Add Version 3.0 to versions

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

README.md

@@ -79,6 +79,12 @@ 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

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"/>
 

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,
@@ -45,12 +58,15 @@ object MyBuild extends Build {
       "com.typesafe.slick" %% "slick" % "2.1.0",
       "com.novell.ldap" % "jldap" % "2009-10-07",
       "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/scala/ScalatraBootstrap.scala

@@ -1,5 +1,9 @@
-import _root_.servlet.{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._
@@ -15,6 +19,11 @@ class ScalatraBootstrap extends LifeCycle {
 
     // 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")
@@ -31,7 +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/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
@@ -103,21 +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 }))
@@ -145,7 +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
   })
 
@@ -189,7 +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
   })
 
@@ -211,7 +214,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
       if(context.loginAccount.isDefined){
         redirect("/")
       } else {
-        account.html.register()
+        html.register()
       }
     } else NotFound
   }
@@ -225,7 +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 =>
@@ -241,7 +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))
     }
   })
 
@@ -290,7 +293,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
    * Show the new repository form.
    */
   get("/new")(usersOnly {
-    account.html.newrepo(getGroupsByUserName(context.loginAccount.get.userName), context.settings.isCreateRepoOptionPublic)
+    html.newrepo(getGroupsByUserName(context.loginAccount.get.userName), context.settings.isCreateRepoOptionPublic)
   })
 
   /**
@@ -366,7 +369,7 @@ trait AccountControllerBase extends AccountManagementControllerBase {
           val members = getGroupMembers(group)
           context.loginAccount.exists(x => members.exists { member => member.userName == x.userName && member.isManager })
         }
-        _root_.helper.html.forkrepository(
+        helper.html.forkrepository(
           repository,
           (groups zip managerPermissions).toMap
         )

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

@@ -1,4 +1,4 @@
-package app
+package gitbucket.core.controller
 
 class AnonymousAccessController extends AnonymousAccessControllerBase
 

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 {

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()
   })
@@ -301,7 +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) = {
@@ -325,13 +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 {
@@ -346,11 +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
@@ -371,7 +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 {
@@ -381,7 +383,7 @@ trait IssuesControllerBase extends ControllerBase {
             }
         }
 
-        issue -> commentId
+        commentId.map( issue -> _ )
       }
     }
   }
@@ -395,7 +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)
@@ -403,7 +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}
@@ -17,7 +22,6 @@ 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
@@ -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
     }
@@ -217,7 +221,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
             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
@@ -233,7 +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),
@@ -260,7 +264,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     val oldLineNumber = params.get("oldLineNumber") map (_.toInt)
     val newLineNumber = params.get("newLineNumber") map (_.toInt)
     val issueId   = params.get("issueId") map (_.toInt)
-    repo.html.commentform(
+    html.commentform(
       commitId = id,
       fileName, oldLineNumber, newLineNumber, issueId,
       hasWritePermission = hasWritePermission(repository.owner, repository.name, context.loginAccount),
@@ -284,7 +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")
@@ -322,14 +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)
   })
 
   /**
@@ -369,7 +370,7 @@ trait RepositoryViewerControllerBase extends ControllerBase {
    * Displays tags.
    */
   get("/:owner/:repository/tags")(referrersOnly {
-    repo.html.tags(_)
+    html.tags(_)
   })
 
   /**
@@ -386,7 +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),
@@ -397,7 +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 {
@@ -420,7 +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
@@ -439,11 +440,11 @@ 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[model.Account] => getGroupsByUserName(account.get.userName)
+                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),
@@ -454,7 +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) = {
 
@@ -562,6 +563,6 @@ trait RepositoryViewerControllerBase extends ControllerBase {
     }
   }
 
-  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

@@ -1,10 +1,11 @@
-package app
+package gitbucket.core.controller
 
-import service.{AccountService, SystemSettingsService}
+import gitbucket.core.admin.html
+import gitbucket.core.service.{AccountService, SystemSettingsService}
+import gitbucket.core.util.AdminAuthenticator
+import gitbucket.core.ssh.SshServer
 import SystemSettingsService._
-import util.AdminAuthenticator
 import jp.sf.amateras.scalatra.forms._
-import ssh.SshServer
 
 class SystemSettingsController extends SystemSettingsControllerBase
   with AccountService with AdminAuthenticator
@@ -59,7 +60,7 @@ trait SystemSettingsControllerBase extends ControllerBase {
   case class PluginForm(pluginIds: List[String])
 
   get("/admin/system")(adminOnly {
-    admin.html.system(flash.get("info"))
+    html.system(flash.get("info"))
   })
 
   post("/admin/system", form)(adminOnly { form =>
@@ -70,7 +71,7 @@ trait SystemSettingsControllerBase extends ControllerBase {
     }
 
     if(form.ssh && !SshServer.isActive && form.baseUrl.isDefined){
-      SshServer.start(request.getServletContext,
+      SshServer.start(
         form.sshPort.getOrElse(SystemSettingsService.DefaultSshPort),
         form.baseUrl.get)
     } else if(!form.ssh && SshServer.isActive){

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
       }
     }

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}]",

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

@@ -1,9 +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}
-import util.JGitUtil
 
 trait PullRequestService { self: IssuesService =>
   import PullRequestService._
@@ -94,6 +94,26 @@ trait PullRequestService { self: IssuesService =>
         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, Label}
-import util.JGitUtil
 
 trait RepositoryService { self: AccountService =>
   import RepositoryService._
@@ -375,7 +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
 

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

@@ -1,16 +1,15 @@
-package servlet
+package gitbucket.core.servlet
 
 import javax.servlet._
 import javax.servlet.http._
-import service.{SystemSettingsService, AccountService, RepositoryService}
-import model._
+import gitbucket.core.service.{RepositoryService, AccountService, SystemSettingsService}
+import gitbucket.core.util.{ControlUtil, Keys, Implicits}
 import org.slf4j.LoggerFactory
-import util.Implicits._
-import util.ControlUtil._
-import util.Keys
+import Implicits._
+import ControlUtil._
 
 /**
- * Provides BASIC Authentication for [[servlet.GitRepositoryServlet]].
+ * Provides BASIC Authentication for [[GitRepositoryServlet]].
  */
 class BasicAuthenticationFilter extends Filter with RepositoryService with AccountService with SystemSettingsService {
 

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 {
 

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

@@ -1,61 +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 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")
@@ -93,8 +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")
@@ -102,20 +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){
@@ -143,8 +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 =>
@@ -193,14 +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 {
+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){
@@ -208,47 +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)
     }
+
   }
 
-  def contextDestroyed(sce: ServletContextEvent): Unit = {
+  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._
@@ -16,7 +17,6 @@ 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
 
@@ -134,6 +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.
    * 
@@ -705,4 +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.

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

@@ -1,17 +1,18 @@
-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 {
 
@@ -19,12 +20,12 @@ object Markdown {
    * Converts Markdown of Wiki pages to HTML.
    */
   def toHtml(markdown: String,
-             repository: service.RepositoryService.RepositoryInfo,
+             repository: RepositoryService.RepositoryInfo,
              enableWikiLink: Boolean,
              enableRefsLink: Boolean,
              enableTaskList: Boolean = false,
              hasWritePermission: Boolean = false,
-             pages: List[String] = Nil)(implicit context: app.Context): String = {
+             pages: List[String] = Nil)(implicit context: Context): String = {
 
     // escape issue id
     val s = if(enableRefsLink){
@@ -45,8 +46,8 @@ object Markdown {
 }
 
 class GitBucketLinkRender(
-    context: app.Context,
-    repository: service.RepositoryService.RepositoryInfo,
+    context: Context,
+    repository: RepositoryService.RepositoryInfo,
     enableWikiLink: Boolean,
     pages: List[String]) extends LinkRenderer with WikiService {
 
@@ -96,13 +97,13 @@ class GitBucketVerbatimSerializer extends VerbatimSerializer {
 
 class GitBucketHtmlSerializer(
     markdown: String,
-    repository: service.RepositoryService.RepositoryInfo,
+    repository: RepositoryService.RepositoryInfo,
     enableWikiLink: Boolean,
     enableRefsLink: Boolean,
     enableTaskList: Boolean,
     hasWritePermission: Boolean,
     pages: List[String]
-  )(implicit val context: app.Context) extends ToHtmlSerializer(
+  )(implicit val context: Context) extends ToHtmlSerializer(
     new GitBucketLinkRender(context, repository, enableWikiLink, pages),
     Map[String, VerbatimSerializer](VerbatimSerializer.DEFAULT -> new GitBucketVerbatimSerializer).asJava
   ) with LinkConverter with RequestCache {

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.
@@ -75,7 +78,7 @@ 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)),
       ".markdown" -> ((filePath, fileContent, branch, repository, enableWikiLink, enableRefsLink, context) => markdown(fileContent, repository, enableWikiLink, enableRefsLink)(context))
@@ -87,17 +90,17 @@ object helpers extends AvatarImageProvider with LinkConverter with RequestCache
    * Converts Markdown of Wiki pages to HTML.
    */
   def markdown(value: String,
-               repository: service.RepositoryService.RepositoryInfo,
+               repository: RepositoryService.RepositoryInfo,
                enableWikiLink: Boolean,
                enableRefsLink: Boolean,
                enableTaskList: Boolean = false,
                hasWritePermission: Boolean = false,
-               pages: List[String] = Nil)(implicit context: app.Context): Html =
+               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 {
@@ -114,20 +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 =
@@ -147,7 +150,7 @@ 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>""")
@@ -170,34 +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 {

src/main/scala/servlet/TransactionFilter.scala

@@ -1,45 +0,0 @@
-package servlet
-
-import javax.servlet._
-import org.slf4j.LoggerFactory
-import javax.servlet.http.HttpServletRequest
-import 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(req.getServletContext) withTransaction { session =>
-        logger.debug("begin transaction")
-        req.setAttribute(Keys.Request.DBSession, session)
-        chain.doFilter(req, res)
-        logger.debug("end transaction")
-      }
-    }
-  }
-
-}
-
-object Database {
-
-  def apply(context: ServletContext): slick.jdbc.JdbcBackend.Database =
-    slick.jdbc.JdbcBackend.Database.forURL(context.getInitParameter("db.url"),
-        context.getInitParameter("db.user"),
-        context.getInitParameter("db.password"))
-
-  def getSession(req: ServletRequest): slick.jdbc.JdbcBackend#Session =
-    req.getAttribute(Keys.Request.DBSession).asInstanceOf[slick.jdbc.JdbcBackend#Session]
-
-}

src/main/twirl/error.scala.html

@@ -1,4 +0,0 @@
-@(title: String)(implicit context: app.Context)
-@main("Error"){
-  <h1>@title</h1>
-}

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

@@ -1,6 +1,8 @@
-@(account: model.Account, groupNames: List[String], activities: List[model.Activity])(implicit context: app.Context)
+@(account: gitbucket.core.model.Account,
+  groupNames: List[String],
+  activities: List[gitbucket.core.model.Activity])(implicit context: gitbucket.core.controller.Context)
 @import context._
-@import view.helpers._
+@import gitbucket.core.view.helpers._
 @main(account, groupNames, "activity"){
   <div class="pull-right">
     <a href="@path/@{account.userName}.atom"><img src="@assets/common/images/feed.png" alt="activities"></a>

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

@@ -1,7 +1,7 @@
-@(account: model.Account, info: Option[Any])(implicit context: app.Context)
+@(account: gitbucket.core.model.Account, info: Option[Any])(implicit context: gitbucket.core.controller.Context)
+@import gitbucket.core.util.LDAPUtil
 @import context._
-@import view.helpers._
-@import util.LDAPUtil
+@import gitbucket.core.view.helpers._
 @html.main("Edit your profile"){
 <div class="container">
   <div class="row-fluid">

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

@@ -1,6 +1,6 @@
-@(account: Option[model.Account], members: List[model.GroupMember])(implicit context: app.Context)
+@(account: Option[gitbucket.core.model.Account], members: List[gitbucket.core.model.GroupMember])(implicit context: gitbucket.core.controller.Context)
 @import context._
-@import view.helpers._
+@import gitbucket.core.view.helpers._
 @html.main(if(account.isEmpty) "Create group" else "Edit group"){
 <div class="container">
   <form id="form" method="post" action="@if(account.isEmpty){@path/groups/new} else {@path/@account.get.userName/_editgroup}" validate="true">

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

@@ -1,7 +1,7 @@
-@(account: model.Account, groupNames: List[String], active: String,
-  isGroupManager: Boolean = false)(body: Html)(implicit context: app.Context)
+@(account: gitbucket.core.model.Account, groupNames: List[String], active: String,
+  isGroupManager: Boolean = false)(body: Html)(implicit context: gitbucket.core.controller.Context)
 @import context._
-@import view.helpers._
+@import gitbucket.core.view.helpers._
 @html.main(account.userName){
   <div class="container">
     <div class="container-fluid">

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

@@ -1,6 +1,6 @@
-@(account: model.Account, members: List[String], isGroupManager: Boolean)(implicit context: app.Context)
+@(account: gitbucket.core.model.Account, members: List[String], isGroupManager: Boolean)(implicit context: gitbucket.core.controller.Context)
 @import context._
-@import view.helpers._
+@import gitbucket.core.view.helpers._
 @main(account, Nil, "members", isGroupManager){
   @if(members.isEmpty){
     No members

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

@@ -1,4 +1,4 @@
-@(active: String, ssh: Boolean)(implicit context: app.Context)
+@(active: String, ssh: Boolean)(implicit context: gitbucket.core.controller.Context)
 @import context._
 <div class="box">
   <ul class="nav nav-tabs nav-stacked side-menu">