Merge remote-tracking branch 'origin/branch-4.5'

Conflicts:
	server/sonar-server/src/main/java/org/sonar/server/rule/index/RuleIndex.java
	sonar-batch/src/main/java/org/sonar/batch/scan2/DefaultFileLinesContextFactory.java

26 files changed, 94 insertions, 113 deletions

diff --git a/debug.sh b/debug-server.sh
index 5dadb3becab..1d1549d9c4d 100755
--- a/debug.sh
+++ b/debug-server.sh
@@ -7,4 +7,4 @@ if ! ls sonarqube-*/bin/sonar-application*.jar &> /dev/null; then
 fi
 
 cd sonarqube-*
-java -jar ./lib/sonar-application*.jar -Dsonar.web.javaOpts=-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=5005
\ No newline at end of file
+java -jar ./lib/sonar-application*.jar -Dsonar.web.javaAdditionalOpts=-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=5005
diff --git a/jacoco_build.sh b/jacoco-build.sh
index 11ceb34f316..11ceb34f316 100644
--- a/jacoco_build.sh
+++ b/jacoco-build.sh
diff --git a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/timemachine/VariationDecorator.java b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/timemachine/VariationDecorator.java
index 19d1dd93207..8f54748066f 100644
--- a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/timemachine/VariationDecorator.java
+++ b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/timemachine/VariationDecorator.java
@@ -95,10 +95,10 @@ public class VariationDecorator implements Decorator {
 
   private void computeVariation(Resource resource, DecoratorContext context, PastSnapshot pastSnapshot) {
     List<Object[]> pastMeasures = pastMeasuresLoader.getPastMeasures(resource, pastSnapshot);
-    compareWithPastMeasures(resource, context, pastSnapshot.getIndex(), pastMeasures);
+    compareWithPastMeasures(context, pastSnapshot.getIndex(), pastMeasures);
   }
 
-  void compareWithPastMeasures(Resource resource, DecoratorContext context, int index, List<Object[]> pastMeasures) {
+  private void compareWithPastMeasures(DecoratorContext context, int index, List<Object[]> pastMeasures) {
     Map<MeasureKey, Object[]> pastMeasuresByKey = Maps.newHashMap();
     for (Object[] pastMeasure : pastMeasures) {
       pastMeasuresByKey.put(new MeasureKey(pastMeasure), pastMeasure);
diff --git a/server/sonar-process-monitor/src/main/java/org/sonar/process/monitor/JavaCommand.java b/server/sonar-process-monitor/src/main/java/org/sonar/process/monitor/JavaCommand.java
index 7750b6deb35..76abf52deba 100644
--- a/server/sonar-process-monitor/src/main/java/org/sonar/process/monitor/JavaCommand.java
+++ b/server/sonar-process-monitor/src/main/java/org/sonar/process/monitor/JavaCommand.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.process.monitor;
 
+import org.apache.commons.lang.StringUtils;
+
 import javax.annotation.Nullable;
 
 import java.io.File;
@@ -84,12 +86,16 @@ public class JavaCommand {
   }
 
   public JavaCommand addJavaOption(String s) {
-    javaOptions.add(s);
+    if (StringUtils.isNotBlank(s)) {
+      javaOptions.add(s);
+    }
     return this;
   }
 
   public JavaCommand addJavaOptions(String s) {
-    Collections.addAll(javaOptions, s.split(" "));
+    for (String opt : s.split(" ")) {
+      addJavaOption(opt);
+    }
     return this;
   }
 
diff --git a/server/sonar-process-monitor/src/test/java/org/sonar/process/monitor/JavaCommandTest.java b/server/sonar-process-monitor/src/test/java/org/sonar/process/monitor/JavaCommandTest.java
index fbfbad11b54..689f061ff06 100644
--- a/server/sonar-process-monitor/src/test/java/org/sonar/process/monitor/JavaCommandTest.java
+++ b/server/sonar-process-monitor/src/test/java/org/sonar/process/monitor/JavaCommandTest.java
@@ -65,8 +65,13 @@ public class JavaCommandTest {
   }
 
   @Test
-  public void split_java_options() throws Exception {
+  public void add_java_options() throws Exception {
     JavaCommand command = new JavaCommand("foo");
+    assertThat(command.getJavaOptions()).isEmpty();
+
+    command.addJavaOptions("");
+    assertThat(command.getJavaOptions()).isEmpty();
+
     command.addJavaOptions("-Xmx512m -Xms256m -Dfoo");
     assertThat(command.getJavaOptions()).containsOnly("-Xmx512m", "-Xms256m", "-Dfoo");
   }
diff --git a/server/sonar-server/src/main/java/org/sonar/server/activity/ws/ActivityMapping.java b/server/sonar-server/src/main/java/org/sonar/server/activity/ws/ActivityMapping.java
index e2910b6c4ea..668b072dad9 100644
--- a/server/sonar-server/src/main/java/org/sonar/server/activity/ws/ActivityMapping.java
+++ b/server/sonar-server/src/main/java/org/sonar/server/activity/ws/ActivityMapping.java
@@ -19,14 +19,12 @@
  */
 package org.sonar.server.activity.ws;
 
-import org.sonar.api.resources.Languages;
 import org.sonar.api.utils.text.JsonWriter;
 import org.sonar.core.activity.Activity;
 import org.sonar.server.activity.index.ActivityDoc;
 import org.sonar.server.activity.index.ActivityNormalizer;
 import org.sonar.server.search.ws.BaseMapping;
 import org.sonar.server.search.ws.SearchOptions;
-import org.sonar.server.text.MacroInterpreter;
 
 import java.util.Map;
 
@@ -35,7 +33,7 @@ import java.util.Map;
  */
 public class ActivityMapping extends BaseMapping<ActivityDoc, Object> {
 
-  public ActivityMapping(Languages languages, MacroInterpreter macroInterpreter) {
+  public ActivityMapping() {
     map("type", ActivityNormalizer.LogFields.TYPE.field());
     map("action", ActivityNormalizer.LogFields.ACTION.field());
     mapDateTime("createdAt", ActivityNormalizer.LogFields.CREATED_AT.field());
diff --git a/server/sonar-server/src/main/java/org/sonar/server/rule/index/RuleIndex.java b/server/sonar-server/src/main/java/org/sonar/server/rule/index/RuleIndex.java
index 968c9b46448..c008bd971d0 100644
--- a/server/sonar-server/src/main/java/org/sonar/server/rule/index/RuleIndex.java
+++ b/server/sonar-server/src/main/java/org/sonar/server/rule/index/RuleIndex.java
@@ -56,7 +56,6 @@ import org.sonar.server.search.Result;
 import org.sonar.server.search.SearchClient;
 
 import javax.annotation.CheckForNull;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -158,7 +157,7 @@ public class RuleIndex extends BaseIndex<Rule, RuleDto, RuleKey> {
   }
 
   /* Build main query (search based) */
-  protected QueryBuilder getQuery(RuleQuery query, QueryContext options) {
+  protected QueryBuilder getQuery(RuleQuery query) {
 
     // No contextual query case
     String queryText = query.getQueryText();
@@ -413,7 +412,7 @@ public class RuleIndex extends BaseIndex<Rule, RuleDto, RuleKey> {
       esSearch.setScroll(TimeValue.timeValueMinutes(3));
     }
 
-    QueryBuilder qb = this.getQuery(query, options);
+    QueryBuilder qb = this.getQuery(query);
     HashMap<String, FilterBuilder> filters = this.getFilters(query, options);
 
     if (options.isFacet()) {
diff --git a/server/sonar-server/src/main/java/org/sonar/server/search/SearchClient.java b/server/sonar-server/src/main/java/org/sonar/server/search/SearchClient.java
index 5cf1ba3dc72..de1234cd280 100644
--- a/server/sonar-server/src/main/java/org/sonar/server/search/SearchClient.java
+++ b/server/sonar-server/src/main/java/org/sonar/server/search/SearchClient.java
@@ -99,7 +99,7 @@ public class SearchClient extends TransportClient implements Startable {
       }
       return response;
     } catch (Exception e) {
-      LOGGER.error("could not execute request: " + response, e);
+      LOGGER.error("could not execute request: {}", request);
       throw new IllegalStateException("ES error: ", e);
     }
   }
diff --git a/server/sonar-server/src/test/java/org/sonar/server/startup/GeneratePluginIndexTest.java b/server/sonar-server/src/test/java/org/sonar/server/startup/GeneratePluginIndexTest.java
index 0fbabca058e..cc96395bc62 100644
--- a/server/sonar-server/src/test/java/org/sonar/server/startup/GeneratePluginIndexTest.java
+++ b/server/sonar-server/src/test/java/org/sonar/server/startup/GeneratePluginIndexTest.java
@@ -22,7 +22,9 @@ package org.sonar.server.startup;
 import org.apache.commons.io.FileUtils;
 import org.hamcrest.core.Is;
 import org.junit.Before;
+import org.junit.Rule;
 import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
 import org.sonar.api.platform.PluginMetadata;
 import org.sonar.api.platform.PluginRepository;
 import org.sonar.core.plugins.DefaultPluginMetadata;
@@ -40,6 +42,9 @@ import static org.mockito.Mockito.when;
 
 public class GeneratePluginIndexTest {
 
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
   private DefaultServerFileSystem fileSystem;
   private File index;
 
@@ -65,10 +70,11 @@ public class GeneratePluginIndexTest {
     assertThat(lines.get(1), containsString("checkstyle"));
   }
 
-  private PluginMetadata newMetadata(String pluginKey) {
+  private PluginMetadata newMetadata(String pluginKey) throws IOException {
     PluginMetadata plugin = mock(DefaultPluginMetadata.class);
     when(plugin.getKey()).thenReturn(pluginKey);
-    when(plugin.getFile()).thenReturn(new File(pluginKey + ".jar"));
+    File pluginFile = temp.newFile(pluginKey + ".jar");
+    when(plugin.getFile()).thenReturn(pluginFile);
     return plugin;
   }
 }
diff --git a/server/sonar-web/src/main/coffee/coding-rules/views/coding-rules-detail-view.coffee b/server/sonar-web/src/main/coffee/coding-rules/views/coding-rules-detail-view.coffee
index 67776649b39..16ba0bb7925 100644
--- a/server/sonar-web/src/main/coffee/coding-rules/views/coding-rules-detail-view.coffee
+++ b/server/sonar-web/src/main/coffee/coding-rules/views/coding-rules-detail-view.coffee
@@ -152,7 +152,7 @@ define [
         @$(@qualityProfilesRegion.el).show()
         @qualityProfilesRegion.show @qualityProfilesView
 
-        if @options.app.getQualityProfile()
+        if @options.app.getQualityProfile() and (@options.app.canWrite or @contextProfile.has('severity'))
           @$(@contextRegion.el).show()
           @contextRegion.show @contextQualityProfileView
         else
diff --git a/server/sonar-web/src/main/coffee/component-viewer/main.coffee b/server/sonar-web/src/main/coffee/component-viewer/main.coffee
index 15e2a13d138..e6da45caa2f 100644
--- a/server/sonar-web/src/main/coffee/component-viewer/main.coffee
+++ b/server/sonar-web/src/main/coffee/component-viewer/main.coffee
@@ -131,7 +131,7 @@ define [
 
       width = @elementToFit.width()
       height = @elementToFit.height()
-      availableWidth = width - workspace.outerWidth(true)
+      availableWidth = width - workspace.outerWidth(true) - 20
       availableHeight = height - @$(@headerRegion.$el).outerHeight(true)
 
       source.removeClass 'overflow'
diff --git a/server/sonar-web/src/main/js/issues/app.js b/server/sonar-web/src/main/js/issues/app.js
index 43411efffb2..861636f8089 100644
--- a/server/sonar-web/src/main/js/issues/app.js
+++ b/server/sonar-web/src/main/js/issues/app.js
@@ -371,7 +371,7 @@ requirejs(
 
           var detailsEl = jQuery('.navigator-details'),
               detailsWidth = jQuery(window).width() - detailsEl.offset().left -
-                  parseInt(detailsEl.css('margin-right'), 10),
+                  parseInt(detailsEl.css('margin-right'), 10) - 20,
               detailsHeight = jQuery(window).height() - detailsEl.offset().top -
                   parseInt(detailsEl.css('margin-bottom'), 10) - footerHeight;
           detailsEl.width(detailsWidth).height(detailsHeight);
diff --git a/sonar-application/src/main/assembly/conf/sonar.properties b/sonar-application/src/main/assembly/conf/sonar.properties
index 3fa9963d19a..b9bee4266e5 100644
--- a/sonar-application/src/main/assembly/conf/sonar.properties
+++ b/sonar-application/src/main/assembly/conf/sonar.properties
@@ -66,8 +66,11 @@ sonar.jdbc.timeBetweenEvictionRunsMillis=30000
 # Use the following property to customize JVM options. Enabling the HotSpot Server VM
 # mode (-server) is recommended.
 # Note that the option -Dfile.encoding=UTF-8 is mandatory.
-#sonar.web.javaOpts=-Xmx768m -XX:MaxPermSize=160m -XX:+HeapDumpOnOutOfMemoryError \
-#  -Djava.awt.headless=true -Dfile.encoding=UTF-8 -Djruby.management.enabled=false
+#sonar.web.javaOpts=-Xmx768m -XX:MaxPermSize=160m -XX:+HeapDumpOnOutOfMemoryError
+
+# Same as previous property, but allows to not repeat all other settings
+# like -Djava.awt.headless=true
+#sonar.web.javaAdditionalOpts=
 
 # Binding IP address. For servers with more than one IP address, this property specifies which
 # address will be used for listening on the specified ports.
@@ -170,8 +173,11 @@ sonar.jdbc.timeBetweenEvictionRunsMillis=30000
 # JVM options. Note that enabling the HotSpot Server VM mode (-server) is recommended.
 #sonar.search.javaOpts=-Xmx256m -Xms256m -Xss256k -Djava.net.preferIPv4Stack=true \
 #  -XX:+UseParNewGC -XX:+UseConcMarkSweepGC -XX:CMSInitiatingOccupancyFraction=75 \
-#  -XX:+UseCMSInitiatingOccupancyOnly -XX:+HeapDumpOnOutOfMemoryError \
-#  -Djava.awt.headless=true
+#  -XX:+UseCMSInitiatingOccupancyOnly -XX:+HeapDumpOnOutOfMemoryError
+
+# Same as previous property, but allows to not repeat all other settings
+# like -Djava.awt.headless=true
+#sonar.search.javaAdditionalOpts=
 
 # Elasticsearch port. Default is 9001. Use 0 to get a free port.
 # This port must be private and must not be exposed to the Internet.
diff --git a/sonar-application/src/main/java/org/sonar/application/App.java b/sonar-application/src/main/java/org/sonar/application/App.java
index 502cf561394..9c027abebdf 100644
--- a/sonar-application/src/main/java/org/sonar/application/App.java
+++ b/sonar-application/src/main/java/org/sonar/application/App.java
@@ -70,7 +70,9 @@ public class App implements Stoppable {
     JavaCommand elasticsearch = new JavaCommand("search");
     elasticsearch
       .setWorkDir(homeDir)
-      .addJavaOptions(props.value(DefaultSettings.SEARCH_JAVA_OPTS))
+      .addJavaOptions("-Djava.awt.headless=true")
+      .addJavaOptions(props.nonNullValue(DefaultSettings.SEARCH_JAVA_OPTS))
+      .addJavaOptions(props.nonNullValue(DefaultSettings.SEARCH_JAVA_ADDITIONAL_OPTS))
       .setTempDir(tempDir.getAbsoluteFile())
       .setClassName("org.sonar.search.SearchServer")
       .setArguments(props.rawProperties())
@@ -82,7 +84,9 @@ public class App implements Stoppable {
     if (StringUtils.isEmpty(props.value(DefaultSettings.CLUSTER_MASTER))) {
       JavaCommand webServer = new JavaCommand("web")
         .setWorkDir(homeDir)
+        .addJavaOptions("-Djava.awt.headless=true -Dfile.encoding=UTF-8 -Djruby.management.enabled=false")
         .addJavaOptions(props.nonNullValue(DefaultSettings.WEB_JAVA_OPTS))
+        .addJavaOptions(props.nonNullValue(DefaultSettings.WEB_JAVA_ADDITIONAL_OPTS))
         .setTempDir(tempDir.getAbsoluteFile())
         // required for logback tomcat valve
         .setEnvVariable("sonar.path.logs", props.nonNullValue("sonar.path.logs"))
diff --git a/sonar-application/src/main/java/org/sonar/application/DefaultSettings.java b/sonar-application/src/main/java/org/sonar/application/DefaultSettings.java
index 701249f5f63..4a936789499 100644
--- a/sonar-application/src/main/java/org/sonar/application/DefaultSettings.java
+++ b/sonar-application/src/main/java/org/sonar/application/DefaultSettings.java
@@ -36,7 +36,9 @@ class DefaultSettings {
   static final String CLUSTER_NODE_NAME = "sonar.node.name";
   static final String SEARCH_PORT = "sonar.search.port";
   static final String SEARCH_JAVA_OPTS = "sonar.search.javaOpts";
+  static final String SEARCH_JAVA_ADDITIONAL_OPTS = "sonar.search.javaAdditionalOpts";
   static final String WEB_JAVA_OPTS = "sonar.web.javaOpts";
+  static final String WEB_JAVA_ADDITIONAL_OPTS = "sonar.web.javaAdditionalOpts";
   static final String JDBC_URL = "sonar.jdbc.url";
   static final String JDBC_LOGIN = "sonar.jdbc.username";
   static final String JDBC_PASSWORD = "sonar.jdbc.password";
@@ -70,9 +72,11 @@ class DefaultSettings {
     defaults.put(SEARCH_JAVA_OPTS, "-Xmx256m -Xms256m -Xss256k -Djava.net.preferIPv4Stack=true " +
       "-XX:+UseParNewGC -XX:+UseConcMarkSweepGC -XX:CMSInitiatingOccupancyFraction=75 -XX:+UseCMSInitiatingOccupancyOnly " +
       "-XX:+HeapDumpOnOutOfMemoryError -Djava.awt.headless=true");
+    defaults.put(SEARCH_JAVA_ADDITIONAL_OPTS, "");
     defaults.put(CLUSTER_NODE_NAME, "sonar-" + System.currentTimeMillis());
     defaults.put(WEB_JAVA_OPTS, "-Xmx768m -XX:MaxPermSize=160m -XX:+HeapDumpOnOutOfMemoryError -Djava.net.preferIPv4Stack=true " +
       "-Djava.awt.headless=true -Dfile.encoding=UTF-8 -Djruby.management.enabled=false");
+    defaults.put(WEB_JAVA_ADDITIONAL_OPTS, "");
     defaults.put(JDBC_URL, "jdbc:h2:tcp://localhost:9092/sonar");
     defaults.put(JDBC_LOGIN, "sonar");
     defaults.put(JDBC_PASSWORD, "sonar");
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/ResourceNotIndexedException.java b/sonar-batch/src/main/java/org/sonar/batch/index/ResourceNotIndexedException.java
deleted file mode 100644
index 16b5ee32a90..00000000000
--- a/sonar-batch/src/main/java/org/sonar/batch/index/ResourceNotIndexedException.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * SonarQube, open source software quality management tool.
- * Copyright (C) 2008-2014 SonarSource
- * mailto:contact AT sonarsource DOT com
- *
- * SonarQube is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
- * version 3 of the License, or (at your option) any later version.
- *
- * SonarQube is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
- */
-package org.sonar.batch.index;
-
-import org.sonar.api.resources.Resource;
-import org.sonar.api.utils.SonarException;
-
-/**
- * @since 2.6
- */
-public class ResourceNotIndexedException extends SonarException {
-
-  public ResourceNotIndexedException(final Resource reference) {
-    super(reference.toString());
-  }
-}
diff --git a/sonar-batch/src/main/java/org/sonar/batch/mediumtest/BatchMediumTester.java b/sonar-batch/src/main/java/org/sonar/batch/mediumtest/BatchMediumTester.java
index 437d778b7fd..61a6a062867 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/mediumtest/BatchMediumTester.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/mediumtest/BatchMediumTester.java
@@ -96,7 +96,7 @@ public class BatchMediumTester {
   public static class BatchMediumTesterBuilder {
     private final FakeGlobalReferentialsLoader globalRefProvider = new FakeGlobalReferentialsLoader();
     private final FakeProjectReferentialsLoader projectRefProvider = new FakeProjectReferentialsLoader();
-    private final FackPluginsReferential pluginsReferential = new FackPluginsReferential();
+    private final FakePluginsReferential pluginsReferential = new FakePluginsReferential();
     private final Map<String, String> bootstrapProperties = new HashMap<String, String>();
 
     public BatchMediumTester build() {
@@ -472,7 +472,7 @@ public class BatchMediumTester {
     }
   }
 
-  private static class FackPluginsReferential implements PluginsReferential {
+  private static class FakePluginsReferential implements PluginsReferential {
 
     private List<RemotePlugin> pluginList = new ArrayList<RemotePlugin>();
     private Map<RemotePlugin, File> pluginFiles = new HashMap<RemotePlugin, File>();
@@ -488,15 +488,15 @@ public class BatchMediumTester {
       return pluginFiles.get(remote);
     }
 
-    public FackPluginsReferential addPlugin(String pluginKey, File location) {
+    public FakePluginsReferential addPlugin(String pluginKey, File location) {
       RemotePlugin plugin = new RemotePlugin(pluginKey, false);
       pluginList.add(plugin);
       pluginFiles.put(plugin, location);
       return this;
     }
 
-    public FackPluginsReferential addPlugin(String pluginKey, SonarPlugin pluginInstance) {
-      localPlugins.put(DefaultPluginMetadata.create(null).setKey(pluginKey), pluginInstance);
+    public FakePluginsReferential addPlugin(String pluginKey, SonarPlugin pluginInstance) {
+      localPlugins.put(DefaultPluginMetadata.create(pluginKey), pluginInstance);
       return this;
     }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactory.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactory.java
index 772f773cb5f..59f1e667edd 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactory.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactory.java
@@ -21,7 +21,6 @@ package org.sonar.batch.scan.filesystem;
 
 import org.sonar.api.BatchComponent;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
-import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.PathResolver;
 import org.sonar.batch.bootstrap.AnalysisMode;
 
@@ -33,17 +32,9 @@ public class InputFileBuilderFactory implements BatchComponent {
   private final StatusDetectionFactory statusDetectionFactory;
   private final AnalysisMode analysisMode;
 
-  public InputFileBuilderFactory(Project module, ProjectDefinition def, PathResolver pathResolver, LanguageDetectionFactory langDetectionFactory,
-    StatusDetectionFactory statusDetectionFactory, AnalysisMode analysisMode) {
-    this(module.getEffectiveKey(), pathResolver, langDetectionFactory, statusDetectionFactory, analysisMode);
-  }
-
-  /**
-   * Used by scan2
-   */
   public InputFileBuilderFactory(ProjectDefinition def, PathResolver pathResolver, LanguageDetectionFactory langDetectionFactory,
     StatusDetectionFactory statusDetectionFactory, AnalysisMode analysisMode) {
-    this(def.getKey(), pathResolver, langDetectionFactory, statusDetectionFactory, analysisMode);
+    this(def.getKeyWithBranch(), pathResolver, langDetectionFactory, statusDetectionFactory, analysisMode);
   }
 
   private InputFileBuilderFactory(String effectiveKey, PathResolver pathResolver, LanguageDetectionFactory langDetectionFactory,
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan2/DefaultFileLinesContextFactory.java b/sonar-batch/src/main/java/org/sonar/batch/scan2/DefaultFileLinesContextFactory.java
index 8b268b14be9..3ea69cad781 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan2/DefaultFileLinesContextFactory.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan2/DefaultFileLinesContextFactory.java
@@ -20,7 +20,6 @@
 package org.sonar.batch.scan2;
 
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
-import org.sonar.api.batch.fs.FileSystem;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.measure.MetricFinder;
 import org.sonar.api.batch.sensor.SensorStorage;
@@ -36,7 +35,7 @@ public class DefaultFileLinesContextFactory implements FileLinesContextFactory {
   private final ProjectDefinition def;
   private final InputPathCache fileCache;
 
-  public DefaultFileLinesContextFactory(InputPathCache fileCache, FileSystem fs, MetricFinder metricFinder, SensorStorage sensorStorage,
+  public DefaultFileLinesContextFactory(InputPathCache fileCache, MetricFinder metricFinder, SensorStorage sensorStorage,
     ProjectDefinition def) {
     this.fileCache = fileCache;
     this.metricFinder = metricFinder;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanContainer.java b/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanContainer.java
index 67e2a37908d..41a2cda0390 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanContainer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanContainer.java
@@ -139,7 +139,7 @@ public class ModuleScanContainer extends ComponentContainer {
 
   @Override
   protected void doAfterStart() {
-    getComponentByType(ModuleScanExecutor.class).execute(moduleDefinition);
+    getComponentByType(ModuleScanExecutor.class).execute();
   }
 
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanExecutor.java b/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanExecutor.java
index 8611bd3b26a..088125818df 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanExecutor.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanExecutor.java
@@ -20,7 +20,6 @@
 package org.sonar.batch.scan2;
 
 import com.google.common.collect.Lists;
-import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.sensor.SensorContext;
 import org.sonar.batch.issue.ignore.scanner.IssueExclusionsLoader;
 import org.sonar.batch.rule.QProfileVerifier;
@@ -60,7 +59,7 @@ public final class ModuleScanExecutor {
   /**
    * Executed on each module
    */
-  public void execute(ProjectDefinition moduleDefinition) {
+  public void execute() {
     fsLogger.log();
 
     // Index and lock the filesystem
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactoryTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactoryTest.java
index e38081b62be..bb78a170c84 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactoryTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactoryTest.java
@@ -22,7 +22,6 @@ package org.sonar.batch.scan.filesystem;
 import org.junit.Test;
 import org.mockito.Mockito;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
-import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.PathResolver;
 import org.sonar.batch.bootstrap.AnalysisMode;
 
@@ -33,14 +32,12 @@ public class InputFileBuilderFactoryTest {
   @Test
   public void create_builder() throws Exception {
     PathResolver pathResolver = new PathResolver();
-    Project project = new Project("struts");
     LanguageDetectionFactory langDetectionFactory = mock(LanguageDetectionFactory.class, Mockito.RETURNS_MOCKS);
     StatusDetectionFactory statusDetectionFactory = mock(StatusDetectionFactory.class, Mockito.RETURNS_MOCKS);
     DefaultModuleFileSystem fs = mock(DefaultModuleFileSystem.class);
     AnalysisMode analysisMode = mock(AnalysisMode.class);
 
-    InputFileBuilderFactory factory = new InputFileBuilderFactory(
-      project, ProjectDefinition.create(), pathResolver, langDetectionFactory,
+    InputFileBuilderFactory factory = new InputFileBuilderFactory(ProjectDefinition.create().setKey("struts"), pathResolver, langDetectionFactory,
       statusDetectionFactory, analysisMode);
     InputFileBuilder builder = factory.create(fs);
 
diff --git a/sonar-core/src/main/java/org/sonar/core/plugins/DefaultPluginMetadata.java b/sonar-core/src/main/java/org/sonar/core/plugins/DefaultPluginMetadata.java
index 55239eb3410..8a4a103cd5a 100644
--- a/sonar-core/src/main/java/org/sonar/core/plugins/DefaultPluginMetadata.java
+++ b/sonar-core/src/main/java/org/sonar/core/plugins/DefaultPluginMetadata.java
@@ -63,6 +63,10 @@ public class DefaultPluginMetadata implements PluginMetadata, Comparable<PluginM
     return new DefaultPluginMetadata().setFile(file);
   }
 
+  public static DefaultPluginMetadata create(String key) {
+    return new DefaultPluginMetadata().setKey(key);
+  }
+
   public File getFile() {
     return file;
   }
diff --git a/sonar-core/src/main/java/org/sonar/core/plugins/RemotePlugin.java b/sonar-core/src/main/java/org/sonar/core/plugins/RemotePlugin.java
index 50903592616..3bc254a3ff1 100644
--- a/sonar-core/src/main/java/org/sonar/core/plugins/RemotePlugin.java
+++ b/sonar-core/src/main/java/org/sonar/core/plugins/RemotePlugin.java
@@ -45,7 +45,7 @@ public class RemotePlugin {
     RemotePlugin result = new RemotePlugin(fields[0], Boolean.parseBoolean(fields[1]));
     if (fields.length > 2) {
       String[] nameAndHash = StringUtils.split(fields[2], "|");
-      result.setFile(nameAndHash[0], nameAndHash.length > 1 ? nameAndHash[1] : null);
+      result.setFile(nameAndHash[0], nameAndHash[1]);
     }
     return result;
   }
@@ -72,7 +72,7 @@ public class RemotePlugin {
   }
 
   public RemotePlugin setFile(File f) {
-    return this.setFile(f.getName(), f.exists() ? new FileHashes().of(f) : null);
+    return this.setFile(f.getName(), new FileHashes().of(f));
   }
 
   public RemotePluginFile file() {
diff --git a/sonar-core/src/test/java/org/sonar/core/plugins/DefaultPluginMetadataTest.java b/sonar-core/src/test/java/org/sonar/core/plugins/DefaultPluginMetadataTest.java
index f7d7dea4e59..d3f819392b5 100644
--- a/sonar-core/src/test/java/org/sonar/core/plugins/DefaultPluginMetadataTest.java
+++ b/sonar-core/src/test/java/org/sonar/core/plugins/DefaultPluginMetadataTest.java
@@ -36,19 +36,19 @@ public class DefaultPluginMetadataTest {
   public void testGettersAndSetters() {
     DefaultPluginMetadata metadata = DefaultPluginMetadata.create(new File("sonar-checkstyle-plugin.jar"));
     metadata.setKey("checkstyle")
-        .setParent("java")
-        .setLicense("LGPL")
-        .setDescription("description")
-        .setHomepage("http://home")
-        .setIssueTrackerUrl("http://jira.codehuas.org")
-        .setMainClass("org.Main")
-        .setOrganization("SonarSource")
-        .setOrganizationUrl("http://sonarsource.org")
-        .setVersion("1.1")
-        .setSonarVersion("3.0")
-        .setUseChildFirstClassLoader(true)
-        .setCore(false)
-        .setImplementationBuild("abcdef");
+      .setParent("java")
+      .setLicense("LGPL")
+      .setDescription("description")
+      .setHomepage("http://home")
+      .setIssueTrackerUrl("http://jira.codehuas.org")
+      .setMainClass("org.Main")
+      .setOrganization("SonarSource")
+      .setOrganizationUrl("http://sonarsource.org")
+      .setVersion("1.1")
+      .setSonarVersion("3.0")
+      .setUseChildFirstClassLoader(true)
+      .setCore(false)
+      .setImplementationBuild("abcdef");
 
     assertThat(metadata.getKey()).isEqualTo("checkstyle");
     assertThat(metadata.getParent()).isEqualTo("java");
@@ -72,8 +72,8 @@ public class DefaultPluginMetadataTest {
   @Test
   public void testDeployedFiles() {
     DefaultPluginMetadata metadata = DefaultPluginMetadata.create(new File("sonar-checkstyle-plugin.jar"))
-        .addDeployedFile(new File("foo.jar"))
-        .addDeployedFile(new File("bar.jar"));
+      .addDeployedFile(new File("foo.jar"))
+      .addDeployedFile(new File("bar.jar"));
 
     assertThat(metadata.getDeployedFiles()).hasSize(2);
   }
@@ -81,7 +81,7 @@ public class DefaultPluginMetadataTest {
   @Test
   public void testInternalPathToDependencies() {
     DefaultPluginMetadata metadata = DefaultPluginMetadata.create(new File("sonar-checkstyle-plugin.jar"))
-        .setPathsToInternalDeps(newArrayList("META-INF/lib/commons-lang.jar", "META-INF/lib/commons-io.jar"));
+      .setPathsToInternalDeps(newArrayList("META-INF/lib/commons-lang.jar", "META-INF/lib/commons-io.jar"));
 
     assertThat(metadata.getPathsToInternalDeps()).containsOnly("META-INF/lib/commons-lang.jar", "META-INF/lib/commons-io.jar");
   }
@@ -99,11 +99,11 @@ public class DefaultPluginMetadataTest {
   @Test
   public void shouldCompare() {
     DefaultPluginMetadata checkstyle = DefaultPluginMetadata.create(new File("sonar-checkstyle-plugin.jar"))
-        .setKey("checkstyle")
-        .setName("Checkstyle");
+      .setKey("checkstyle")
+      .setName("Checkstyle");
     DefaultPluginMetadata pmd = DefaultPluginMetadata.create(new File("sonar-pmd-plugin.jar"))
-        .setKey("pmd")
-        .setName("PMD");
+      .setKey("pmd")
+      .setName("PMD");
     List<DefaultPluginMetadata> plugins = Arrays.asList(pmd, checkstyle);
 
     assertThat(natural().sortedCopy(plugins)).onProperty("key").containsExactly("checkstyle", "pmd");
@@ -141,6 +141,6 @@ public class DefaultPluginMetadataTest {
   }
 
   static DefaultPluginMetadata pluginWithVersion(String version) {
-    return DefaultPluginMetadata.create(null).setSonarVersion(version);
+    return DefaultPluginMetadata.create("foo").setSonarVersion(version);
   }
 }
diff --git a/sonar-core/src/test/java/org/sonar/core/plugins/PluginClassloadersTest.java b/sonar-core/src/test/java/org/sonar/core/plugins/PluginClassloadersTest.java
index 95bb9da245c..120680b1998 100644
--- a/sonar-core/src/test/java/org/sonar/core/plugins/PluginClassloadersTest.java
+++ b/sonar-core/src/test/java/org/sonar/core/plugins/PluginClassloadersTest.java
@@ -62,8 +62,8 @@ public class PluginClassloadersTest {
 
   @Test
   public void shouldImport() throws Exception {
-    classloaders.add(DefaultPluginMetadata.create(null).setKey("foo").addDeployedFile(getFile("PluginClassloadersTest/foo.jar")));
-    classloaders.add(DefaultPluginMetadata.create(null).setKey("bar").addDeployedFile(getFile("PluginClassloadersTest/bar.jar")));
+    classloaders.add(DefaultPluginMetadata.create("foo").addDeployedFile(getFile("PluginClassloadersTest/foo.jar")));
+    classloaders.add(DefaultPluginMetadata.create("bar").addDeployedFile(getFile("PluginClassloadersTest/bar.jar")));
     classloaders.done();
 
     String resourceName = "org/sonar/plugins/bar/api/resource.txt";
@@ -74,8 +74,7 @@ public class PluginClassloadersTest {
   @Test
   public void shouldCreateBaseClassloader() {
     classloaders = new PluginClassloaders(getClass().getClassLoader());
-    DefaultPluginMetadata checkstyle = DefaultPluginMetadata.create(null)
-      .setKey("checkstyle")
+    DefaultPluginMetadata checkstyle = DefaultPluginMetadata.create("checkstyle")
       .setMainClass("org.sonar.plugins.checkstyle.CheckstylePlugin")
       .addDeployedFile(getFile("sonar-checkstyle-plugin-2.8.jar"));
 
@@ -90,13 +89,11 @@ public class PluginClassloadersTest {
   public void shouldExtendPlugin() {
     classloaders = new PluginClassloaders(getClass().getClassLoader());
 
-    DefaultPluginMetadata checkstyle = DefaultPluginMetadata.create(null)
-      .setKey("checkstyle")
+    DefaultPluginMetadata checkstyle = DefaultPluginMetadata.create("checkstyle")
       .setMainClass("org.sonar.plugins.checkstyle.CheckstylePlugin")
       .addDeployedFile(getFile("sonar-checkstyle-plugin-2.8.jar"));
 
-    DefaultPluginMetadata checkstyleExt = DefaultPluginMetadata.create(null)
-      .setKey("checkstyle-ext")
+    DefaultPluginMetadata checkstyleExt = DefaultPluginMetadata.create("checkstyle-ext")
       .setBasePlugin("checkstyle")
       .setMainClass("com.mycompany.sonar.checkstyle.CheckstyleExtensionsPlugin")
       .addDeployedFile(getFile("sonar-checkstyle-extensions-plugin-0.1-SNAPSHOT.jar"));
@@ -119,8 +116,7 @@ public class PluginClassloadersTest {
 
     classloaders = new PluginClassloaders(getClass().getClassLoader(), world);
 
-    DefaultPluginMetadata checkstyle = DefaultPluginMetadata.create(null)
-      .setKey("checkstyle")
+    DefaultPluginMetadata checkstyle = DefaultPluginMetadata.create("checkstyle")
       .setMainClass("org.sonar.plugins.checkstyle.CheckstylePlugin")
       .addDeployedFile(getFile("sonar-checkstyle-plugin-2.8.jar"));