._
 import org.eclipse.jgit.revwalk.RevWalk
 import org.eclipse.jgit.treewalk.TreeWalk
 import org.eclipse.jgit.lib.FileMode
 import org.eclipse.jgit.api.Git
-import model.Profile._
+import gitbucket.core.model.Profile._
 import profile.simple._
 
 trait RepositorySearchService { self: IssuesService =>
@@ -108,7 +110,7 @@ object RepositorySearchService {
 
   case class SearchResult(
     files : List[(String, String)],
-    issues: List[(model.Issue, Int, String)])
+    issues: List[(Issue, Int, String)])
 
   case class IssueSearchResult(
     issueId: Int,

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

@@ -1,9 +1,9 @@
-package service
+package gitbucket.core.service
 
-import model.Profile._
+import gitbucket.core.model.{Collaborator, Repository, Account}
+import gitbucket.core.model.Profile._
+import gitbucket.core.util.JGitUtil
 import profile.simple._
-import model.{Repository, Account, Collaborator}
-import util.JGitUtil
 
 trait RepositoryService { self: AccountService =>
   import RepositoryService._
@@ -94,9 +94,17 @@ trait RepositoryService { self: AccountService =>
         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)) :_*)
-        IssueLabels   .insertAll(issueLabels   .map(_.copy(userName = newUserName, repositoryName = newRepositoryName)) :_*)
         CommitComments.insertAll(commitComments.map(_.copy(userName = newUserName, repositoryName = 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
+        )) :_*)
+
         if(account.isGroupAccount){
           Collaborators.insertAll(getGroupMembers(newUserName).map(m => Collaborator(newUserName, newRepositoryName, m.userName)) :_*)
         } else {
@@ -189,7 +197,7 @@ trait RepositoryService { self: AccountService =>
       new RepositoryInfo(
         JGitUtil.getRepositoryInfo(repository.userName, repository.repositoryName, baseUrl),
         repository,
-        issues.size,
+        issues.count(_ == false),
         issues.count(_ == true),
         getForkedCount(
           repository.originUserName.getOrElse(repository.userName),
@@ -367,7 +375,7 @@ object RepositoryService {
 
   case class RepositoryInfo(owner: String, name: String, httpUrl: String, repository: Repository,
     issueCount: Int, pullCount: Int, commitCount: Int, forkedCount: Int,
-    branchList: Seq[String], tags: Seq[util.JGitUtil.TagInfo], managers: Seq[String]){
+    branchList: Seq[String], tags: Seq[JGitUtil.TagInfo], managers: Seq[String]){
 
     lazy val host = """^https?://(.+?)(:\d+)?/""".r.findFirstMatchIn(httpUrl).get.group(1)
 

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

@@ -1,7 +1,9 @@
-package service
+package gitbucket.core.service
 
-import model.{Account, Issue, Session}
-import util.Implicits.request2Session
+import gitbucket.core.model.{Session, Issue, Account}
+import gitbucket.core.util.Implicits
+import gitbucket.core.controller.Context
+import Implicits.request2Session
 
 /**
  * This service is used for a view helper mainly.
@@ -11,25 +13,22 @@ import util.Implicits.request2Session
  */
 trait RequestCache extends SystemSettingsService with AccountService with IssuesService {
 
-  private implicit def context2Session(implicit context: app.Context): Session =
+  private implicit def context2Session(implicit context: Context): Session =
     request2Session(context.request)
 
-  def getIssue(userName: String, repositoryName: String, issueId: String)
-              (implicit context: app.Context): Option[Issue] = {
+  def getIssue(userName: String, repositoryName: String, issueId: String)(implicit context: Context): Option[Issue] = {
     context.cache(s"issue.${userName}/${repositoryName}#${issueId}"){
       super.getIssue(userName, repositoryName, issueId)
     }
   }
 
-  def getAccountByUserName(userName: String)
-                          (implicit context: app.Context): Option[Account] = {
+  def getAccountByUserName(userName: String)(implicit context: Context): Option[Account] = {
     context.cache(s"account.${userName}"){
       super.getAccountByUserName(userName)
     }
   }
 
-  def getAccountByMailAddress(mailAddress: String)
-                             (implicit context: app.Context): Option[Account] = {
+  def getAccountByMailAddress(mailAddress: String)(implicit context: Context): Option[Account] = {
     context.cache(s"account.${mailAddress}"){
       super.getAccountByMailAddress(mailAddress)
     }

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

@@ -1,8 +1,8 @@
-package service
+package gitbucket.core.service
 
-import model.Profile._
+import gitbucket.core.model.SshKey
+import gitbucket.core.model.Profile._
 import profile.simple._
-import model.SshKey
 
 trait SshKeyService {
 

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

@@ -1,7 +1,8 @@
-package service
+package gitbucket.core.service
 
-import util.Directory._
-import util.ControlUtil._
+import gitbucket.core.util.{Directory, ControlUtil}
+import Directory._
+import ControlUtil._
 import SystemSettingsService._
 import javax.servlet.http.HttpServletRequest
 
@@ -14,6 +15,8 @@ trait SystemSettingsService {
       settings.baseUrl.foreach(x => props.setProperty(BaseURL, x.replaceFirst("/\\Z", "")))
       settings.information.foreach(x => props.setProperty(Information, x))
       props.setProperty(AllowAccountRegistration, settings.allowAccountRegistration.toString)
+      props.setProperty(AllowAnonymousAccess, settings.allowAnonymousAccess.toString)
+      props.setProperty(IsCreateRepoOptionPublic, settings.isCreateRepoOptionPublic.toString)
       props.setProperty(Gravatar, settings.gravatar.toString)
       props.setProperty(Notification, settings.notification.toString)
       props.setProperty(Ssh, settings.ssh.toString)
@@ -42,6 +45,7 @@ trait SystemSettingsService {
           ldap.fullNameAttribute.foreach(x => props.setProperty(LdapFullNameAttribute, x))
           ldap.mailAttribute.foreach(x => props.setProperty(LdapMailAddressAttribute, x))
           ldap.tls.foreach(x => props.setProperty(LdapTls, x.toString))
+          ldap.ssl.foreach(x => props.setProperty(LdapSsl, x.toString))
           ldap.keystore.foreach(x => props.setProperty(LdapKeystore, x))
         }
       }
@@ -63,6 +67,8 @@ trait SystemSettingsService {
         getOptionValue[String](props, BaseURL, None).map(x => x.replaceFirst("/\\Z", "")),
         getOptionValue[String](props, Information, None),
         getValue(props, AllowAccountRegistration, false),
+        getValue(props, AllowAnonymousAccess, true),
+        getValue(props, IsCreateRepoOptionPublic, true),
         getValue(props, Gravatar, true),
         getValue(props, Notification, false),
         getValue(props, Ssh, false),
@@ -92,6 +98,7 @@ trait SystemSettingsService {
             getOptionValue(props, LdapFullNameAttribute, None),
             getOptionValue(props, LdapMailAddressAttribute, None),
             getOptionValue[Boolean](props, LdapTls, None),
+            getOptionValue[Boolean](props, LdapSsl, None),
             getOptionValue(props, LdapKeystore, None)))
         } else {
           None
@@ -109,6 +116,8 @@ object SystemSettingsService {
     baseUrl: Option[String],
     information: Option[String],
     allowAccountRegistration: Boolean,
+    allowAnonymousAccess: Boolean,
+    isCreateRepoOptionPublic: Boolean,
     gravatar: Boolean,
     notification: Boolean,
     ssh: Boolean,
@@ -134,6 +143,7 @@ object SystemSettingsService {
     fullNameAttribute: Option[String],
     mailAttribute: Option[String],
     tls: Option[Boolean],
+    ssl: Option[Boolean],
     keystore: Option[String])
 
   case class Smtp(
@@ -152,6 +162,8 @@ object SystemSettingsService {
   private val BaseURL = "base_url"
   private val Information = "information"
   private val AllowAccountRegistration = "allow_account_registration"
+  private val AllowAnonymousAccess = "allow_anonymous_access"
+  private val IsCreateRepoOptionPublic = "is_create_repository_option_public"
   private val Gravatar = "gravatar"
   private val Notification = "notification"
   private val Ssh = "ssh"
@@ -174,6 +186,7 @@ object SystemSettingsService {
   private val LdapFullNameAttribute = "ldap.fullname_attribute"
   private val LdapMailAddressAttribute = "ldap.mail_attribute"
   private val LdapTls = "ldap.tls"
+  private val LdapSsl = "ldap.ssl"
   private val LdapKeystore = "ldap.keystore"
 
   private def getValue[A: ClassTag](props: java.util.Properties, key: String, default: A): A =
@@ -195,7 +208,7 @@ object SystemSettingsService {
       else value
     }
 
-  // TODO temporary flag
-  val enablePluginSystem = Option(System.getProperty("enable.plugin")).getOrElse("false").toBoolean
+//  // TODO temporary flag
+//  val enablePluginSystem = Option(System.getProperty("enable.plugin")).getOrElse("false").toBoolean
 
 }

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

@@ -1,13 +1,14 @@
-package service
+package gitbucket.core.service
 
-import model.Profile._
+import gitbucket.core.model.{WebHook, Account}
+import gitbucket.core.model.Profile._
+import gitbucket.core.service.RepositoryService.RepositoryInfo
+import gitbucket.core.util.JGitUtil
 import profile.simple._
-import model.{WebHook, Account}
 import org.slf4j.LoggerFactory
-import service.RepositoryService.RepositoryInfo
-import util.JGitUtil
+import RepositoryService.RepositoryInfo
 import org.eclipse.jgit.diff.DiffEntry
-import util.JGitUtil.CommitInfo
+import JGitUtil.CommitInfo
 import org.eclipse.jgit.api.Git
 import org.apache.http.message.BasicNameValuePair
 import org.apache.http.client.entity.UrlEncodedFormEntity

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

@@ -1,9 +1,10 @@
-package service
+package gitbucket.core.service
 
 import java.util.Date
+import gitbucket.core.model.Account
+import gitbucket.core.util._
+import gitbucket.core.util.ControlUtil._
 import org.eclipse.jgit.api.Git
-import util._
-import _root_.util.ControlUtil._
 import org.eclipse.jgit.treewalk.CanonicalTreeParser
 import org.eclipse.jgit.lib._
 import org.eclipse.jgit.dircache.DirCache
@@ -12,7 +13,7 @@ import java.io.ByteArrayInputStream
 import org.eclipse.jgit.patch._
 import org.eclipse.jgit.api.errors.PatchFormatException
 import scala.collection.JavaConverters._
-import service.RepositoryService.RepositoryInfo
+import RepositoryService.RepositoryInfo
 
 object WikiService {
   
@@ -46,7 +47,7 @@ object WikiService {
 trait WikiService {
   import WikiService._
 
-  def createWikiRepository(loginAccount: model.Account, owner: String, repository: String): Unit =
+  def createWikiRepository(loginAccount: Account, owner: String, repository: String): Unit =
     LockUtil.lock(s"${owner}/${repository}/wiki"){
       defining(Directory.getWikiRepositoryDir(owner, repository)){ dir =>
         if(!dir.exists){
@@ -102,7 +103,7 @@ trait WikiService {
    * Reverts specified changes.
    */
   def revertWikiPage(owner: String, repository: String, from: String, to: String,
-                     committer: model.Account, pageName: Option[String]): Boolean = {
+                     committer: Account, pageName: Option[String]): Boolean = {
 
     case class RevertInfo(operation: String, filePath: String, source: String)
 
@@ -204,7 +205,7 @@ trait WikiService {
    * Save the wiki page.
    */
   def saveWikiPage(owner: String, repository: String, currentPageName: String, newPageName: String,
-      content: String, committer: model.Account, message: String, currentId: Option[String]): Option[String] = {
+      content: String, committer: Account, message: String, currentId: Option[String]): Option[String] = {
     LockUtil.lock(s"${owner}/${repository}/wiki"){
       using(Git.open(Directory.getWikiRepositoryDir(owner, repository))){ git =>
         val builder  = DirCache.newInCore.builder()

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

@@ -0,0 +1,91 @@
+package gitbucket.core.servlet
+
+import javax.servlet._
+import javax.servlet.http._
+import gitbucket.core.service.{RepositoryService, AccountService, SystemSettingsService}
+import gitbucket.core.util.{ControlUtil, Keys, Implicits}
+import org.slf4j.LoggerFactory
+import Implicits._
+import ControlUtil._
+
+/**
+ * Provides BASIC Authentication for [[GitRepositoryServlet]].
+ */
+class BasicAuthenticationFilter extends Filter with RepositoryService with AccountService with SystemSettingsService {
+
+  private val logger = LoggerFactory.getLogger(classOf[BasicAuthenticationFilter])
+
+  def init(config: FilterConfig) = {}
+  
+  def destroy(): Unit = {}
+  
+  def doFilter(req: ServletRequest, res: ServletResponse, chain: FilterChain): Unit = {
+    implicit val request  = req.asInstanceOf[HttpServletRequest]
+    val response = res.asInstanceOf[HttpServletResponse]
+
+    val wrappedResponse = new HttpServletResponseWrapper(response){
+      override def setCharacterEncoding(encoding: String) = {}
+    }
+
+    val isUpdating = request.getRequestURI.endsWith("/git-receive-pack") || "service=git-receive-pack".equals(request.getQueryString)
+
+    val settings = loadSystemSettings()
+
+    try {
+      defining(request.paths){
+        case Array(_, repositoryOwner, repositoryName, _*) =>
+          getRepository(repositoryOwner, repositoryName.replaceFirst("\\.wiki\\.git$|\\.git$", ""), "") match {
+            case Some(repository) => {
+              if(!isUpdating && !repository.repository.isPrivate && settings.allowAnonymousAccess){
+                chain.doFilter(req, wrappedResponse)
+              } else {
+                request.getHeader("Authorization") match {
+                  case null => requireAuth(response)
+                  case auth => decodeAuthHeader(auth).split(":") match {
+                    case Array(username, password) => {
+                      authenticate(settings, username, password) match {
+                        case Some(account) => {
+                          if(isUpdating && hasWritePermission(repository.owner, repository.name, Some(account))){
+                            request.setAttribute(Keys.Request.UserName, account.userName)
+                          }
+                          chain.doFilter(req, wrappedResponse)
+                        }
+                        case None => requireAuth(response)
+                      }
+                    }
+                    case _ => requireAuth(response)
+                  }
+                }
+              }
+            }
+            case None => {
+              logger.debug(s"Repository ${repositoryOwner}/${repositoryName} is not found.")
+              response.sendError(HttpServletResponse.SC_NOT_FOUND)
+            }
+          }
+        case _ => {
+          logger.debug(s"Not enough path arguments: ${request.paths}")
+          response.sendError(HttpServletResponse.SC_NOT_FOUND)
+        }
+      }
+    } catch {
+      case ex: Exception => {
+        logger.error("error", ex)
+        requireAuth(response)
+      }
+    }
+  }
+
+  private def requireAuth(response: HttpServletResponse): Unit = {
+    response.setHeader("WWW-Authenticate", "BASIC realm=\"GitBucket\"")
+    response.sendError(HttpServletResponse.SC_UNAUTHORIZED)
+  }
+  
+  private def decodeAuthHeader(header: String): String = {
+    try {
+      new String(new sun.misc.BASE64Decoder().decodeBuffer(header.substring(6)))
+    } catch {
+      case _: Throwable => ""
+    }
+  }
+}

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

@@ -1,5 +1,8 @@
-package servlet
+package gitbucket.core.servlet
 
+import gitbucket.core.model.Session
+import gitbucket.core.service._
+import gitbucket.core.util._
 import org.eclipse.jgit.http.server.GitServlet
 import org.eclipse.jgit.lib._
 import org.eclipse.jgit.transport._
@@ -9,21 +12,19 @@ import org.slf4j.LoggerFactory
 import javax.servlet.ServletConfig
 import javax.servlet.ServletContext
 import javax.servlet.http.{HttpServletResponse, HttpServletRequest}
-import util.{StringUtil, Keys, JGitUtil, Directory}
-import util.ControlUtil._
-import util.Implicits._
-import service._
+import gitbucket.core.util.StringUtil
+import gitbucket.core.util.ControlUtil._
+import gitbucket.core.util.Implicits._
 import WebHookService._
 import org.eclipse.jgit.api.Git
-import util.JGitUtil.CommitInfo
-import service.IssuesService.IssueSearchCondition
-import model.Session
+import JGitUtil.CommitInfo
+import IssuesService.IssueSearchCondition
 
 /**
  * Provides Git repository via HTTP.
  * 
  * This servlet provides only Git repository functionality.
- * Authentication is provided by [[servlet.BasicAuthenticationFilter]].
+ * Authentication is provided by [[BasicAuthenticationFilter]].
  */
 class GitRepositoryServlet extends GitServlet with SystemSettingsService {
 
@@ -174,7 +175,7 @@ class CommitLogHook(owner: String, repository: String, pusher: String, baseUrl:
               case ReceiveCommand.Type.CREATE |
                    ReceiveCommand.Type.UPDATE |
                    ReceiveCommand.Type.UPDATE_NONFASTFORWARD =>
-                updatePullRequests(branchName)
+                updatePullRequests(owner, repository, branchName)
               case _ =>
             }
           }
@@ -211,26 +212,4 @@ class CommitLogHook(owner: String, repository: String, pusher: String, baseUrl:
       }
     }
   }
-
-  /**
-   * Fetch pull request contents into refs/pull/${issueId}/head and update pull request table.
-   */
-  private def updatePullRequests(branch: String) =
-    getPullRequestsByRequest(owner, repository, branch, false).foreach { pullreq =>
-      if(getRepository(pullreq.userName, pullreq.repositoryName, baseUrl).isDefined){
-        using(Git.open(Directory.getRepositoryDir(pullreq.userName, pullreq.repositoryName)),
-              Git.open(Directory.getRepositoryDir(pullreq.requestUserName, pullreq.requestRepositoryName))){ (oldGit, newGit) =>
-          oldGit.fetch
-            .setRemote(Directory.getRepositoryDir(owner, repository).toURI.toString)
-            .setRefSpecs(new RefSpec(s"refs/heads/${branch}:refs/pull/${pullreq.issueId}/head").setForceUpdate(true))
-            .call
-
-          val commitIdTo = oldGit.getRepository.resolve(s"refs/pull/${pullreq.issueId}/head").getName
-          val commitIdFrom = JGitUtil.getForkedCommitId(oldGit, newGit,
-            pullreq.userName, pullreq.repositoryName, pullreq.branch,
-            pullreq.requestUserName, pullreq.requestRepositoryName, pullreq.requestBranch)
-          updateCommitId(pullreq.userName, pullreq.repositoryName, pullreq.issueId, commitIdTo, commitIdFrom)
-        }
-      }
-    }
 }

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

@@ -1,62 +1,31 @@
-package servlet
+package gitbucket.core.servlet
 
 import java.io.File
 import java.sql.{DriverManager, Connection}
+import gitbucket.core.plugin.PluginRegistry
+import gitbucket.core.util._
 import org.apache.commons.io.FileUtils
-import javax.servlet.{ServletContext, ServletContextListener, ServletContextEvent}
-import org.apache.commons.io.IOUtils
+import javax.servlet.{ServletContextListener, ServletContextEvent}
 import org.slf4j.LoggerFactory
-import util.Directory._
-import util.ControlUtil._
-import util.JDBCUtil._
+import Directory._
+import ControlUtil._
+import JDBCUtil._
 import org.eclipse.jgit.api.Git
-import util.Directory
-import plugin.PluginUpdateJob
-import service.SystemSettingsService
+import gitbucket.core.util.Versions
+import gitbucket.core.util.Directory
+import gitbucket.core.plugin._
 
 object AutoUpdate {
-  
-  /**
-   * Version of GitBucket
-   * 
-   * @param majorVersion the major version
-   * @param minorVersion the minor version
-   */
-  case class Version(majorVersion: Int, minorVersion: Int){
-    
-    private val logger = LoggerFactory.getLogger(classOf[servlet.AutoUpdate.Version])
-    
-    /**
-     * Execute update/MAJOR_MINOR.sql to update schema to this version.
-     * If corresponding SQL file does not exist, this method do nothing.
-     */
-    def update(conn: Connection): Unit = {
-      val sqlPath = s"update/${majorVersion}_${minorVersion}.sql"
-
-      using(Thread.currentThread.getContextClassLoader.getResourceAsStream(sqlPath)){ in =>
-        if(in != null){
-          val sql = IOUtils.toString(in, "UTF-8")
-          using(conn.createStatement()){ stmt =>
-            logger.debug(sqlPath + "=" + sql)
-            stmt.executeUpdate(sql)
-          }
-        }
-      }
-    }
-    
-    /**
-     * MAJOR.MINOR
-     */
-    val versionString = s"${majorVersion}.${minorVersion}"
-  }
 
   /**
    * The history of versions. A head of this sequence is the current BitBucket version.
    */
   val versions = Seq(
+    new Version(3, 0),
+    new Version(2, 8),
     new Version(2, 7) {
-      override def update(conn: Connection): Unit = {
-        super.update(conn)
+      override def update(conn: Connection, cl: ClassLoader): Unit = {
+        super.update(conn, cl)
         conn.select("SELECT * FROM REPOSITORY"){ rs =>
           // Rename attached files directory from /issues to /comments
           val userName = rs.getString("USER_NAME")
@@ -94,8 +63,8 @@ object AutoUpdate {
     new Version(2, 5),
     new Version(2, 4),
     new Version(2, 3) {
-      override def update(conn: Connection): Unit = {
-        super.update(conn)
+      override def update(conn: Connection, cl: ClassLoader): Unit = {
+        super.update(conn, cl)
         conn.select("SELECT ACTIVITY_ID, ADDITIONAL_INFO FROM ACTIVITY WHERE ACTIVITY_TYPE='push'"){ rs =>
           val curInfo = rs.getString("ADDITIONAL_INFO")
           val newInfo = curInfo.split("\n").filter(_ matches "^[0-9a-z]{40}:.*").mkString("\n")
@@ -103,20 +72,22 @@ object AutoUpdate {
             conn.update("UPDATE ACTIVITY SET ADDITIONAL_INFO = ? WHERE ACTIVITY_ID = ?", newInfo, rs.getInt("ACTIVITY_ID"))
           }
         }
-        FileUtils.deleteDirectory(Directory.getPluginCacheDir())
-        FileUtils.deleteDirectory(new File(Directory.PluginHome))
+        ignore {
+          FileUtils.deleteDirectory(Directory.getPluginCacheDir())
+          //FileUtils.deleteDirectory(new File(Directory.PluginHome))
+        }
       }
     },
     new Version(2, 2),
     new Version(2, 1),
     new Version(2, 0){
-      override def update(conn: Connection): Unit = {
+      override def update(conn: Connection, cl: ClassLoader): Unit = {
         import eu.medsea.mimeutil.{MimeUtil2, MimeType}
 
         val mimeUtil = new MimeUtil2()
         mimeUtil.registerMimeDetector("eu.medsea.mimeutil.detector.MagicMimeMimeDetector")
 
-        super.update(conn)
+        super.update(conn, cl)
         conn.select("SELECT USER_NAME, REPOSITORY_NAME FROM REPOSITORY"){ rs =>
           defining(Directory.getAttachedDir(rs.getString("USER_NAME"), rs.getString("REPOSITORY_NAME"))){ dir =>
             if(dir.exists && dir.isDirectory){
@@ -144,8 +115,8 @@ object AutoUpdate {
     Version(1, 5),
     Version(1, 4),
     new Version(1, 3){
-      override def update(conn: Connection): Unit = {
-        super.update(conn)
+      override def update(conn: Connection, cl: ClassLoader): Unit = {
+        super.update(conn, cl)
         // Fix wiki repository configuration
         conn.select("SELECT USER_NAME, REPOSITORY_NAME FROM REPOSITORY"){ rs =>
           using(Git.open(getWikiRepositoryDir(rs.getString("USER_NAME"), rs.getString("REPOSITORY_NAME")))){ git =>
@@ -194,15 +165,14 @@ object AutoUpdate {
 }
 
 /**
- * Update database schema automatically in the context initializing.
+ * Initialize GitBucket system.
+ * Update database schema and load plug-ins automatically in the context initializing.
  */
-class AutoUpdateListener extends ServletContextListener {
-  import org.quartz.impl.StdSchedulerFactory
+class InitializeListener extends ServletContextListener {
   import AutoUpdate._
 
-  private val logger = LoggerFactory.getLogger(classOf[AutoUpdateListener])
-  private val scheduler = StdSchedulerFactory.getDefaultScheduler
-  
+  private val logger = LoggerFactory.getLogger(classOf[InitializeListener])
+
   override def contextInitialized(event: ServletContextEvent): Unit = {
     val dataDir = event.getServletContext.getInitParameter("gitbucket.home")
     if(dataDir != null){
@@ -210,69 +180,28 @@ class AutoUpdateListener extends ServletContextListener {
     }
     org.h2.Driver.load()
 
-    val context = event.getServletContext
-    context.setInitParameter("db.url", s"jdbc:h2:${DatabaseHome};MVCC=true")
-
-    defining(getConnection(event.getServletContext)){ conn =>
+    defining(getConnection()){ conn =>
+      // Migration
       logger.debug("Start schema update")
-      try {
-        defining(getCurrentVersion()){ currentVersion =>
-          if(currentVersion == headVersion){
-            logger.debug("No update")
-          } else if(!versions.contains(currentVersion)){
-            logger.warn(s"Skip migration because ${currentVersion.versionString} is illegal version.")
-          } else {
-            versions.takeWhile(_ != currentVersion).reverse.foreach(_.update(conn))
-            FileUtils.writeStringToFile(versionFile, headVersion.versionString, "UTF-8")
-            logger.debug(s"Updated from ${currentVersion.versionString} to ${headVersion.versionString}")
-          }
-        }
-      } catch {
-        case ex: Throwable => {
-          logger.error("Failed to schema update", ex)
-          ex.printStackTrace()
-          conn.rollback()
-        }
+      Versions.update(conn, headVersion, getCurrentVersion(), versions, Thread.currentThread.getContextClassLoader){ conn =>
+        FileUtils.writeStringToFile(versionFile, headVersion.versionString, "UTF-8")
       }
-      logger.debug("End schema update")
+      // Load plugins
+      logger.debug("Initialize plugins")
+      PluginRegistry.initialize(event.getServletContext, conn)
     }
 
-    if(SystemSettingsService.enablePluginSystem){
-      getDatabase(context).withSession { implicit session =>
-        logger.debug("Starting plugin system...")
-        try {
-          plugin.PluginSystem.init()
-
-          scheduler.start()
-          PluginUpdateJob.schedule(scheduler)
-          logger.debug("PluginUpdateJob is started.")
-
-          logger.debug("Plugin system is initialized.")
-        } catch {
-          case ex: Throwable => {
-            logger.error("Failed to initialize plugin system", ex)
-            ex.printStackTrace()
-            throw ex
-          }
-        }
-      }
-    }
   }
 
-  def contextDestroyed(sce: ServletContextEvent): Unit = {
-    scheduler.shutdown()
+  def contextDestroyed(event: ServletContextEvent): Unit = {
+    // Shutdown plugins
+    PluginRegistry.shutdown(event.getServletContext)
   }
 
-  private def getConnection(servletContext: ServletContext): Connection =
+  private def getConnection(): Connection =
     DriverManager.getConnection(
-      servletContext.getInitParameter("db.url"),
-      servletContext.getInitParameter("db.user"),
-      servletContext.getInitParameter("db.password"))
-
-  private def getDatabase(servletContext: ServletContext): scala.slick.jdbc.JdbcBackend.Database =
-    slick.jdbc.JdbcBackend.Database.forURL(
-      servletContext.getInitParameter("db.url"),
-      servletContext.getInitParameter("db.user"),
-      servletContext.getInitParameter("db.password"))
+      DatabaseConfig.url,
+      DatabaseConfig.user,
+      DatabaseConfig.password)
 
 }

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

@@ -1,8 +1,9 @@
-package servlet
+package gitbucket.core.servlet
 
 import javax.servlet.http.{HttpSessionEvent, HttpSessionListener}
+import gitbucket.core.util.Directory
 import org.apache.commons.io.FileUtils
-import util.Directory._
+import Directory._
 
 /**
  * Removes session associated temporary files when session is destroyed.

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

@@ -0,0 +1,60 @@
+package gitbucket.core.servlet
+
+import javax.servlet._
+import javax.servlet.http.HttpServletRequest
+import com.mchange.v2.c3p0.ComboPooledDataSource
+import gitbucket.core.util.DatabaseConfig
+import org.slf4j.LoggerFactory
+import slick.jdbc.JdbcBackend.{Database => SlickDatabase, Session}
+import gitbucket.core.util.Keys
+
+/**
+ * Controls the transaction with the open session in view pattern.
+ */
+class TransactionFilter extends Filter {
+
+  private val logger = LoggerFactory.getLogger(classOf[TransactionFilter])
+
+  def init(config: FilterConfig) = {}
+
+  def destroy(): Unit = {}
+
+  def doFilter(req: ServletRequest, res: ServletResponse, chain: FilterChain): Unit = {
+    if(req.asInstanceOf[HttpServletRequest].getRequestURI().startsWith("/assets/")){
+      // assets don't need transaction
+      chain.doFilter(req, res)
+    } else {
+      Database() withTransaction { session =>
+        logger.debug("begin transaction")
+        req.setAttribute(Keys.Request.DBSession, session)
+        chain.doFilter(req, res)
+        logger.debug("end transaction")
+      }
+    }
+  }
+
+}
+
+object Database {
+
+  private val logger = LoggerFactory.getLogger(Database.getClass)
+
+  private val db: SlickDatabase = {
+    val datasource = new ComboPooledDataSource
+
+    datasource.setDriverClass(DatabaseConfig.driver)
+    datasource.setJdbcUrl(DatabaseConfig.url)
+    datasource.setUser(DatabaseConfig.user)
+    datasource.setPassword(DatabaseConfig.password)
+
+    logger.debug("load database connection pool")
+
+    SlickDatabase.forDataSource(datasource)
+  }
+
+  def apply(): SlickDatabase = db
+
+  def getSession(req: ServletRequest): Session =
+    req.getAttribute(Keys.Request.DBSession).asInstanceOf[Session]
+
+}

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

@@ -1,24 +1,24 @@
-package ssh
+package gitbucket.core.ssh
 
+import gitbucket.core.model.Session
+import gitbucket.core.service.{RepositoryService, AccountService, SystemSettingsService}
+import gitbucket.core.servlet.{Database, CommitLogHook}
+import gitbucket.core.util.{Directory, ControlUtil}
 import org.apache.sshd.server.{CommandFactory, Environment, ExitCallback, Command}
 import org.slf4j.LoggerFactory
 import java.io.{InputStream, OutputStream}
-import util.ControlUtil._
+import ControlUtil._
 import org.eclipse.jgit.api.Git
-import util.Directory._
+import Directory._
 import org.eclipse.jgit.transport.{ReceivePack, UploadPack}
 import org.apache.sshd.server.command.UnknownCommand
-import servlet.{Database, CommitLogHook}
-import service.{AccountService, RepositoryService, SystemSettingsService}
 import org.eclipse.jgit.errors.RepositoryNotFoundException
-import javax.servlet.ServletContext
-import model.Session
 
 object GitCommand {
   val CommandRegex = """\Agit-(upload|receive)-pack '/([a-zA-Z0-9\-_.]+)/([a-zA-Z0-9\-_.]+).git'\Z""".r
 }
 
-abstract class GitCommand(val context: ServletContext, val owner: String, val repoName: String) extends Command {
+abstract class GitCommand(val owner: String, val repoName: String) extends Command {
   self: RepositoryService with AccountService =>
 
   private val logger = LoggerFactory.getLogger(classOf[GitCommand])
@@ -31,7 +31,7 @@ abstract class GitCommand(val context: ServletContext, val owner: String, val re
 
   private def newTask(user: String): Runnable = new Runnable {
     override def run(): Unit = {
-      Database(context) withSession { implicit session =>
+      Database() withSession { implicit session =>
         try {
           runTask(user)
           callback.onExit(0)
@@ -80,7 +80,7 @@ abstract class GitCommand(val context: ServletContext, val owner: String, val re
 
 }
 
-class GitUploadPack(context: ServletContext, owner: String, repoName: String, baseUrl: String) extends GitCommand(context, owner, repoName)
+class GitUploadPack(owner: String, repoName: String, baseUrl: String) extends GitCommand(owner, repoName)
     with RepositoryService with AccountService {
 
   override protected def runTask(user: String)(implicit session: Session): Unit = {
@@ -97,7 +97,7 @@ class GitUploadPack(context: ServletContext, owner: String, repoName: String, ba
 
 }
 
-class GitReceivePack(context: ServletContext, owner: String, repoName: String, baseUrl: String) extends GitCommand(context, owner, repoName)
+class GitReceivePack(owner: String, repoName: String, baseUrl: String) extends GitCommand(owner, repoName)
     with SystemSettingsService with RepositoryService with AccountService {
 
   override protected def runTask(user: String)(implicit session: Session): Unit = {
@@ -119,15 +119,15 @@ class GitReceivePack(context: ServletContext, owner: String, repoName: String, b
 
 }
 
-class GitCommandFactory(context: ServletContext, baseUrl: String) extends CommandFactory {
+class GitCommandFactory(baseUrl: String) extends CommandFactory {
   private val logger = LoggerFactory.getLogger(classOf[GitCommandFactory])
 
   override def createCommand(command: String): Command = {
     logger.debug(s"command: $command")
     command match {
-      case GitCommand.CommandRegex("upload", owner, repoName) => new GitUploadPack(context, owner, repoName, baseUrl)
-      case GitCommand.CommandRegex("receive", owner, repoName) => new GitReceivePack(context, owner, repoName, baseUrl)
+      case GitCommand.CommandRegex("upload", owner, repoName) => new GitUploadPack(owner, repoName, baseUrl)
+      case GitCommand.CommandRegex("receive", owner, repoName) => new GitReceivePack(owner, repoName, baseUrl)
       case _ => new UnknownCommand(command)
     }
   }
-}
+}

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

@@ -1,10 +1,10 @@
-package ssh
+package gitbucket.core.ssh
 
+import gitbucket.core.service.SystemSettingsService
 import org.apache.sshd.common.Factory
 import org.apache.sshd.server.{Environment, ExitCallback, Command}
 import java.io.{OutputStream, InputStream}
 import org.eclipse.jgit.lib.Constants
-import service.SystemSettingsService
 
 class NoShell extends Factory[Command] with SystemSettingsService {
   override def create(): Command = new Command() {

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

@@ -1,16 +1,15 @@
-package ssh
+package gitbucket.core.ssh
 
+import gitbucket.core.service.SshKeyService
+import gitbucket.core.servlet.Database
 import org.apache.sshd.server.PublickeyAuthenticator
 import org.apache.sshd.server.session.ServerSession
 import java.security.PublicKey
-import service.SshKeyService
-import servlet.Database
-import javax.servlet.ServletContext
 
-class PublicKeyAuthenticator(context: ServletContext) extends PublickeyAuthenticator with SshKeyService {
+class PublicKeyAuthenticator extends PublickeyAuthenticator with SshKeyService {
 
   override def authenticate(username: String, key: PublicKey, session: ServerSession): Boolean = {
-    Database(context) withSession { implicit session =>
+    Database() withSession { implicit session =>
       getPublicKeys(username).exists { sshKey =>
         SshUtil.str2PublicKey(sshKey.publicKey) match {
           case Some(publicKey) => key.equals(publicKey)

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

@@ -1,10 +1,10 @@
-package ssh
+package gitbucket.core.ssh
 
-import javax.servlet.{ServletContext, ServletContextEvent, ServletContextListener}
+import javax.servlet.{ServletContextEvent, ServletContextListener}
+import gitbucket.core.service.SystemSettingsService
+import gitbucket.core.util.Directory
 import org.apache.sshd.server.keyprovider.SimpleGeneratorHostKeyProvider
 import org.slf4j.LoggerFactory
-import util.Directory
-import service.SystemSettingsService
 import java.util.concurrent.atomic.AtomicBoolean
 
 object SshServer {
@@ -12,17 +12,17 @@ object SshServer {
   private val server = org.apache.sshd.SshServer.setUpDefaultServer()
   private val active = new AtomicBoolean(false)
 
-  private def configure(context: ServletContext, port: Int, baseUrl: String) = {
+  private def configure(port: Int, baseUrl: String) = {
     server.setPort(port)
     server.setKeyPairProvider(new SimpleGeneratorHostKeyProvider(s"${Directory.GitBucketHome}/gitbucket.ser"))
-    server.setPublickeyAuthenticator(new PublicKeyAuthenticator(context))
-    server.setCommandFactory(new GitCommandFactory(context, baseUrl))
+    server.setPublickeyAuthenticator(new PublicKeyAuthenticator)
+    server.setCommandFactory(new GitCommandFactory(baseUrl))
     server.setShellFactory(new NoShell)
   }
 
-  def start(context: ServletContext, port: Int, baseUrl: String) = {
+  def start(port: Int, baseUrl: String) = {
     if(active.compareAndSet(false, true)){
-      configure(context, port, baseUrl)
+      configure(port, baseUrl)
       server.start()
       logger.info(s"Start SSH Server Listen on ${server.getPort}")
     }
@@ -55,8 +55,7 @@ class SshServerListener extends ServletContextListener with SystemSettingsServic
         case None =>
           logger.error("Could not start SshServer because the baseUrl is not configured.")
         case Some(baseUrl) =>
-          SshServer.start(sce.getServletContext,
-            settings.sshPort.getOrElse(SystemSettingsService.DefaultSshPort), baseUrl)
+          SshServer.start(settings.sshPort.getOrElse(SystemSettingsService.DefaultSshPort), baseUrl)
       }
     }
   }

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

@@ -1,4 +1,4 @@
-package ssh
+package gitbucket.core.ssh
 
 import java.security.PublicKey
 import org.slf4j.LoggerFactory

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

@@ -1,10 +1,10 @@
-package util
+package gitbucket.core.util
 
-import app.ControllerBase
-import service._
+import gitbucket.core.controller.ControllerBase
+import gitbucket.core.service.{RepositoryService, AccountService}
 import RepositoryService.RepositoryInfo
-import util.Implicits._
-import util.ControlUtil._
+import Implicits._
+import ControlUtil._
 
 /**
  * Allows only oneself and administrators.

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

@@ -1,4 +1,4 @@
-package util
+package gitbucket.core.util
 
 import org.eclipse.jgit.api.Git
 import org.eclipse.jgit.revwalk.RevWalk
@@ -37,4 +37,10 @@ object ControlUtil {
   def using[T](treeWalk: TreeWalk)(f: TreeWalk => T): T =
     try f(treeWalk) finally treeWalk.release()
 
+  def ignore[T](f: => Unit): Unit = try {
+    f
+  } catch {
+    case e: Exception => ()
+  }
+
 }

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

@@ -0,0 +1,19 @@
+package gitbucket.core.util
+
+import com.typesafe.config.ConfigFactory
+import Directory.DatabaseHome
+
+object DatabaseConfig {
+
+  private val config = ConfigFactory.load("database")
+  private val dbUrl = config.getString("db.url")
+
+  def url(directory: Option[String]): String =
+    dbUrl.replace("${DatabaseHome}", directory.getOrElse(DatabaseHome))
+
+  val url: String = url(None)
+  val user: String = config.getString("db.user")
+  val password: String = config.getString("db.password")
+  val driver: String = config.getString("db.driver")
+
+}

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

@@ -1,7 +1,7 @@
-package util
+package gitbucket.core.util
 
 import java.io.File
-import util.ControlUtil._
+import ControlUtil._
 import org.apache.commons.io.FileUtils
 
 /**

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

@@ -1,9 +1,9 @@
-package util
+package gitbucket.core.util
 
 import org.apache.commons.io.FileUtils
 import java.net.URLConnection
 import java.io.File
-import util.ControlUtil._
+import ControlUtil._
 import scala.util.Random
 
 object FileUtil {

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

@@ -1,9 +1,10 @@
-package util
+package gitbucket.core.util
+
+import gitbucket.core.servlet.Database
 
 import scala.util.matching.Regex
 import scala.util.control.Exception._
 import slick.jdbc.JdbcBackend
-import servlet.Database
 import javax.servlet.http.{HttpSession, HttpServletRequest}
 
 /**

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

@@ -1,7 +1,7 @@
-package util
+package gitbucket.core.util
 
 import java.sql._
-import util.ControlUtil._
+import ControlUtil._
 import scala.collection.mutable.ListBuffer
 
 /**
@@ -18,6 +18,14 @@ object JDBCUtil {
       }
     }
 
+    def find[T](sql: String, params: Any*)(f: ResultSet => T): Option[T] = {
+      execute(sql, params: _*){ stmt =>
+        using(stmt.executeQuery()){ rs =>
+          if(rs.next) Some(f(rs)) else None
+        }
+      }
+    }
+
     def select[T](sql: String, params: Any*)(f: ResultSet => T): Seq[T] = {
       execute(sql, params: _*){ stmt =>
         using(stmt.executeQuery()){ rs =>

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

@@ -1,9 +1,10 @@
-package util
+package gitbucket.core.util
 
+import gitbucket.core.service.RepositoryService
 import org.eclipse.jgit.api.Git
-import util.Directory._
-import util.StringUtil._
-import util.ControlUtil._
+import Directory._
+import StringUtil._
+import ControlUtil._
 import scala.annotation.tailrec
 import scala.collection.JavaConverters._
 import org.eclipse.jgit.lib._
@@ -13,9 +14,9 @@ import org.eclipse.jgit.treewalk._
 import org.eclipse.jgit.treewalk.filter._
 import org.eclipse.jgit.diff.DiffEntry.ChangeType
 import org.eclipse.jgit.errors.{ConfigInvalidException, MissingObjectException}
+import org.eclipse.jgit.transport.RefSpec
 import java.util.Date
 import org.eclipse.jgit.api.errors.{JGitInternalException, InvalidRefNameException, RefAlreadyExistsException, NoHeadException}
-import service.RepositoryService
 import org.eclipse.jgit.dircache.DirCacheEntry
 import org.slf4j.LoggerFactory
 
@@ -133,6 +134,10 @@ object JGitUtil {
    */
   case class SubmoduleInfo(name: String, path: String, url: String)
 
+  case class BranchMergeInfo(ahead: Int, behind: Int, isMerged: Boolean)
+
+  case class BranchInfo(name: String, committerName: String, commitTime: Date, committerEmailAddress:String, mergeInfo: Option[BranchMergeInfo], commitId: String)
+
   /**
    * Returns RevCommit from the commit or tag id.
    * 
@@ -674,6 +679,25 @@ object JGitUtil {
       }.head.id
     }
 
+  /**
+   * Fetch pull request contents into refs/pull/${issueId}/head and return (commitIdTo, commitIdFrom)
+   */
+  def updatePullRequest(userName: String, repositoryName:String, branch: String, issueId: Int,
+                        requestUserName: String, requestRepositoryName: String, requestBranch: String):(String, String) =
+    using(Git.open(Directory.getRepositoryDir(userName, repositoryName)),
+          Git.open(Directory.getRepositoryDir(requestUserName, requestRepositoryName))){ (oldGit, newGit) =>
+      oldGit.fetch
+        .setRemote(Directory.getRepositoryDir(requestUserName, requestRepositoryName).toURI.toString)
+        .setRefSpecs(new RefSpec(s"refs/heads/${requestBranch}:refs/pull/${issueId}/head").setForceUpdate(true))
+        .call
+
+      val commitIdTo = oldGit.getRepository.resolve(s"refs/pull/${issueId}/head").getName
+      val commitIdFrom = getForkedCommitId(oldGit, newGit,
+        userName, repositoryName, branch,
+        requestUserName, requestRepositoryName, requestBranch)
+      (commitIdTo, commitIdFrom)
+    }
+
   /**
    * Returns the last modified commit of specified path
    * @param git the Git object
@@ -685,4 +709,43 @@ object JGitUtil {
     return git.log.add(startCommit).addPath(path).setMaxCount(1).call.iterator.next
   }
 
+  def getBranches(owner: String, name: String, defaultBranch: String): Seq[BranchInfo] = {
+    using(Git.open(getRepositoryDir(owner, name))){ git =>
+      val repo = git.getRepository
+      val defaultObject = repo.resolve(defaultBranch)
+      git.branchList.call.asScala.map { ref =>
+        val walk = new RevWalk(repo)
+        try{
+          val defaultCommit = walk.parseCommit(defaultObject)
+          val branchName = ref.getName.stripPrefix("refs/heads/")
+          val branchCommit = if(branchName == defaultBranch){
+            defaultCommit
+          }else{
+            walk.parseCommit(ref.getObjectId)
+          }
+          val when = branchCommit.getCommitterIdent.getWhen
+          val committer = branchCommit.getCommitterIdent.getName
+          val committerEmail = branchCommit.getCommitterIdent.getEmailAddress
+          val mergeInfo = if(branchName==defaultBranch){
+            None
+          }else{
+            walk.reset()
+            walk.setRevFilter( RevFilter.MERGE_BASE )
+            walk.markStart(branchCommit)
+            walk.markStart(defaultCommit)
+            val mergeBase = walk.next()
+            walk.reset()
+            walk.setRevFilter(RevFilter.ALL)
+            Some(BranchMergeInfo(
+              ahead    = RevWalkUtils.count(walk, branchCommit, mergeBase),
+              behind   = RevWalkUtils.count(walk, defaultCommit, mergeBase),
+              isMerged = walk.isMergedInto(branchCommit, defaultCommit)))
+          }
+          BranchInfo(branchName, committer, when, committerEmail, mergeInfo, ref.getObjectId.name)
+        } finally {
+          walk.dispose();
+        }
+      }
+    }
+  }
 }

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

@@ -1,4 +1,4 @@
-package util
+package gitbucket.core.util
 
 /**
  * Define key strings for request attributes, session attributes or flash attributes.

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

@@ -1,13 +1,13 @@
-package util
+package gitbucket.core.util
 
-import util.ControlUtil._
-import service.SystemSettingsService
+import gitbucket.core.model.Account
+import ControlUtil._
+import gitbucket.core.service.SystemSettingsService
+import gitbucket.core.service.SystemSettingsService.Ldap
 import com.novell.ldap._
 import java.security.Security
 import org.slf4j.LoggerFactory
-import service.SystemSettingsService.Ldap
 import scala.annotation.tailrec
-import model.Account
 
 /**
  * Utility for LDAP authentication.
@@ -48,6 +48,7 @@ object LDAPUtil {
       dn       = ldapSettings.bindDN.getOrElse(""),
       password = ldapSettings.bindPassword.getOrElse(""),
       tls      = ldapSettings.tls.getOrElse(false),
+      ssl      = ldapSettings.ssl.getOrElse(false),
       keystore = ldapSettings.keystore.getOrElse(""),
       error    = "System LDAP authentication failed."
     ){ conn =>
@@ -65,6 +66,7 @@ object LDAPUtil {
       dn       = userDN,
       password = password,
       tls      = ldapSettings.tls.getOrElse(false),
+      ssl      = ldapSettings.ssl.getOrElse(false),
       keystore = ldapSettings.keystore.getOrElse(""),
       error    = "User LDAP Authentication Failed."
     ){ conn =>
@@ -96,7 +98,7 @@ object LDAPUtil {
     }).replaceAll("[^a-zA-Z0-9\\-_.]", "").replaceAll("^[_\\-]", "")
   }
 
-  private def bind[A](host: String, port: Int, dn: String, password: String, tls: Boolean, keystore: String, error: String)
+  private def bind[A](host: String, port: Int, dn: String, password: String, tls: Boolean, ssl: Boolean, keystore: String, error: String)
                   (f: LDAPConnection => Either[String, A]): Either[String, A] = {
     if (tls) {
       // Dynamically set Sun as the security provider
@@ -109,7 +111,13 @@ object LDAPUtil {
       }
     }
 
-    val conn: LDAPConnection = new LDAPConnection(new LDAPJSSEStartTLSFactory())
+    val conn: LDAPConnection = 
+	if(ssl) {
+		new LDAPConnection(new LDAPJSSESecureSocketFactory()) 
+	}else {
+		new LDAPConnection(new LDAPJSSEStartTLSFactory())
+	}
+
     try {
       // Connect to the server
       conn.connect(host, port)

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

@@ -1,8 +1,8 @@
-package util
+package gitbucket.core.util
 
 import java.util.concurrent.ConcurrentHashMap
 import java.util.concurrent.locks.{ReentrantLock, Lock}
-import util.ControlUtil._
+import ControlUtil._
 
 object LockUtil {
 

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

@@ -1,22 +1,24 @@
-package util
+package gitbucket.core.util
+
+import gitbucket.core.model.{Session, Issue}
+import gitbucket.core.service.{RepositoryService, AccountService, IssuesService, SystemSettingsService}
+import gitbucket.core.servlet.Database
+import gitbucket.core.view.Markdown
 
 import scala.concurrent._
 import ExecutionContext.Implicits.global
 import org.apache.commons.mail.{DefaultAuthenticator, HtmlEmail}
 import org.slf4j.LoggerFactory
 
-import app.Context
-import model.Session
-import service.{AccountService, RepositoryService, IssuesService, SystemSettingsService}
-import servlet.Database
+import gitbucket.core.controller.Context
 import SystemSettingsService.Smtp
-import _root_.util.ControlUtil.defining
+import ControlUtil.defining
 
 trait Notifier extends RepositoryService with AccountService with IssuesService {
   def toNotify(r: RepositoryService.RepositoryInfo, issueId: Int, content: String)
       (msg: String => String)(implicit context: Context): Unit
 
-  protected def recipients(issue: model.Issue)(notify: String => Unit)(implicit session: Session, context: Context) =
+  protected def recipients(issue: Issue)(notify: String => Unit)(implicit session: Session, context: Context) =
     (
         // individual repository's owner
         issue.userName ::
@@ -27,7 +29,7 @@ trait Notifier extends RepositoryService with AccountService with IssuesService
         getComments(issue.userName, issue.repositoryName, issue.issueId).map(_.commentedUserName)
     )
     .distinct
-    .withFilter ( _ != context.loginAccount.get.userName )	// the operation in person is excluded
+    .withFilter ( _ != context.loginAccount.get.userName )  // the operation in person is excluded
     .foreach ( getAccountByUserName(_) filterNot (_.isGroupAccount) filterNot (LDAPUtil.isDummyMailAddress(_)) foreach (x => notify(x.mailAddress)) )
 
 }
@@ -67,14 +69,14 @@ class Mailer(private val smtp: Smtp) extends Notifier {
 
   def toNotify(r: RepositoryService.RepositoryInfo, issueId: Int, content: String)
       (msg: String => String)(implicit context: Context) = {
-    val database = Database(context.request.getServletContext)
+    val database = Database()
 
     val f = Future {
       database withSession { implicit session =>
         getIssue(r.owner, r.name, issueId.toString) foreach { issue =>
           defining(
               s"[${r.name}] ${issue.title} (#${issueId})" ->
-              msg(view.Markdown.toHtml(content, r, false, true))) { case (subject, msg) =>
+              msg(Markdown.toHtml(content, r, false, true))) { case (subject, msg) =>
             recipients(issue) { to =>
               val email = new HtmlEmail
               email.setHostName(smtp.host)
@@ -113,4 +115,4 @@ class Mailer(private val smtp: Smtp) extends Notifier {
 class MockMailer extends Notifier {
   def toNotify(r: RepositoryService.RepositoryInfo, issueId: Int, content: String)
       (msg: String => String)(implicit context: Context): Unit = {}
-}
+}

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

@@ -1,8 +1,8 @@
-package util
+package gitbucket.core.util
 
 import java.net.{URLDecoder, URLEncoder}
 import org.mozilla.universalchardet.UniversalDetector
-import util.ControlUtil._
+import ControlUtil._
 import org.apache.commons.io.input.BOMInputStream
 import org.apache.commons.io.IOUtils
 
@@ -30,7 +30,7 @@ object StringUtil {
     value.replace("&", "&amp;").replace("<", "&lt;").replace(">", "&gt;").replace("\"", "&quot;")
 
   /**
-   * Make string from byte array. Character encoding is detected automatically by [[util.StringUtil.detectEncoding]].
+   * Make string from byte array. Character encoding is detected automatically by [[StringUtil.detectEncoding]].
    * And if given bytes contains UTF-8 BOM, it's removed from returned string.
    */
   def convertFromByteArray(content: Array[Byte]): String =

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

@@ -1,4 +1,4 @@
-package util
+package gitbucket.core.util
 
 import jp.sf.amateras.scalatra.forms._
 import org.scalatra.i18n.Messages

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

@@ -0,0 +1,67 @@
+package gitbucket.core.util
+
+import java.sql.Connection
+
+import org.apache.commons.io.IOUtils
+import org.slf4j.LoggerFactory
+import ControlUtil._
+
+case class Version(majorVersion: Int, minorVersion: Int) {
+
+  private val logger = LoggerFactory.getLogger(classOf[Version])
+
+  /**
+   * Execute update/MAJOR_MINOR.sql to update schema to this version.
+   * If corresponding SQL file does not exist, this method do nothing.
+   */
+  def update(conn: Connection, cl: ClassLoader): Unit = {
+    val sqlPath = s"update/${majorVersion}_${minorVersion}.sql"
+
+    using(cl.getResourceAsStream(sqlPath)){ in =>
+      if(in != null){
+        val sql = IOUtils.toString(in, "UTF-8")
+        using(conn.createStatement()){ stmt =>
+          logger.debug(sqlPath + "=" + sql)
+          stmt.executeUpdate(sql)
+        }
+      }
+    }
+  }
+
+
+  /**
+   * MAJOR.MINOR
+   */
+  val versionString = s"${majorVersion}.${minorVersion}"
+
+}
+
+object Versions {
+
+  private val logger = LoggerFactory.getLogger(Versions.getClass)
+
+  def update(conn: Connection, headVersion: Version, currentVersion: Version, versions: Seq[Version], cl: ClassLoader)
+            (save: Connection => Unit): Unit = {
+    logger.debug("Start schema update")
+    try {
+      if(currentVersion == headVersion){
+        logger.debug("No update")
+      } else if(currentVersion.versionString != "0.0" && !versions.contains(currentVersion)){
+        logger.warn(s"Skip migration because ${currentVersion.versionString} is illegal version.")
+      } else {
+        versions.takeWhile(_ != currentVersion).reverse.foreach(_.update(conn, cl))
+        save(conn)
+        logger.debug(s"Updated from ${currentVersion.versionString} to ${headVersion.versionString}")
+      }
+    } catch {
+      case ex: Throwable => {
+        logger.error("Failed to schema update", ex)
+        ex.printStackTrace()
+        conn.rollback()
+      }
+    }
+    logger.debug("End schema update")
+  }
+
+}
+

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

@@ -1,8 +1,9 @@
-package view
+package gitbucket.core.view
 
-import service.RequestCache
+import gitbucket.core.controller.Context
+import gitbucket.core.service.RequestCache
+import gitbucket.core.util.StringUtil
 import play.twirl.api.Html
-import util.StringUtil
 
 trait AvatarImageProvider { self: RequestCache =>
 
@@ -11,7 +12,7 @@ trait AvatarImageProvider { self: RequestCache =>
    * Looks up Gravatar if avatar icon has not been configured in user settings.
    */
   protected def getAvatarImageHtml(userName: String, size: Int,
-      mailAddress: String = "", tooltip: Boolean = false)(implicit context: app.Context): Html = {
+      mailAddress: String = "", tooltip: Boolean = false)(implicit context: Context): Html = {
 
     val src = if(mailAddress.isEmpty){
       // by user name

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

@@ -1,15 +1,17 @@
-package view
+package gitbucket.core.view
 
-import service.RequestCache
-import util.Implicits.RichString
+import gitbucket.core.controller.Context
+import gitbucket.core.service.{RepositoryService, RequestCache}
+import gitbucket.core.util.Implicits
+import gitbucket.core.util.Implicits.RichString
 
 trait LinkConverter { self: RequestCache =>
 
   /**
    * Converts issue id, username and commit id to link.
    */
-  protected def convertRefsLinks(value: String, repository: service.RepositoryService.RepositoryInfo,
-                                 issueIdPrefix: String =  "#")(implicit context: app.Context): String = {
+  protected def convertRefsLinks(value: String, repository: RepositoryService.RepositoryInfo,
+                                 issueIdPrefix: String =  "#")(implicit context: Context): String = {
     value
       // escape HTML tags
       .replace("&", "&amp;").replace("<", "&lt;").replace(">", "&gt;").replace("\"", "&quot;")

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

@@ -1,26 +1,32 @@
-package view
+package gitbucket.core.view
 
-import util.StringUtil
-import util.ControlUtil._
-import util.Directory._
-import org.parboiled.common.StringUtils
-import org.pegdown._
-import org.pegdown.ast._
-import org.pegdown.LinkRenderer.Rendering
 import java.text.Normalizer
 import java.util.Locale
 import java.util.regex.Pattern
+
+import gitbucket.core.controller.Context
+import gitbucket.core.service.{RepositoryService, RequestCache, WikiService}
+import gitbucket.core.util.StringUtil
+import org.parboiled.common.StringUtils
+import org.pegdown.LinkRenderer.Rendering
+import org.pegdown._
+import org.pegdown.ast._
+
 import scala.collection.JavaConverters._
-import service.{RequestCache, WikiService}
 
 object Markdown {
 
   /**
    * Converts Markdown of Wiki pages to HTML.
    */
-  def toHtml(markdown: String, repository: service.RepositoryService.RepositoryInfo,
-             enableWikiLink: Boolean, enableRefsLink: Boolean,
-             enableTaskList: Boolean = false, hasWritePermission: Boolean = false)(implicit context: app.Context): String = {
+  def toHtml(markdown: String,
+             repository: RepositoryService.RepositoryInfo,
+             enableWikiLink: Boolean,
+             enableRefsLink: Boolean,
+             enableTaskList: Boolean = false,
+             hasWritePermission: Boolean = false,
+             pages: List[String] = Nil)(implicit context: Context): String = {
+
     // escape issue id
     val s = if(enableRefsLink){
       markdown.replaceAll("(?<=(\\W|^))#(\\d+)(?=(\\W|$))", "issue:$2")
@@ -35,12 +41,16 @@ object Markdown {
       Extensions.AUTOLINKS | Extensions.WIKILINKS | Extensions.FENCED_CODE_BLOCKS | Extensions.TABLES | Extensions.HARDWRAPS | Extensions.SUPPRESS_ALL_HTML
     ).parseMarkdown(source.toCharArray)
 
-    new GitBucketHtmlSerializer(markdown, repository, enableWikiLink, enableRefsLink, enableTaskList, hasWritePermission).toHtml(rootNode)
+    new GitBucketHtmlSerializer(markdown, repository, enableWikiLink, enableRefsLink, enableTaskList, hasWritePermission, pages).toHtml(rootNode)
   }
 }
 
-class GitBucketLinkRender(context: app.Context, repository: service.RepositoryService.RepositoryInfo,
-                          enableWikiLink: Boolean) extends LinkRenderer with WikiService {
+class GitBucketLinkRender(
+    context: Context,
+    repository: RepositoryService.RepositoryInfo,
+    enableWikiLink: Boolean,
+    pages: List[String]) extends LinkRenderer with WikiService {
+
   override def render(node: WikiLinkNode): Rendering = {
     if(enableWikiLink){
       try {
@@ -54,7 +64,7 @@ class GitBucketLinkRender(context: app.Context, repository: service.RepositorySe
 
         val url = repository.httpUrl.replaceFirst("/git/", "/").stripSuffix(".git") + "/wiki/" + StringUtil.urlEncode(page)
 
-        if(getWikiPage(repository.owner, repository.name, page).isDefined){
+        if(pages.contains(page)){
           new Rendering(url, label)
         } else {
           new Rendering(url, label).withAttribute("class", "absent")
@@ -87,13 +97,14 @@ class GitBucketVerbatimSerializer extends VerbatimSerializer {
 
 class GitBucketHtmlSerializer(
     markdown: String,
-    repository: service.RepositoryService.RepositoryInfo,
+    repository: RepositoryService.RepositoryInfo,
     enableWikiLink: Boolean,
     enableRefsLink: Boolean,
     enableTaskList: Boolean,
-    hasWritePermission: Boolean
-  )(implicit val context: app.Context) extends ToHtmlSerializer(
-    new GitBucketLinkRender(context, repository, enableWikiLink),
+    hasWritePermission: Boolean,
+    pages: List[String]
+  )(implicit val context: Context) extends ToHtmlSerializer(
+    new GitBucketLinkRender(context, repository, enableWikiLink, pages),
     Map[String, VerbatimSerializer](VerbatimSerializer.DEFAULT -> new GitBucketVerbatimSerializer).asJava
   ) with LinkConverter with RequestCache {
 
@@ -185,6 +196,32 @@ class GitBucketHtmlSerializer(
       printTag(node, "li")
     }
   }
+
+  override def visit(node: ExpLinkNode) {
+    printLink(linkRenderer.render(node, printLinkChildrenToString(node)))
+  }
+
+  def printLinkChildrenToString(node: SuperNode) = {
+    val priorPrinter = printer
+    printer = new Printer()
+    visitLinkChildren(node)
+    val result = printer.getString()
+    printer = priorPrinter
+    result
+  }
+
+  def visitLinkChildren(node: SuperNode) {
+    import scala.collection.JavaConversions._
+    node.getChildren.foreach(child => child match {
+      case node: ExpImageNode => visitLinkChild(node)
+      case node: SuperNode => visitLinkChildren(node)
+      case _ => child.accept(this)
+    })
+  }
+
+  def visitLinkChild(node: ExpImageNode) {
+    printer.print("<img src=\"").print(fixUrl(node.url, true)).print("\"  alt=\"").printEncoded(printChildrenToString(node)).print("\"/>")
+  }
 }
 
 object GitBucketHtmlSerializer {

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

@@ -1,4 +1,4 @@
-package view
+package gitbucket.core.view
 
 /**
  * Provides control information for pagination.

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

@@ -1,9 +1,12 @@
-package view
-import java.util.{Locale, Date, TimeZone}
+package gitbucket.core.view
+
 import java.text.SimpleDateFormat
+import java.util.{Date, Locale, TimeZone}
+
+import gitbucket.core.controller.Context
+import gitbucket.core.service.{RepositoryService, RequestCache}
+import gitbucket.core.util.{JGitUtil, StringUtil}
 import play.twirl.api.Html
-import util.StringUtil
-import service.RequestCache
 
 /**
  * Provides helper methods for Twirl templates.
@@ -38,10 +41,8 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
   }
 
   /**
-   *
    * Format java.util.Date to "x {seconds/minutes/hours/days} ago"
    * If duration over 1 month, format to "d MMM (yyyy)"
-   *
    */
   def datetimeAgoRecentOnly(date: Date): String = {
     val duration = new Date().getTime - date.getTime
@@ -77,9 +78,9 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
   def plural(count: Int, singular: String, plural: String = ""): String =
     if(count == 1) singular else if(plural.isEmpty) singular + "s" else plural
 
-  private[this] val renderersBySuffix: Seq[(String, (List[String], String, String, service.RepositoryService.RepositoryInfo, Boolean, Boolean, app.Context) => Html)] =
+  private[this] val renderersBySuffix: Seq[(String, (List[String], String, String, RepositoryService.RepositoryInfo, Boolean, Boolean, Context) => Html)] =
     Seq(
-      ".md" -> ((filePath, fileContent, branch, repository, enableWikiLink, enableRefsLink, context) => markdown(fileContent, repository, enableWikiLink, enableRefsLink)(context)),
+      ".md"       -> ((filePath, fileContent, branch, repository, enableWikiLink, enableRefsLink, context) => markdown(fileContent, repository, enableWikiLink, enableRefsLink)(context)),
       ".markdown" -> ((filePath, fileContent, branch, repository, enableWikiLink, enableRefsLink, context) => markdown(fileContent, repository, enableWikiLink, enableRefsLink)(context))
     )
 
@@ -88,13 +89,18 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
   /**
    * Converts Markdown of Wiki pages to HTML.
    */
-  def markdown(value: String, repository: service.RepositoryService.RepositoryInfo,
-               enableWikiLink: Boolean, enableRefsLink: Boolean, enableTaskList: Boolean = false, hasWritePermission: Boolean = false)(implicit context: app.Context): Html =
-    Html(Markdown.toHtml(value, repository, enableWikiLink, enableRefsLink, enableTaskList, hasWritePermission))
+  def markdown(value: String,
+               repository: RepositoryService.RepositoryInfo,
+               enableWikiLink: Boolean,
+               enableRefsLink: Boolean,
+               enableTaskList: Boolean = false,
+               hasWritePermission: Boolean = false,
+               pages: List[String] = Nil)(implicit context: Context): Html =
+    Html(Markdown.toHtml(value, repository, enableWikiLink, enableRefsLink, enableTaskList, hasWritePermission, pages))
 
   def renderMarkup(filePath: List[String], fileContent: String, branch: String,
-                   repository: service.RepositoryService.RepositoryInfo,
-                   enableWikiLink: Boolean, enableRefsLink: Boolean)(implicit context: app.Context): Html = {
+                   repository: RepositoryService.RepositoryInfo,
+                   enableWikiLink: Boolean, enableRefsLink: Boolean)(implicit context: Context): Html = {
 
     val fileNameLower = filePath.reverse.head.toLowerCase
     renderersBySuffix.find { case (suffix, _) => fileNameLower.endsWith(suffix) } match {
@@ -111,20 +117,20 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
    * Returns <img> which displays the avatar icon for the given user name.
    * This method looks up Gravatar if avatar icon has not been configured in user settings.
    */
-  def avatar(userName: String, size: Int, tooltip: Boolean = false)(implicit context: app.Context): Html =
+  def avatar(userName: String, size: Int, tooltip: Boolean = false)(implicit context: Context): Html =
     getAvatarImageHtml(userName, size, "", tooltip)
 
   /**
    * Returns <img> which displays the avatar icon for the given mail address.
    * This method looks up Gravatar if avatar icon has not been configured in user settings.
    */
-  def avatar(commit: util.JGitUtil.CommitInfo, size: Int)(implicit context: app.Context): Html =
+  def avatar(commit: JGitUtil.CommitInfo, size: Int)(implicit context: Context): Html =
     getAvatarImageHtml(commit.authorName, size, commit.authorEmailAddress)
 
   /**
    * Converts commit id, issue id and username to the link.
    */
-  def link(value: String, repository: service.RepositoryService.RepositoryInfo)(implicit context: app.Context): Html =
+  def link(value: String, repository: RepositoryService.RepositoryInfo)(implicit context: Context): Html =
     Html(convertRefsLinks(value, repository))
 
   def cut(value: String, length: Int): String =
@@ -144,14 +150,14 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
   /**
    * Convert link notations in the activity message.
    */
-  def activityMessage(message: String)(implicit context: app.Context): Html =
+  def activityMessage(message: String)(implicit context: Context): Html =
     Html(message
-      .replaceAll("\\[issue:([^\\s]+?)/([^\\s]+?)#((\\d+))\\]"   , s"""<a href="${context.path}/$$1/$$2/issues/$$3">$$1/$$2#$$3</a>""")
-      .replaceAll("\\[pullreq:([^\\s]+?)/([^\\s]+?)#((\\d+))\\]" , s"""<a href="${context.path}/$$1/$$2/pull/$$3">$$1/$$2#$$3</a>""")
-      .replaceAll("\\[repo:([^\\s]+?)/([^\\s]+?)\\]"             , s"""<a href="${context.path}/$$1/$$2\">$$1/$$2</a>""")
-      .replaceAll("\\[branch:([^\\s]+?)/([^\\s]+?)#([^\\s]+?)\\]", (m: Match) => s"""<a href="${context.path}/${m.group(1)}/${m.group(2)}/tree/${encodeRefName(m.group(3))}">${m.group(3)}</a>""")
-      .replaceAll("\\[tag:([^\\s]+?)/([^\\s]+?)#([^\\s]+?)\\]"   , (m: Match) => s"""<a href="${context.path}/${m.group(1)}/${m.group(2)}/tree/${encodeRefName(m.group(3))}">${m.group(3)}</a>""")
-      .replaceAll("\\[user:([^\\s]+?)\\]"                        , (m: Match) => user(m.group(1)).body)
+      .replaceAll("\\[issue:([^\\s]+?)/([^\\s]+?)#((\\d+))\\]"     , s"""<a href="${context.path}/$$1/$$2/issues/$$3">$$1/$$2#$$3</a>""")
+      .replaceAll("\\[pullreq:([^\\s]+?)/([^\\s]+?)#((\\d+))\\]"   , s"""<a href="${context.path}/$$1/$$2/pull/$$3">$$1/$$2#$$3</a>""")
+      .replaceAll("\\[repo:([^\\s]+?)/([^\\s]+?)\\]"               , s"""<a href="${context.path}/$$1/$$2\">$$1/$$2</a>""")
+      .replaceAll("\\[branch:([^\\s]+?)/([^\\s]+?)#([^\\s]+?)\\]"  , (m: Match) => s"""<a href="${context.path}/${m.group(1)}/${m.group(2)}/tree/${encodeRefName(m.group(3))}">${m.group(3)}</a>""")
+      .replaceAll("\\[tag:([^\\s]+?)/([^\\s]+?)#([^\\s]+?)\\]"     , (m: Match) => s"""<a href="${context.path}/${m.group(1)}/${m.group(2)}/tree/${encodeRefName(m.group(3))}">${m.group(3)}</a>""")
+      .replaceAll("\\[user:([^\\s]+?)\\]"                          , (m: Match) => user(m.group(1)).body)
       .replaceAll("\\[commit:([^\\s]+?)/([^\\s]+?)\\@([^\\s]+?)\\]", (m: Match) => 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>""")
     )
 
@@ -167,34 +173,34 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
   /**
    * Generates the url to the repository.
    */
-  def url(repository: service.RepositoryService.RepositoryInfo)(implicit context: app.Context): String =
+  def url(repository: RepositoryService.RepositoryInfo)(implicit context: Context): String =
     s"${context.path}/${repository.owner}/${repository.name}"
 
   /**
    * Generates the url to the account page.
    */
-  def url(userName: String)(implicit context: app.Context): String = s"${context.path}/${userName}"
+  def url(userName: String)(implicit context: Context): String = s"${context.path}/${userName}"
 
   /**
    * Returns the url to the root of assets.
    */
-  def assets(implicit context: app.Context): String = s"${context.path}/assets"
+  def assets(implicit context: Context): String = s"${context.path}/assets"
 
   /**
    * Generates the text link to the account page.
    * 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: app.Context): Html =
+  def user(userName: String, mailAddress: String = "", styleClass: String = "")(implicit context: Context): Html =
     userWithContent(userName, mailAddress, styleClass)(Html(userName))
 
   /**
    * Generates the avatar link to the account page.
    * If user does not exist or disabled, this method returns avatar image without link.
    */
-  def avatarLink(userName: String, size: Int, mailAddress: String = "", tooltip: Boolean = false)(implicit context: app.Context): Html =
+  def avatarLink(userName: String, size: Int, mailAddress: String = "", tooltip: Boolean = false)(implicit context: Context): Html =
     userWithContent(userName, mailAddress)(avatar(userName, size, tooltip))
 
-  private def userWithContent(userName: String, mailAddress: String = "", styleClass: String = "")(content: Html)(implicit context: app.Context): Html =
+  private def userWithContent(userName: String, mailAddress: String = "", styleClass: String = "")(content: Html)(implicit context: Context): Html =
     (if(mailAddress.isEmpty){
       getAccountByUserName(userName)
     } else {
@@ -247,6 +253,8 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
     }
   }
 
+  def pre(value: Html): Html = Html(s"<pre>${value.body.trim.split("\n").map(_.trim).mkString("\n")}</pre>")
+
   /**
    * Implicit conversion to add mkHtml() to Seq[Html].
    */

src/main/scala/plugin/Plugin.scala

@@ -1,22 +0,0 @@
-package plugin
-
-import plugin.PluginSystem._
-import java.sql.Connection
-
-trait Plugin {
-  val id: String
-  val version: String
-  val author: String
-  val url: String
-  val description: String
-
-  def repositoryMenus       : List[RepositoryMenu]
-  def globalMenus           : List[GlobalMenu]
-  def repositoryActions     : List[RepositoryAction]
-  def globalActions         : List[Action]
-  def javaScripts           : List[JavaScript]
-}
-
-object PluginConnectionHolder {
-  val threadLocal = new ThreadLocal[Connection]
-}

src/main/scala/plugin/PluginSystem.scala

@@ -1,194 +0,0 @@
-package plugin
-
-import javax.servlet.http.{HttpServletResponse, HttpServletRequest}
-import org.slf4j.LoggerFactory
-import java.util.concurrent.atomic.AtomicBoolean
-import util.Directory._
-import util.ControlUtil._
-import org.apache.commons.io.{IOUtils, FileUtils}
-import Security._
-import service.PluginService
-import model.Profile._
-import profile.simple._
-import java.io.FileInputStream
-import java.sql.Connection
-import app.Context
-import service.RepositoryService.RepositoryInfo
-
-/**
- * Provides extension points to plug-ins.
- */
-object PluginSystem extends PluginService {
-
-  private val logger = LoggerFactory.getLogger(PluginSystem.getClass)
-
-  private val initialized = new AtomicBoolean(false)
-  private val pluginsMap = scala.collection.mutable.Map[String, Plugin]()
-  private val repositoriesList = scala.collection.mutable.ListBuffer[PluginRepository]()
-
-  def install(plugin: Plugin): Unit = {
-    pluginsMap.put(plugin.id, plugin)
-  }
-
-  def plugins: List[Plugin] = pluginsMap.values.toList
-
-  def uninstall(id: String)(implicit session: Session): Unit = {
-    pluginsMap.remove(id)
-
-    // Delete from PLUGIN table
-    deletePlugin(id)
-
-    // Drop tables
-    val pluginDir = new java.io.File(PluginHome)
-    val sqlFile = new java.io.File(pluginDir, s"${id}/sql/drop.sql")
-    if(sqlFile.exists){
-      val sql = IOUtils.toString(new FileInputStream(sqlFile), "UTF-8")
-      using(session.conn.createStatement()){ stmt =>
-        stmt.executeUpdate(sql)
-      }
-    }
-  }
-
-  def repositories: List[PluginRepository] = repositoriesList.toList
-
-  /**
-   * Initializes the plugin system. Load scripts from GITBUCKET_HOME/plugins.
-   */
-  def init()(implicit session: Session): Unit = {
-    if(initialized.compareAndSet(false, true)){
-      // Load installed plugins
-      val pluginDir = new java.io.File(PluginHome)
-      if(pluginDir.exists && pluginDir.isDirectory){
-        pluginDir.listFiles.filter(f => f.isDirectory && !f.getName.startsWith(".")).foreach { dir =>
-          installPlugin(dir.getName)
-        }
-      }
-      // Add default plugin repositories
-      repositoriesList += PluginRepository("central", "https://github.com/takezoe/gitbucket_plugins.git")
-    }
-  }
-
-  // TODO Method name seems to not so good.
-  def installPlugin(id: String)(implicit session: Session): Unit = {
-    val pluginHome = new java.io.File(PluginHome)
-    val pluginDir  = new java.io.File(pluginHome, id)
-
-    val scalaFile = new java.io.File(pluginDir, "plugin.scala")
-    if(scalaFile.exists && scalaFile.isFile){
-      val properties = new java.util.Properties()
-      using(new java.io.FileInputStream(new java.io.File(pluginDir, "plugin.properties"))){ in =>
-        properties.load(in)
-      }
-
-      val pluginId     = properties.getProperty("id")
-      val version      = properties.getProperty("version")
-      val author       = properties.getProperty("author")
-      val url          = properties.getProperty("url")
-      val description  = properties.getProperty("description")
-
-      val source = s"""
-        |val id          = "${pluginId}"
-        |val version     = "${version}"
-        |val author      = "${author}"
-        |val url         = "${url}"
-        |val description = "${description}"
-      """.stripMargin + FileUtils.readFileToString(scalaFile, "UTF-8")
-
-      try {
-        // Compile and eval Scala source code
-        ScalaPlugin.eval(pluginDir.listFiles.filter(_.getName.endsWith(".scala.html")).map { file =>
-          ScalaPlugin.compileTemplate(
-            id.replace("-", ""),
-            file.getName.stripSuffix(".scala.html"),
-            IOUtils.toString(new FileInputStream(file)))
-        }.mkString("\n") + source)
-
-        // Migrate database
-        val plugin = getPlugin(pluginId)
-        if(plugin.isEmpty){
-          registerPlugin(model.Plugin(pluginId, version))
-          migrate(session.conn, pluginId, "0.0")
-        } else {
-          updatePlugin(model.Plugin(pluginId, version))
-          migrate(session.conn, pluginId, plugin.get.version)
-        }
-      } catch {
-        case e: Throwable => logger.warn(s"Error in plugin loading for ${scalaFile.getAbsolutePath}", e)
-      }
-    }
-  }
-
-  // TODO Should PluginSystem provide a way to migrate resources other than H2?
-  private def migrate(conn: Connection, pluginId: String, current: String): Unit = {
-    val pluginDir = new java.io.File(PluginHome)
-
-    // TODO Is ot possible to use this migration system in GitBucket migration?
-    val dim = current.split("\\.")
-    val currentVersion = Version(dim(0).toInt, dim(1).toInt)
-
-    val sqlDir = new java.io.File(pluginDir, s"${pluginId}/sql")
-    if(sqlDir.exists && sqlDir.isDirectory){
-      sqlDir.listFiles.filter(_.getName.endsWith(".sql")).map { file =>
-        val array = file.getName.replaceFirst("\\.sql", "").split("_")
-        Version(array(0).toInt, array(1).toInt)
-      }
-      .sorted.reverse.takeWhile(_ > currentVersion)
-      .reverse.foreach { version =>
-        val sqlFile = new java.io.File(pluginDir, s"${pluginId}/sql/${version.major}_${version.minor}.sql")
-        val sql = IOUtils.toString(new FileInputStream(sqlFile), "UTF-8")
-        using(conn.createStatement()){ stmt =>
-          stmt.executeUpdate(sql)
-        }
-      }
-    }
-  }
-
-  case class Version(major: Int, minor: Int) extends Ordered[Version] {
-
-    override def compare(that: Version): Int = {
-      if(major != that.major){
-        major.compare(that.major)
-      } else{
-        minor.compare(that.minor)
-      }
-    }
-
-    def displayString: String = major + "." + minor
-  }
-
-  def repositoryMenus       : List[RepositoryMenu]   = pluginsMap.values.flatMap(_.repositoryMenus).toList
-  def globalMenus           : List[GlobalMenu]       = pluginsMap.values.flatMap(_.globalMenus).toList
-  def repositoryActions     : List[RepositoryAction] = pluginsMap.values.flatMap(_.repositoryActions).toList
-  def globalActions         : List[Action]           = pluginsMap.values.flatMap(_.globalActions).toList
-  def javaScripts           : List[JavaScript]       = pluginsMap.values.flatMap(_.javaScripts).toList
-
-  // Case classes to hold plug-ins information internally in GitBucket
-  case class PluginRepository(id: String, url: String)
-  case class GlobalMenu(label: String, url: String, icon: String, condition: Context => Boolean)
-  case class RepositoryMenu(label: String, name: String, url: String, icon: String, condition: Context => Boolean)
-  case class Action(method: String, path: String, security: Security, function: (HttpServletRequest, HttpServletResponse, Context) => Any)
-  case class RepositoryAction(method: String, path: String, security: Security, function: (HttpServletRequest, HttpServletResponse, Context, RepositoryInfo) => Any)
-  case class Button(label: String, href: String)
-  case class JavaScript(filter: String => Boolean, script: String)
-
-  /**
-   * Checks whether the plugin is updatable.
-   */
-  def isUpdatable(oldVersion: String, newVersion: String): Boolean = {
-    if(oldVersion == newVersion){
-      false
-    } else {
-      val dim1 = oldVersion.split("\\.").map(_.toInt)
-      val dim2 = newVersion.split("\\.").map(_.toInt)
-      dim1.zip(dim2).foreach { case (a, b) =>
-        if(a < b){
-          return true
-        } else if(a > b){
-          return false
-        }
-      }
-      return false
-    }
-  }
-
-}

src/main/scala/plugin/PluginUpdateJob.scala

@@ -1,66 +0,0 @@
-package plugin
-
-import util.Directory._
-import org.eclipse.jgit.api.Git
-import org.slf4j.LoggerFactory
-import org.quartz.{Scheduler, JobExecutionContext, Job}
-import org.quartz.JobBuilder._
-import org.quartz.TriggerBuilder._
-import org.quartz.SimpleScheduleBuilder._
-
-class PluginUpdateJob extends Job {
-
-  private val logger = LoggerFactory.getLogger(classOf[PluginUpdateJob])
-  private var failedCount = 0
-
-  /**
-   * Clone or pull all plugin repositories
-   *
-   * TODO Support plugin repository access through the proxy server
-   */
-  override def execute(context: JobExecutionContext): Unit = {
-    try {
-      if(failedCount > 3){
-        logger.error("Skip plugin information updating because failed count is over limit")
-      } else {
-        logger.info("Start plugin information updating")
-        PluginSystem.repositories.foreach { repository =>
-          logger.info(s"Updating ${repository.id}: ${repository.url}...")
-          val dir = getPluginCacheDir()
-          val repo = new java.io.File(dir, repository.id)
-          if(repo.exists){
-            // pull if the repository is already cloned
-            Git.open(repo).pull().call()
-          } else {
-            // clone if the repository is not exist
-            Git.cloneRepository().setURI(repository.url).setDirectory(repo).call()
-          }
-        }
-        logger.info("End plugin information updating")
-      }
-    } catch {
-      case e: Exception => {
-        failedCount = failedCount + 1
-        logger.error("Failed to update plugin information", e)
-      }
-    }
-  }
-}
-
-object PluginUpdateJob {
-
-  def schedule(scheduler: Scheduler): Unit = {
-    val job = newJob(classOf[PluginUpdateJob])
-      .withIdentity("pluginUpdateJob")
-      .build()
-
-    val trigger = newTrigger()
-      .withIdentity("pluginUpdateTrigger")
-      .startNow()
-      .withSchedule(simpleSchedule().withIntervalInHours(24).repeatForever())
-      .build()
-
-    scheduler.scheduleJob(job, trigger)
-  }
-
-}

src/main/scala/plugin/ScalaPlugin.scala

@@ -1,77 +0,0 @@
-package plugin
-
-import scala.collection.mutable.ListBuffer
-import javax.servlet.http.{HttpServletResponse, HttpServletRequest}
-import app.Context
-import plugin.PluginSystem._
-import plugin.PluginSystem.RepositoryMenu
-import plugin.Security._
-import service.RepositoryService.RepositoryInfo
-import scala.reflect.runtime.currentMirror
-import scala.tools.reflect.ToolBox
-import play.twirl.compiler.TwirlCompiler
-import scala.io.Codec
-
-// TODO This is a sample implementation for Scala based plug-ins.
-class ScalaPlugin(val id: String, val version: String,
-                  val author: String, val url: String, val description: String) extends Plugin {
-
-  private val repositoryMenuList   = ListBuffer[RepositoryMenu]()
-  private val globalMenuList       = ListBuffer[GlobalMenu]()
-  private val repositoryActionList = ListBuffer[RepositoryAction]()
-  private val globalActionList     = ListBuffer[Action]()
-  private val javaScriptList       = ListBuffer[JavaScript]()
-
-  def repositoryMenus       : List[RepositoryMenu]   = repositoryMenuList.toList
-  def globalMenus           : List[GlobalMenu]       = globalMenuList.toList
-  def repositoryActions     : List[RepositoryAction] = repositoryActionList.toList
-  def globalActions         : List[Action]           = globalActionList.toList
-  def javaScripts           : List[JavaScript]       = javaScriptList.toList
-
-  def addRepositoryMenu(label: String, name: String, url: String, icon: String)(condition: (Context) => Boolean): Unit = {
-    repositoryMenuList += RepositoryMenu(label, name, url, icon, condition)
-  }
-
-  def addGlobalMenu(label: String, url: String, icon: String)(condition: (Context) => Boolean): Unit = {
-    globalMenuList += GlobalMenu(label, url, icon, condition)
-  }
-
-  def addGlobalAction(method: String, path: String, security: Security = All())(function: (HttpServletRequest, HttpServletResponse, Context) => Any): Unit = {
-    globalActionList += Action(method, path, security, function)
-  }
-
-  def addRepositoryAction(method: String, path: String, security: Security = All())(function: (HttpServletRequest, HttpServletResponse, Context, RepositoryInfo) => Any): Unit = {
-    repositoryActionList += RepositoryAction(method, path, security, function)
-  }
-
-  def addJavaScript(filter: String => Boolean, script: String): Unit = {
-    javaScriptList += JavaScript(filter, script)
-  }
-
-}
-
-object ScalaPlugin {
-
-  def define(id: String, version: String, author: String, url: String, description: String)
-    = new ScalaPlugin(id, version, author, url, description)
-
-  def eval(source: String): Any = {
-    val toolbox = currentMirror.mkToolBox()
-    val tree = toolbox.parse(source)
-    toolbox.eval(tree)
-  }
-
-  def compileTemplate(packageName: String, name: String, source: String): String = {
-    val result = TwirlCompiler.parseAndGenerateCodeNewParser(
-      Array(packageName, name),
-      source.getBytes("UTF-8"),
-      Codec(scala.util.Properties.sourceEncoding),
-      "",
-      "play.twirl.api.HtmlFormat.Appendable",
-      "play.twirl.api.HtmlFormat",
-      "",
-      false)
-
-    result.replaceFirst("package .*", "")
-  }
-}

src/main/scala/plugin/Security.scala

@@ -1,36 +0,0 @@
-package plugin
-
-/**
- * Defines enum case classes to specify permission for actions which is provided by plugin.
- */
-object Security {
-
-  sealed trait Security
-
-  /**
-   * All users and guests
-   */
-  case class All() extends Security
-
-  /**
-   * Only signed-in users
-   */
-  case class Login() extends Security
-
-  /**
-   * Only repository owner and collaborators
-   */
-  case class Member() extends Security
-
-  /**
-   * Only repository owner and managers of group repository
-   */
-  case class Owner() extends Security
-
-  /**
-   * Only administrators
-   */
-  case class Admin() extends Security
-
-}
-