SONAR-2298 Add support for multi-modules for non-Maven projects

* Use ProjectDefinition in ProjectTree instead of MavenProject

* Allow to specify extensions for project's container via
  ProjectDefinition, so MavenProject not passed directly to batch in mojos

* ProjectDefinition should store all information in properties

* Replace DefaultProjectFileSystem by DefaultProjectFileSystem2, which
  works not only for Maven projects

* Add DefaultProjectClasspath, which works not only for Maven projects

* Enable ProjectLinksSensor only for Maven

22 files changed, 683 insertions, 541 deletions

diff --git a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/sensors/ProjectLinksSensor.java b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/sensors/ProjectLinksSensor.java
index c9ef33368dc..5f0ace5847f 100644
--- a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/sensors/ProjectLinksSensor.java
+++ b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/sensors/ProjectLinksSensor.java
@@ -26,9 +26,11 @@ import org.apache.maven.model.Scm;
 import org.apache.maven.project.MavenProject;
 import org.sonar.api.batch.Sensor;
 import org.sonar.api.batch.SensorContext;
+import org.sonar.api.batch.SupportedEnvironment;
 import org.sonar.api.resources.Project;
 import org.sonar.api.resources.ProjectLink;
 
+@SupportedEnvironment("maven")
 public class ProjectLinksSensor implements Sensor {
 
   public static final String KEY_HOME = "homepage";
diff --git a/sonar-batch/src/main/java/org/sonar/batch/DefaultProjectClasspath.java b/sonar-batch/src/main/java/org/sonar/batch/DefaultProjectClasspath.java
new file mode 100644
index 00000000000..978acf4b5d5
--- /dev/null
+++ b/sonar-batch/src/main/java/org/sonar/batch/DefaultProjectClasspath.java
@@ -0,0 +1,61 @@
+/*
+ * Sonar, open source software quality management tool.
+ * Copyright (C) 2008-2011 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * Sonar 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.
+ *
+ * Sonar 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 Sonar; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02
+ */
+package org.sonar.batch;
+
+import com.google.common.collect.Lists;
+import org.apache.maven.project.MavenProject;
+import org.sonar.api.batch.ProjectClasspath;
+import org.sonar.api.resources.ProjectFileSystem;
+import org.sonar.batch.bootstrapper.ProjectDefinition;
+
+import java.io.File;
+import java.util.List;
+
+public class DefaultProjectClasspath extends ProjectClasspath {
+
+  private ProjectDefinition def;
+  private ProjectFileSystem projectFileSystem;
+
+  public DefaultProjectClasspath(ProjectDefinition def, ProjectFileSystem projectFileSystem) {
+    this(def, projectFileSystem, null);
+  }
+
+  public DefaultProjectClasspath(ProjectDefinition def, ProjectFileSystem projectFileSystem, MavenProject pom) {
+    super(pom);
+    this.def = def;
+    this.projectFileSystem = projectFileSystem;
+  }
+
+  @Override
+  protected List<File> createElements() {
+    if (pom != null) {
+      return super.createElements();
+    } else {
+      List<File> elements = Lists.newArrayList();
+      for (String path : def.getBinaries()) {
+        elements.add(projectFileSystem.resolvePath(path));
+      }
+      for (String path : def.getLibraries()) {
+        elements.add(projectFileSystem.resolvePath(path));
+      }
+      return elements;
+    }
+  }
+}
diff --git a/sonar-batch/src/main/java/org/sonar/batch/DefaultProjectFileSystem2.java b/sonar-batch/src/main/java/org/sonar/batch/DefaultProjectFileSystem2.java
new file mode 100644
index 00000000000..82302af4973
--- /dev/null
+++ b/sonar-batch/src/main/java/org/sonar/batch/DefaultProjectFileSystem2.java
@@ -0,0 +1,166 @@
+/*
+ * Sonar, open source software quality management tool.
+ * Copyright (C) 2008-2011 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * Sonar 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.
+ *
+ * Sonar 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 Sonar; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02
+ */
+package org.sonar.batch;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.maven.project.MavenProject;
+import org.sonar.api.resources.DefaultProjectFileSystem;
+import org.sonar.api.resources.Languages;
+import org.sonar.api.resources.Project;
+import org.sonar.api.resources.ProjectFileSystem;
+import org.sonar.api.utils.SonarException;
+import org.sonar.batch.bootstrapper.ProjectDefinition;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
+/**
+ * Implementation of {@link ProjectFileSystem} based on {@link ProjectDefinition} and {@link MavenProject}.
+ */
+public class DefaultProjectFileSystem2 extends DefaultProjectFileSystem {
+
+  private ProjectDefinition def;
+  private MavenProject pom;
+
+  public DefaultProjectFileSystem2(Project project, Languages languages, ProjectDefinition def) {
+    super(project, languages);
+    this.def = def;
+  }
+
+  /**
+   * For Maven.
+   */
+  public DefaultProjectFileSystem2(Project project, Languages languages, ProjectDefinition def, MavenProject pom) {
+    this(project, languages, def);
+    this.pom = pom;
+  }
+
+  public File getBasedir() {
+    if (pom != null) {
+      return pom.getBasedir();
+    } else {
+      return def.getBaseDir();
+    }
+  }
+
+  public File getBuildDir() {
+    if (pom != null) {
+      return resolvePath(pom.getBuild().getDirectory());
+    } else {
+      // TODO workaround
+      return new File(getSonarWorkingDirectory(), "target");
+    }
+  }
+
+  public File getBuildOutputDir() {
+    if (pom != null) {
+      return resolvePath(pom.getBuild().getOutputDirectory());
+    } else {
+      if (def.getBinaries().isEmpty()) {
+        // workaround for IndexOutOfBoundsException
+        return new File(getBuildDir(), "classes");
+      }
+      // TODO we assume that there is only one directory which contains compiled code
+      return resolvePath(def.getBinaries().get(0));
+    }
+  }
+
+  public List<File> getSourceDirs() {
+    if (pom != null) {
+      // Maven can modify source directories during Sonar execution - see MavenPhaseExecutor.
+      return resolvePaths(pom.getCompileSourceRoots());
+    } else {
+      return resolvePaths(def.getSourceDirs());
+    }
+  }
+
+  /**
+   * @deprecated since 2.6, because should be immutable
+   */
+  @Deprecated
+  public DefaultProjectFileSystem addSourceDir(File dir) {
+    if (dir == null) {
+      throw new IllegalArgumentException("Can not add null to project source dirs");
+    }
+    if (pom != null) {
+      pom.getCompileSourceRoots().add(0, dir.getAbsolutePath());
+    } else {
+      def.addSourceDir(dir.getAbsolutePath());
+    }
+    return this;
+  }
+
+  /**
+   * Maven can modify test directories during Sonar execution - see MavenPhaseExecutor.
+   */
+  public List<File> getTestDirs() {
+    if (pom != null) {
+      // Maven can modify test directories during Sonar execution - see MavenPhaseExecutor.
+      return resolvePaths(pom.getTestCompileSourceRoots());
+    } else {
+      return resolvePaths(def.getTestDirs());
+    }
+  }
+
+  /**
+   * @deprecated since 2.6, because should be immutable
+   */
+  @Deprecated
+  public DefaultProjectFileSystem addTestDir(File dir) {
+    if (dir == null) {
+      throw new IllegalArgumentException("Can not add null to project test dirs");
+    }
+    if (pom != null) {
+      pom.getTestCompileSourceRoots().add(0, dir.getAbsolutePath());
+    } else {
+      def.addTestDir(dir.getAbsolutePath());
+    }
+    return this;
+  }
+
+  /**
+   * TODO Godin: seems that used only by Cobertura and Clover
+   */
+  public File getReportOutputDir() {
+    if (pom != null) {
+      return resolvePath(pom.getReporting().getOutputDirectory());
+    } else {
+      return new File(getBuildDir(), "site");
+    }
+  }
+
+  @Override
+  public File getSonarWorkingDirectory() {
+    if (pom != null) {
+      try {
+        File dir = new File(getBuildDir(), "sonar");
+        FileUtils.forceMkdir(dir);
+        return dir;
+
+      } catch (IOException e) {
+        throw new SonarException("Unable to retrieve Sonar working directory.", e);
+      }
+    } else {
+      return def.getWorkDir();
+    }
+  }
+
+}
diff --git a/sonar-batch/src/main/java/org/sonar/batch/InMemoryPomCreator.java b/sonar-batch/src/main/java/org/sonar/batch/InMemoryPomCreator.java
deleted file mode 100644
index 73c79ad8548..00000000000
--- a/sonar-batch/src/main/java/org/sonar/batch/InMemoryPomCreator.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- * Sonar, open source software quality management tool.
- * Copyright (C) 2008-2011 SonarSource
- * mailto:contact AT sonarsource DOT com
- *
- * Sonar 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.
- *
- * Sonar 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 Sonar; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02
- */
-package org.sonar.batch;
-
-import org.apache.commons.lang.StringUtils;
-import org.apache.maven.artifact.DependencyResolutionRequiredException;
-import org.apache.maven.model.Reporting;
-import org.apache.maven.project.MavenProject;
-import org.sonar.api.CoreProperties;
-import org.sonar.api.utils.SonarException;
-import org.sonar.batch.bootstrapper.ProjectDefinition;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Properties;
-
-/**
- * This is a dirty hack for for non-Maven environments,
- * which allows to create {@link MavenProject} based on {@link ProjectDefinition}.
- */
-public class InMemoryPomCreator {
-
-  private ProjectDefinition project;
-
-  public InMemoryPomCreator(ProjectDefinition project) {
-    this.project = project;
-  }
-
-  public MavenProject create() {
-    File workDir = project.getWorkDir();
-    String buildDirectory = workDir.getAbsolutePath() + "/target";
-    Properties properties = project.getProperties();
-
-    if (project.getBinaries().size() == 0) {
-      project.addBinaryDir(buildDirectory + "/classes");
-    }
-
-    final MavenProject pom = new MavenProject() {
-      /**
-       * This allows to specify base directory without specifying location of a pom.xml
-       */
-      @Override
-      public File getBasedir() {
-        return project.getBaseDir();
-      };
-
-      /**
-       * This allows to specify project classpath (binaries + libraries).
-       */
-      @Override
-      public List<String> getCompileClasspathElements() throws DependencyResolutionRequiredException {
-        List<String> cp = new ArrayList<String>();
-        cp.addAll(project.getBinaries());
-        cp.addAll(project.getLibraries());
-        return cp;
-      }
-    };
-
-    String key = getPropertyOrDie(properties, CoreProperties.PROJECT_KEY_PROPERTY);
-    String[] keys = key.split(":");
-    pom.setGroupId(keys[0]);
-    pom.setArtifactId(keys[1]);
-    pom.setVersion(getPropertyOrDie(properties, CoreProperties.PROJECT_VERSION_PROPERTY));
-
-    pom.setName(properties.getProperty(CoreProperties.PROJECT_NAME_PROPERTY, "Unnamed - " + key));
-    pom.setDescription(properties.getProperty(CoreProperties.PROJECT_DESCRIPTION_PROPERTY, ""));
-
-    pom.getModel().setProperties(properties);
-
-    pom.setArtifacts(Collections.EMPTY_SET);
-
-    // Configure fake directories
-    pom.getBuild().setDirectory(buildDirectory);
-    pom.getBuild().setOutputDirectory(project.getBinaries().get(0));
-    Reporting reporting = new Reporting();
-    String reportingOutputDirectory = buildDirectory + "/site";
-    reporting.setOutputDirectory(reportingOutputDirectory);
-    pom.setReporting(reporting);
-
-    // Configure source directories
-    for (String dir : project.getSourceDirs()) {
-      pom.addCompileSourceRoot(dir);
-    }
-
-    // Configure test directories
-    for (String dir : project.getTestDirs()) {
-      pom.addTestCompileSourceRoot(dir);
-    }
-
-    return pom;
-  }
-
-  private static String getPropertyOrDie(Properties properties, String key) {
-    String value = properties.getProperty(key);
-    if (StringUtils.isBlank(value)) {
-      throw new SonarException("Property '" + key + "' must be specified");
-    }
-    return value;
-  }
-
-}
diff --git a/sonar-batch/src/main/java/org/sonar/batch/MavenProjectBuilder.java b/sonar-batch/src/main/java/org/sonar/batch/MavenProjectBuilder.java
index 0086f1015c0..48bc41730b0 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/MavenProjectBuilder.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/MavenProjectBuilder.java
@@ -19,14 +19,9 @@
  */
 package org.sonar.batch;
 
-import java.text.DateFormat;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.Date;
-
 import org.apache.commons.configuration.*;
+import org.apache.commons.lang.StringUtils;
 import org.apache.commons.lang.time.DateUtils;
-import org.apache.maven.project.MavenProject;
 import org.sonar.api.CoreProperties;
 import org.sonar.api.database.DatabaseSession;
 import org.sonar.api.database.model.ResourceModel;
@@ -34,7 +29,14 @@ import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.resources.Java;
 import org.sonar.api.resources.Project;
 import org.sonar.api.utils.SonarException;
+import org.sonar.batch.bootstrapper.ProjectDefinition;
+
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Date;
 
+// TODO Godin: rename to ProjectBuilder ?
 public class MavenProjectBuilder {
 
   private DatabaseSession databaseSession;
@@ -43,43 +45,55 @@ public class MavenProjectBuilder {
     this.databaseSession = databaseSession;
   }
 
-  public Project create(MavenProject pom) {
-    Configuration configuration = getStartupConfiguration(pom);
-    return new Project(loadProjectKey(pom), loadProjectBranch(configuration), pom.getName())
-        .setPom(pom)
-        .setDescription(pom.getDescription())
-        .setPackaging(pom.getPackaging());
+  public Project create(ProjectDefinition project) {
+    Configuration configuration = getStartupConfiguration(project);
+    return new Project(loadProjectKey(project), loadProjectBranch(configuration), loadProjectName(project))
+        .setDescription(project.getProperties().getProperty(CoreProperties.PROJECT_DESCRIPTION_PROPERTY))
+        .setPackaging("jar"); // FIXME http://jira.codehaus.org/browse/SONAR-2341
   }
 
-  Configuration getStartupConfiguration(MavenProject pom) {
+  Configuration getStartupConfiguration(ProjectDefinition project) {
     CompositeConfiguration configuration = new CompositeConfiguration();
     configuration.addConfiguration(new SystemConfiguration());
     configuration.addConfiguration(new EnvironmentConfiguration());
-    configuration.addConfiguration(new MapConfiguration(pom.getModel().getProperties()));
+    configuration.addConfiguration(new MapConfiguration(project.getProperties()));
     return configuration;
   }
 
-  String loadProjectKey(MavenProject pom) {
-    return new StringBuilder().append(pom.getGroupId()).append(":").append(pom.getArtifactId()).toString();
+  private String getPropertyOrDie(ProjectDefinition project, String key) {
+    String value = project.getProperties().getProperty(key);
+    if (StringUtils.isBlank(value)) {
+      throw new SonarException("Property '" + key + "' must be specified");
+    }
+    return value;
+  }
+
+  String loadProjectKey(ProjectDefinition projectDefinition) {
+    return getPropertyOrDie(projectDefinition, CoreProperties.PROJECT_KEY_PROPERTY);
+  }
+
+  String loadProjectName(ProjectDefinition projectDefinition) {
+    return projectDefinition.getProperties().getProperty(
+        CoreProperties.PROJECT_NAME_PROPERTY,
+        "Unnamed - " + loadProjectKey(projectDefinition));
   }
 
   String loadProjectBranch(Configuration configuration) {
     return configuration.getString(CoreProperties.PROJECT_BRANCH_PROPERTY, configuration.getString("branch" /* deprecated property */));
   }
 
-  public void configure(Project project) {
-    ProjectConfiguration projectConfiguration = new ProjectConfiguration(databaseSession, project);
+  public void configure(Project project, ProjectDefinition def) {
+    ProjectConfiguration projectConfiguration = new ProjectConfiguration(databaseSession, project, def.getProperties());
     configure(project, projectConfiguration);
   }
 
   void configure(Project project, Configuration projectConfiguration) {
     Date analysisDate = loadAnalysisDate(projectConfiguration);
-    MavenProject pom = project.getPom();
     project.setConfiguration(projectConfiguration)
         .setExclusionPatterns(loadExclusionPatterns(projectConfiguration))
         .setAnalysisDate(analysisDate)
         .setLatestAnalysis(isLatestAnalysis(project.getKey(), analysisDate))
-        .setAnalysisVersion(loadAnalysisVersion(projectConfiguration, pom))
+        .setAnalysisVersion(loadAnalysisVersion(projectConfiguration))
         .setAnalysisType(loadAnalysisType(projectConfiguration))
         .setLanguageKey(loadLanguageKey(projectConfiguration));
   }
@@ -133,12 +147,8 @@ public class MavenProjectBuilder {
     return Project.AnalysisType.STATIC;
   }
 
-  String loadAnalysisVersion(Configuration configuration, MavenProject pom) {
-    String version = configuration.getString(CoreProperties.PROJECT_VERSION_PROPERTY);
-    if (version == null && pom != null) {
-      version = pom.getVersion();
-    }
-    return version;
+  String loadAnalysisVersion(Configuration configuration) {
+    return configuration.getString(CoreProperties.PROJECT_VERSION_PROPERTY);
   }
 
   String loadLanguageKey(Configuration configuration) {
diff --git a/sonar-batch/src/main/java/org/sonar/batch/MavenProjectConverter.java b/sonar-batch/src/main/java/org/sonar/batch/MavenProjectConverter.java
new file mode 100644
index 00000000000..450509870be
--- /dev/null
+++ b/sonar-batch/src/main/java/org/sonar/batch/MavenProjectConverter.java
@@ -0,0 +1,85 @@
+/*
+ * Sonar, open source software quality management tool.
+ * Copyright (C) 2008-2011 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * Sonar 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.
+ *
+ * Sonar 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 Sonar; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02
+ */
+package org.sonar.batch;
+
+import com.google.common.collect.Maps;
+import org.apache.maven.project.MavenProject;
+import org.sonar.api.CoreProperties;
+import org.sonar.api.utils.SonarException;
+import org.sonar.batch.bootstrapper.ProjectDefinition;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+public class MavenProjectConverter {
+
+  private MavenProjectConverter() {
+  }
+
+  public static ProjectDefinition convert(List<MavenProject> poms) {
+    Map<String, MavenProject> paths = Maps.newHashMap(); // projects by canonical path
+    Map<MavenProject, ProjectDefinition> defs = Maps.newHashMap();
+
+    try {
+      for (MavenProject pom : poms) {
+        String basedir = pom.getBasedir().getCanonicalPath();
+        paths.put(basedir, pom);
+        defs.put(pom, convert(pom));
+      }
+
+      for (Map.Entry<String, MavenProject> entry : paths.entrySet()) {
+        MavenProject pom = entry.getValue();
+        for (Object moduleId : pom.getModules()) {
+          File modulePath = new File(pom.getBasedir(), (String) moduleId);
+          MavenProject module = paths.get(modulePath.getCanonicalPath());
+          defs.get(pom).addModule(defs.get(module));
+        }
+      }
+    } catch (IOException e) {
+      throw new SonarException(e);
+    }
+
+    return defs.get(poms.get(0));
+  }
+
+  public static ProjectDefinition convert(MavenProject pom) {
+    Properties properties = new Properties();
+
+    String key = new StringBuilder().append(pom.getGroupId()).append(":").append(pom.getArtifactId()).toString();
+    setProperty(properties, CoreProperties.PROJECT_KEY_PROPERTY, key);
+    setProperty(properties, CoreProperties.PROJECT_VERSION_PROPERTY, pom.getVersion());
+    setProperty(properties, CoreProperties.PROJECT_NAME_PROPERTY, pom.getName());
+    setProperty(properties, CoreProperties.PROJECT_DESCRIPTION_PROPERTY, pom.getDescription());
+    properties.putAll(pom.getModel().getProperties());
+
+    ProjectDefinition def = new ProjectDefinition(pom.getBasedir(), null, properties); // TODO work directory ?
+    def.addContainerExtension(pom);
+    return def;
+  }
+
+  private static void setProperty(Properties properties, String key, String value) {
+    if (value != null) {
+      properties.setProperty(key, value);
+    }
+  }
+}
diff --git a/sonar-batch/src/main/java/org/sonar/batch/MavenProjectFileSystem.java b/sonar-batch/src/main/java/org/sonar/batch/MavenProjectFileSystem.java
deleted file mode 100644
index 39ac4ad7c18..00000000000
--- a/sonar-batch/src/main/java/org/sonar/batch/MavenProjectFileSystem.java
+++ /dev/null
@@ -1,114 +0,0 @@
-/*
- * Sonar, open source software quality management tool.
- * Copyright (C) 2008-2011 SonarSource
- * mailto:contact AT sonarsource DOT com
- *
- * Sonar 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.
- *
- * Sonar 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 Sonar; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02
- */
-package org.sonar.batch;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.maven.project.MavenProject;
-import org.sonar.api.resources.DefaultProjectFileSystem;
-import org.sonar.api.resources.Languages;
-import org.sonar.api.resources.Project;
-import org.sonar.api.resources.ProjectFileSystem;
-import org.sonar.api.utils.SonarException;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.List;
-
-/**
- * Implementation of {@link ProjectFileSystem} based on {@link MavenProject}.
- */
-public class MavenProjectFileSystem extends DefaultProjectFileSystem {
-
-  private MavenProject pom;
-
-  public MavenProjectFileSystem(Project project, Languages languages) {
-    super(project, languages);
-    this.pom = project.getPom();
-  }
-
-  @Override
-  public File getBasedir() {
-    return pom.getBasedir();
-  }
-
-  @Override
-  public File getBuildDir() {
-    return resolvePath(pom.getBuild().getDirectory());
-  }
-
-  @Override
-  public File getBuildOutputDir() {
-    return resolvePath(pom.getBuild().getOutputDirectory());
-  }
-
-  /**
-   * Maven can modify source directories during Sonar execution - see MavenPhaseExecutor.
-   */
-  @Override
-  public List<File> getSourceDirs() {
-    return resolvePaths(pom.getCompileSourceRoots());
-  }
-
-  @Override
-  public DefaultProjectFileSystem addSourceDir(File dir) {
-    if (dir == null) {
-      throw new IllegalArgumentException("Can not add null to project source dirs");
-    }
-    pom.getCompileSourceRoots().add(0, dir.getAbsolutePath());
-    return this;
-  }
-
-  /**
-   * Maven can modify test directories during Sonar execution - see MavenPhaseExecutor.
-   */
-  @Override
-  public List<File> getTestDirs() {
-    return resolvePaths(pom.getTestCompileSourceRoots());
-  }
-
-  /**
-   * @deprecated since 2.6, because should be immutable
-   */
-  @Override
-  public DefaultProjectFileSystem addTestDir(File dir) {
-    if (dir == null) {
-      throw new IllegalArgumentException("Can not add null to project test dirs");
-    }
-    pom.getTestCompileSourceRoots().add(0, dir.getAbsolutePath());
-    return this;
-  }
-
-  @Override
-  public File getReportOutputDir() {
-    return resolvePath(pom.getReporting().getOutputDirectory());
-  }
-
-  @Override
-  public File getSonarWorkingDirectory() {
-    try {
-      File dir = new File(getBuildDir(), "sonar");
-      FileUtils.forceMkdir(dir);
-      return dir;
-
-    } catch (IOException e) {
-      throw new SonarException("Unable to retrieve Sonar working directory.", e);
-    }
-  }
-}
diff --git a/sonar-batch/src/main/java/org/sonar/batch/MavenReactor.java b/sonar-batch/src/main/java/org/sonar/batch/MavenReactor.java
deleted file mode 100644
index fff85d35e34..00000000000
--- a/sonar-batch/src/main/java/org/sonar/batch/MavenReactor.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Sonar, open source software quality management tool.
- * Copyright (C) 2008-2011 SonarSource
- * mailto:contact AT sonarsource DOT com
- *
- * Sonar 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.
- *
- * Sonar 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 Sonar; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02
- */
-package org.sonar.batch;
-
-import org.apache.maven.execution.MavenSession;
-import org.apache.maven.project.MavenProject;
-
-import java.util.List;
-
-public class MavenReactor {
-
-  private List<MavenProject> sortedProjects;
-
-  public MavenReactor(MavenSession mavenSession) {
-    this.sortedProjects = mavenSession.getSortedProjects();
-  }
-
-  public MavenReactor(List<MavenProject> sortedProjects) {
-    this.sortedProjects = sortedProjects;
-  }
-
-  public List<MavenProject> getSortedProjects() {
-    return sortedProjects;
-  }
-
-}
diff --git a/sonar-batch/src/main/java/org/sonar/batch/ProjectBatch.java b/sonar-batch/src/main/java/org/sonar/batch/ProjectBatch.java
index 95355bc08ef..7a6ea61b454 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/ProjectBatch.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/ProjectBatch.java
@@ -19,8 +19,8 @@
  */
 package org.sonar.batch;
 
+import org.apache.maven.project.MavenProject;
 import org.sonar.api.batch.BatchExtensionDictionnary;
-import org.sonar.api.batch.ProjectClasspath;
 import org.sonar.api.measures.CoreMetrics;
 import org.sonar.api.measures.Metric;
 import org.sonar.api.measures.Metrics;
@@ -32,6 +32,7 @@ import org.sonar.api.resources.ProjectFileSystem;
 import org.sonar.api.rules.DefaultRulesManager;
 import org.sonar.api.utils.SonarException;
 import org.sonar.batch.bootstrap.BatchPluginRepository;
+import org.sonar.batch.bootstrapper.ProjectDefinition;
 import org.sonar.batch.components.PastViolationsLoader;
 import org.sonar.batch.components.TimeMachineConfiguration;
 import org.sonar.batch.events.EventBus;
@@ -103,10 +104,21 @@ public class ProjectBatch {
 
     @Override
     protected void configure() {
+      ProjectDefinition projectDefinition = getComponent(ProjectTree.class).getProjectDefinition(project.getKey());
+      addComponent(projectDefinition);
+      for (Object component : projectDefinition.getContainerExtensions()) {
+        addComponent(component);
+        if (component instanceof MavenProject) {
+          // For backward compatibility we must set POM and actual packaging
+          MavenProject pom = (MavenProject) component;
+          project.setPom(pom);
+          project.setPackaging(pom.getPackaging());
+        }
+      }
+
       addComponent(project);
-      addComponent(project.getPom());
-      addComponent(ProjectClasspath.class);
-      addComponent(MavenProjectFileSystem.class);
+      addComponent(DefaultProjectClasspath.class);
+      addComponent(DefaultProjectFileSystem2.class);
       addComponent(project.getConfiguration());
 
       // need to be registered after the Configuration
diff --git a/sonar-batch/src/main/java/org/sonar/batch/ProjectConfiguration.java b/sonar-batch/src/main/java/org/sonar/batch/ProjectConfiguration.java
index ddae656f1d8..f89e9d644fa 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/ProjectConfiguration.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/ProjectConfiguration.java
@@ -20,20 +20,26 @@
 package org.sonar.batch;
 
 import org.apache.commons.configuration.*;
-import org.apache.maven.project.MavenProject;
 import org.sonar.api.database.DatabaseSession;
 import org.sonar.api.resources.Project;
 
+import java.util.Properties;
+
 public class ProjectConfiguration extends CompositeConfiguration {
   private PropertiesConfiguration runtimeConfiguration;
 
+  // FIXME remove
   public ProjectConfiguration(DatabaseSession session, Project project) {
+    this(session, project, project.getPom().getProperties());
+  }
+
+  public ProjectConfiguration(DatabaseSession session, Project project, Properties properties) {
     runtimeConfiguration = new PropertiesConfiguration();
     addConfiguration(runtimeConfiguration);
 
     loadSystemSettings();
     loadProjectDatabaseSettings(session, project);
-    loadMavenSettings(project.getPom());
+    addConfiguration(new MapConfiguration(properties));
     loadGlobalDatabaseSettings(session);
   }
 
@@ -56,13 +62,8 @@ public class ProjectConfiguration extends CompositeConfiguration {
     addConfiguration(new EnvironmentConfiguration());
   }
 
-  private void loadMavenSettings(MavenProject pom) {
-    addConfiguration(new MapConfiguration(pom.getModel().getProperties()));
-  }
-
   @Override
   public void setProperty(String s, Object o) {
     runtimeConfiguration.setProperty(s, o);
   }
 }
-
diff --git a/sonar-batch/src/main/java/org/sonar/batch/ProjectTree.java b/sonar-batch/src/main/java/org/sonar/batch/ProjectTree.java
index 4a03586a2e8..ac2db745ec3 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/ProjectTree.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/ProjectTree.java
@@ -21,42 +21,30 @@ package org.sonar.batch;
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
+import org.apache.commons.lang.StringUtils;
 import org.apache.maven.project.MavenProject;
 import org.slf4j.LoggerFactory;
+import org.sonar.api.CoreProperties;
 import org.sonar.api.database.DatabaseSession;
 import org.sonar.api.resources.Project;
 import org.sonar.batch.bootstrapper.ProjectDefinition;
 import org.sonar.batch.bootstrapper.Reactor;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.*;
 
 public class ProjectTree {
 
   private List<Project> projects;
-  private List<MavenProject> poms;
   private MavenProjectBuilder projectBuilder;
+  private List<ProjectDefinition> definitions;
 
-  public ProjectTree(MavenReactor mavenReactor, DatabaseSession databaseSession) {
-    this.poms = mavenReactor.getSortedProjects();
-    this.projectBuilder = new MavenProjectBuilder(databaseSession);
-  }
-
-  /**
-   * Hack for non-Maven environments.
-   */
   public ProjectTree(Reactor sonarReactor, DatabaseSession databaseSession) {
-    this(createMavenReactor(sonarReactor), databaseSession);
-  }
-
-  private static MavenReactor createMavenReactor(Reactor sonarReactor) {
-    List<ProjectDefinition> sonarProjects = sonarReactor.getSortedProjects();
-    List<MavenProject> mavenProjects = Lists.newArrayList();
-    for (ProjectDefinition project : sonarProjects) {
-      mavenProjects.add(new InMemoryPomCreator(project).create());
+    this.projectBuilder = new MavenProjectBuilder(databaseSession);
+    definitions = Lists.newArrayList();
+    for (ProjectDefinition project : sonarReactor.getSortedProjects()) {
+      collectProjects(project, definitions);
     }
-    return new MavenReactor(mavenProjects);
   }
 
   /**
@@ -64,7 +52,8 @@ public class ProjectTree {
    */
   protected ProjectTree(MavenProjectBuilder projectBuilder, List<MavenProject> poms) {
     this.projectBuilder = projectBuilder;
-    this.poms = poms;
+    definitions = Lists.newArrayList();
+    collectProjects(MavenProjectConverter.convert(poms), definitions);
   }
 
   /**
@@ -74,36 +63,40 @@ public class ProjectTree {
     this.projects = new ArrayList<Project>(projects);
   }
 
+  /**
+   * Populates list of projects from hierarchy.
+   */
+  private static void collectProjects(ProjectDefinition root, List<ProjectDefinition> collected) {
+    collected.add(root);
+    for (ProjectDefinition module : root.getModules()) {
+      collectProjects(module, collected);
+    }
+  }
+
   public void start() throws IOException {
     projects = Lists.newArrayList();
-    Map<String, Project> paths = Maps.newHashMap(); // projects by canonical path
+    Map<ProjectDefinition, Project> map = Maps.newHashMap();
 
-    for (MavenProject pom : poms) {
-      Project project = projectBuilder.create(pom);
+    for (ProjectDefinition def : definitions) {
+      Project project = projectBuilder.create(def);
+      map.put(def, project);
       projects.add(project);
-      paths.put(pom.getBasedir().getCanonicalPath(), project);
     }
 
-    for (Map.Entry<String, Project> entry : paths.entrySet()) {
+    for (Map.Entry<ProjectDefinition, Project> entry : map.entrySet()) {
+      ProjectDefinition def = entry.getKey();
       Project project = entry.getValue();
-      MavenProject pom = project.getPom();
-      for (Object moduleId : pom.getModules()) {
-        File modulePath = new File(pom.getBasedir(), (String) moduleId);
-        Project module = paths.get(modulePath.getCanonicalPath());
-        if (module != null) {
-          module.setParent(project);
-        }
+      for (ProjectDefinition module : def.getModules()) {
+        map.get(module).setParent(project);
       }
     }
 
-    configureProjects();
-    applyModuleExclusions();
-  }
-
-  private void configureProjects() {
-    for (Project project : projects) {
-      projectBuilder.configure(project);
+    // Configure
+    for (Map.Entry<ProjectDefinition, Project> entry : map.entrySet()) {
+      projectBuilder.configure(entry.getValue(), entry.getKey());
     }
+
+    applyModuleExclusions();
   }
 
   void applyModuleExclusions() {
@@ -125,7 +118,7 @@ public class ProjectTree {
 
       if (!includedModulesIdSet.isEmpty()) {
         for (Project currentProject : projects) {
-          if (!includedModulesIdSet.contains(currentProject.getPom().getArtifactId())) {
+          if (!includedModulesIdSet.contains(getArtifactId(currentProject))) {
             exclude(currentProject);
           }
         }
@@ -160,9 +153,19 @@ public class ProjectTree {
     return projects;
   }
 
+  private String getArtifactId(Project project) {
+    String key = project.getKey();
+    if (StringUtils.isNotBlank(project.getBranch())) {
+      // remove branch part
+      key = StringUtils.removeEnd(project.getKey(), ":" + project.getBranch());
+    }
+    return StringUtils.substringAfterLast(key, ":");
+  }
+
   public Project getProjectByArtifactId(String artifactId) {
     for (Project project : projects) {
-      if (project.getPom().getArtifactId().equals(artifactId)) {
+      // TODO see http://jira.codehaus.org/browse/SONAR-2324
+      if (StringUtils.equals(getArtifactId(project), artifactId)) {
         return project;
       }
     }
@@ -177,4 +180,27 @@ public class ProjectTree {
     }
     throw new IllegalStateException("Can not find the root project from the list of Maven modules");
   }
-}
\ No newline at end of file
+
+  private String getProjectKey(ProjectDefinition def) {
+    String key = def.getProperties().getProperty(CoreProperties.PROJECT_KEY_PROPERTY);
+    String branch = def.getProperties().getProperty(CoreProperties.PROJECT_BRANCH_PROPERTY);
+    if (StringUtils.isNotBlank(branch)) {
+      return key + ":" + branch;
+    } else {
+      return key;
+    }
+  }
+
+  public ProjectDefinition getProjectDefinition(String key) {
+    for (ProjectDefinition def : definitions) {
+      if (StringUtils.equals(key, getProjectKey(def))) {
+        return def;
+      }
+    }
+    return null;
+  }
+
+  public List<Object> getProjectExtensions(String key) {
+    return getProjectDefinition(key).getContainerExtensions();
+  }
+}
diff --git a/sonar-batch/src/main/java/org/sonar/batch/bootstrapper/ProjectDefinition.java b/sonar-batch/src/main/java/org/sonar/batch/bootstrapper/ProjectDefinition.java
index b632feb60ac..907f30940ac 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/bootstrapper/ProjectDefinition.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/bootstrapper/ProjectDefinition.java
@@ -19,12 +19,14 @@
  */
 package org.sonar.batch.bootstrapper;
 
+import com.google.common.collect.Lists;
+import org.apache.commons.lang.StringUtils;
+
 import java.io.File;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Properties;
 
-import com.google.common.collect.Lists;
-
 /**
  * Describes project in a form suitable to bootstrap Sonar batch.
  * We assume that project is just a set of configuration properties and directories.
@@ -33,13 +35,19 @@ import com.google.common.collect.Lists;
  */
 public class ProjectDefinition {
 
+  private static final String PROJECT_SOURCES_PROPERTY = "sonar.sources";
+  private static final String PROJECT_TESTS_PROPERTY = "sonar.tests";
+  private static final String PROJECT_BINARIES_PROPERTY = "sonar.binaries";
+  private static final String PROJECT_LIBRARIES_PROPERTY = "sonar.libraries";
+
+  private static final char SEPARATOR = ',';
+
   private File baseDir;
   private File workDir;
   private Properties properties;
-  private List<String> sourceDirs = Lists.newArrayList();
-  private List<String> testDirs = Lists.newArrayList();
-  private List<String> binaries = Lists.newArrayList();
-  private List<String> libraries = Lists.newArrayList();
+  private List<ProjectDefinition> modules = Lists.newArrayList();
+
+  private List<Object> containerExtensions = Lists.newArrayList();
 
   /**
    * @param baseDir project base directory
@@ -63,8 +71,14 @@ public class ProjectDefinition {
     return properties;
   }
 
+  private void appendProperty(String key, String value) {
+    String newValue = properties.getProperty(key, "") + SEPARATOR + value;
+    properties.put(key, newValue);
+  }
+
   public List<String> getSourceDirs() {
-    return sourceDirs;
+    String sources = properties.getProperty(PROJECT_SOURCES_PROPERTY, "");
+    return Arrays.asList(StringUtils.split(sources, SEPARATOR));
   }
 
   /**
@@ -72,11 +86,12 @@ public class ProjectDefinition {
    *          It can be absolute or relative to project directory.
    */
   public void addSourceDir(String path) {
-    sourceDirs.add(path);
+    appendProperty(PROJECT_SOURCES_PROPERTY, path);
   }
 
   public List<String> getTestDirs() {
-    return testDirs;
+    String sources = properties.getProperty(PROJECT_TESTS_PROPERTY, "");
+    return Arrays.asList(StringUtils.split(sources, SEPARATOR));
   }
 
   /**
@@ -84,11 +99,12 @@ public class ProjectDefinition {
    *          It can be absolute or relative to project directory.
    */
   public void addTestDir(String path) {
-    testDirs.add(path);
+    appendProperty(PROJECT_TESTS_PROPERTY, path);
   }
 
   public List<String> getBinaries() {
-    return binaries;
+    String sources = properties.getProperty(PROJECT_BINARIES_PROPERTY, "");
+    return Arrays.asList(StringUtils.split(sources, SEPARATOR));
   }
 
   /**
@@ -97,11 +113,12 @@ public class ProjectDefinition {
    * @TODO currently Sonar supports only one such directory due to dependency on MavenProject
    */
   public void addBinaryDir(String path) {
-    binaries.add(path);
+    appendProperty(PROJECT_BINARIES_PROPERTY, path);
   }
 
   public List<String> getLibraries() {
-    return libraries;
+    String sources = properties.getProperty(PROJECT_LIBRARIES_PROPERTY, "");
+    return Arrays.asList(StringUtils.split(sources, SEPARATOR));
   }
 
   /**
@@ -109,6 +126,36 @@ public class ProjectDefinition {
    *          It can be absolute or relative to project directory.
    */
   public void addLibrary(String path) {
-    libraries.add(path);
+    appendProperty(PROJECT_LIBRARIES_PROPERTY, path);
+  }
+
+  /**
+   * Adds an extension, which would be available in PicoContainer during analysis of this project.
+   * 
+   * @since 2.8
+   */
+  public void addContainerExtension(Object extension) {
+    containerExtensions.add(extension);
+  }
+
+  /**
+   * @since 2.8
+   */
+  public List<Object> getContainerExtensions() {
+    return containerExtensions;
+  }
+
+  /**
+   * @since 2.8
+   */
+  public void addModule(ProjectDefinition projectDefinition) {
+    modules.add(projectDefinition);
+  }
+
+  /**
+   * @since 2.8
+   */
+  public List<ProjectDefinition> getModules() {
+    return modules;
   }
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/phases/MavenPluginsConfigurator.java b/sonar-batch/src/main/java/org/sonar/batch/phases/MavenPluginsConfigurator.java
index 49560b6126e..ab6c9915123 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/phases/MavenPluginsConfigurator.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/phases/MavenPluginsConfigurator.java
@@ -60,16 +60,18 @@ public class MavenPluginsConfigurator implements BatchComponent {
 
   protected void savePom(Project project) {
     MavenProject pom = project.getPom();
-    File targetPom = new File(project.getFileSystem().getSonarWorkingDirectory(), "sonar-pom.xml");
-    FileWriter fileWriter = null;
-    try {
-      fileWriter = new FileWriter(targetPom, false);
-      pom.writeModel(fileWriter);
+    if (pom != null) {
+      File targetPom = new File(project.getFileSystem().getSonarWorkingDirectory(), "sonar-pom.xml");
+      FileWriter fileWriter = null;
+      try {
+        fileWriter = new FileWriter(targetPom, false);
+        pom.writeModel(fileWriter);
 
-    } catch (IOException e) {
-      throw new SonarException("Can not save pom to " + targetPom, e);
-    } finally {
-      IOUtils.closeQuietly(fileWriter);
+      } catch (IOException e) {
+        throw new SonarException("Can not save pom to " + targetPom, e);
+      } finally {
+        IOUtils.closeQuietly(fileWriter);
+      }
     }
   }
 }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/InMemoryPomCreatorTest.java b/sonar-batch/src/test/java/org/sonar/batch/InMemoryPomCreatorTest.java
deleted file mode 100644
index e7787f5e05b..00000000000
--- a/sonar-batch/src/test/java/org/sonar/batch/InMemoryPomCreatorTest.java
+++ /dev/null
@@ -1,137 +0,0 @@
-/*
- * Sonar, open source software quality management tool.
- * Copyright (C) 2008-2011 SonarSource
- * mailto:contact AT sonarsource DOT com
- *
- * Sonar 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.
- *
- * Sonar 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 Sonar; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02
- */
-package org.sonar.batch;
-
-import org.apache.maven.project.MavenProject;
-import org.junit.Before;
-import org.junit.Test;
-import org.sonar.api.CoreProperties;
-import org.sonar.api.utils.SonarException;
-import org.sonar.batch.bootstrapper.ProjectDefinition;
-
-import java.io.File;
-import java.util.List;
-import java.util.Properties;
-
-import static org.hamcrest.Matchers.is;
-import static org.junit.Assert.assertThat;
-
-public class InMemoryPomCreatorTest {
-
-  private Properties properties;
-  private ProjectDefinition project;
-
-  @Before
-  public void setUp() {
-    properties = new Properties();
-    File baseDir = new File(".");
-    File workDir = new File(baseDir, "sonar");
-    project = new ProjectDefinition(baseDir, workDir, properties);
-  }
-
-  @Test
-  public void minimal() {
-    createRequiredProperties();
-
-    MavenProject pom = create();
-
-    assertThat(pom.getBasedir(), is(project.getBaseDir()));
-    assertThat(pom.getGroupId(), is("org.example"));
-    assertThat(pom.getArtifactId(), is("example"));
-    assertThat(pom.getName(), is("Unnamed - org.example:example"));
-    assertThat(pom.getDescription(), is(""));
-    assertThat(pom.getProperties(), is(project.getProperties()));
-    assertThat(pom.getBasedir(), is(project.getBaseDir()));
-    String buildDirectory = project.getWorkDir().getAbsolutePath() + "/target";
-    assertThat(pom.getBuild().getDirectory(), is(buildDirectory));
-    assertThat(pom.getBuild().getOutputDirectory(), is(buildDirectory + "/classes"));
-    assertThat(pom.getReporting().getOutputDirectory(), is(buildDirectory + "/site"));
-  }
-
-  @Test
-  public void nameAndDescription() {
-    createRequiredProperties();
-
-    properties.setProperty(CoreProperties.PROJECT_NAME_PROPERTY, "Foo");
-    properties.setProperty(CoreProperties.PROJECT_DESCRIPTION_PROPERTY, "Bar");
-
-    MavenProject pom = create();
-
-    assertThat(pom.getName(), is("Foo"));
-    assertThat(pom.getDescription(), is("Bar"));
-  }
-
-  @Test
-  public void sourceDirectories() {
-    createRequiredProperties();
-    project.addSourceDir("src");
-    project.addTestDir("test");
-
-    MavenProject pom = create();
-
-    assertThat(pom.getCompileSourceRoots().size(), is(1));
-    assertThat((String) pom.getCompileSourceRoots().get(0), is("src"));
-
-    assertThat(pom.getTestCompileSourceRoots().size(), is(1));
-    assertThat((String) pom.getTestCompileSourceRoots().get(0), is("test"));
-  }
-
-  @Test
-  public void classpath() throws Exception {
-    createRequiredProperties();
-    project.addBinaryDir("/classes");
-    project.addLibrary("junit.jar");
-
-    MavenProject pom = create();
-
-    List<String> cp = pom.getCompileClasspathElements();
-    assertThat(cp.size(), is(2));
-    assertThat(cp.get(0), is("/classes"));
-    assertThat(cp.get(1), is("junit.jar"));
-  }
-
-  @Test
-  public void shouldNotFailIfNoBinaries() throws Exception {
-    createRequiredProperties();
-
-    MavenProject pom = create();
-    assertThat(pom.getCompileClasspathElements().size(), is(1));
-  }
-
-  private void createRequiredProperties() {
-    properties.setProperty(CoreProperties.PROJECT_KEY_PROPERTY, "org.example:example");
-    properties.setProperty(CoreProperties.PROJECT_VERSION_PROPERTY, "1.0-SNAPSHOT");
-  }
-
-  @Test(expected = SonarException.class)
-  public void shouldFailWhenKeyNotSpecified() {
-    create();
-  }
-
-  @Test(expected = SonarException.class)
-  public void shouldFailWhenVersionNotSpecified() {
-    properties.setProperty(CoreProperties.PROJECT_KEY_PROPERTY, "org.example:example");
-    create();
-  }
-
-  private MavenProject create() {
-    return new InMemoryPomCreator(project).create();
-  }
-}
diff --git a/sonar-batch/src/test/java/org/sonar/batch/MavenProjectConverterTest.java b/sonar-batch/src/test/java/org/sonar/batch/MavenProjectConverterTest.java
new file mode 100644
index 00000000000..c9a2c4124fb
--- /dev/null
+++ b/sonar-batch/src/test/java/org/sonar/batch/MavenProjectConverterTest.java
@@ -0,0 +1,63 @@
+/*
+ * Sonar, open source software quality management tool.
+ * Copyright (C) 2008-2011 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * Sonar 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.
+ *
+ * Sonar 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 Sonar; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02
+ */
+package org.sonar.batch;
+
+import static org.hamcrest.Matchers.is;
+import static org.junit.Assert.assertThat;
+
+import org.apache.maven.project.MavenProject;
+import org.junit.Test;
+import org.sonar.api.CoreProperties;
+import org.sonar.batch.bootstrapper.ProjectDefinition;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.Properties;
+
+public class MavenProjectConverterTest {
+  @Test
+  public void test2() {
+    MavenProject root = new MavenProject();
+    root.setFile(new File("/foo/pom.xml"));
+    root.getModules().add("module");
+    MavenProject module = new MavenProject();
+    module.setFile(new File("/foo/module/pom.xml"));
+    ProjectDefinition project = MavenProjectConverter.convert(Arrays.asList(root, module));
+
+    assertThat(project.getModules().size(), is(1));
+  }
+
+  @Test
+  public void test() {
+    MavenProject pom = new MavenProject();
+    pom.setGroupId("foo");
+    pom.setArtifactId("bar");
+    pom.setVersion("1.0.1");
+    pom.setName("Test");
+    pom.setDescription("just test");
+    ProjectDefinition project = MavenProjectConverter.convert(pom);
+
+    Properties properties = project.getProperties();
+    assertThat(properties.getProperty(CoreProperties.PROJECT_KEY_PROPERTY), is("foo:bar"));
+    assertThat(properties.getProperty(CoreProperties.PROJECT_VERSION_PROPERTY), is("1.0.1"));
+    assertThat(properties.getProperty(CoreProperties.PROJECT_NAME_PROPERTY), is("Test"));
+    assertThat(properties.getProperty(CoreProperties.PROJECT_DESCRIPTION_PROPERTY), is("just test"));
+  }
+}
diff --git a/sonar-batch/src/test/java/org/sonar/batch/ProjectTreeTest.java b/sonar-batch/src/test/java/org/sonar/batch/ProjectTreeTest.java
index ef3b087ffac..c494dfb02bc 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/ProjectTreeTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/ProjectTreeTest.java
@@ -19,6 +19,11 @@
  */
 package org.sonar.batch;
 
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.core.Is.is;
+import static org.junit.Assert.assertNull;
+import static org.junit.internal.matchers.IsCollectionContaining.hasItem;
+
 import org.apache.commons.configuration.PropertiesConfiguration;
 import org.apache.commons.io.FileUtils;
 import org.apache.maven.model.Model;
@@ -26,8 +31,8 @@ import org.apache.maven.model.io.xpp3.MavenXpp3Reader;
 import org.apache.maven.project.MavenProject;
 import org.codehaus.plexus.util.xml.pull.XmlPullParserException;
 import org.junit.Test;
-import org.sonar.jpa.test.AbstractDbUnitTestCase;
 import org.sonar.api.resources.Project;
+import org.sonar.jpa.test.AbstractDbUnitTestCase;
 
 import java.io.File;
 import java.io.IOException;
@@ -35,12 +40,6 @@ import java.io.StringReader;
 import java.net.URISyntaxException;
 import java.util.Arrays;
 
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.core.Is.is;
-import static org.junit.Assert.assertNull;
-import static org.junit.internal.matchers.IsCollectionContaining.hasItem;
-
-
 public class ProjectTreeTest extends AbstractDbUnitTestCase {
 
   @Test
@@ -71,7 +70,6 @@ public class ProjectTreeTest extends AbstractDbUnitTestCase {
     ProjectTree tree = new ProjectTree(newProjectBuilder(), Arrays.asList(parent, module1, module2));
     tree.start();
 
-
     Project root = tree.getRootProject();
     assertThat(root.getModules().size(), is(2));
     assertThat(root.getKey(), is("org.test:parent"));
@@ -105,7 +103,6 @@ public class ProjectTreeTest extends AbstractDbUnitTestCase {
     assertThat(tree.getRootProject().getName(), is("Project BRANCH-1.X"));
   }
 
-
   @Test
   public void keyIncludesDeprecatedBranch() throws IOException, XmlPullParserException, URISyntaxException {
     MavenProject pom = loadProject("/org/sonar/batch/ProjectTreeTest/keyIncludesDeprecatedBranch/pom.xml", true);
@@ -130,7 +127,7 @@ public class ProjectTreeTest extends AbstractDbUnitTestCase {
   }
 
   @Test
-  public void skipModule() {
+  public void skipModule() throws IOException {
     Project root = newProjectWithArtifactId("root");
     root.getConfiguration().setProperty("sonar.skippedModules", "sub1");
     Project sub1 = newProjectWithArtifactId("sub1");
@@ -191,7 +188,7 @@ public class ProjectTreeTest extends AbstractDbUnitTestCase {
   private Project newProjectWithArtifactId(String artifactId) {
     MavenProject pom = new MavenProject();
     pom.setArtifactId(artifactId);
-    return new Project(artifactId).setPom(pom).setConfiguration(new PropertiesConfiguration());
+    return new Project("org.example:" + artifactId).setPom(pom).setConfiguration(new PropertiesConfiguration());
   }
 
   private MavenProject loadProject(String pomPath, boolean isRoot) throws URISyntaxException, IOException, XmlPullParserException {
diff --git a/sonar-batch/src/test/java/org/sonar/batch/bootstrapper/ProjectDefinitionTest.java b/sonar-batch/src/test/java/org/sonar/batch/bootstrapper/ProjectDefinitionTest.java
new file mode 100644
index 00000000000..df584f312b6
--- /dev/null
+++ b/sonar-batch/src/test/java/org/sonar/batch/bootstrapper/ProjectDefinitionTest.java
@@ -0,0 +1,71 @@
+/*
+ * Sonar, open source software quality management tool.
+ * Copyright (C) 2008-2011 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * Sonar 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.
+ *
+ * Sonar 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 Sonar; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02
+ */
+package org.sonar.batch.bootstrapper;
+
+import static org.hamcrest.Matchers.is;
+import static org.junit.Assert.assertThat;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.List;
+import java.util.Properties;
+
+public class ProjectDefinitionTest {
+  private ProjectDefinition def;
+
+  @Before
+  public void setUp() {
+    def = new ProjectDefinition(new File("."), new File("."), new Properties());
+  }
+
+  @Test
+  public void defaultValues() {
+    assertThat(def.getSourceDirs().size(), is(0));
+    assertThat(def.getTestDirs().size(), is(0));
+    assertThat(def.getBinaries().size(), is(0));
+    assertThat(def.getLibraries().size(), is(0));
+  }
+
+  @Test
+  public void shouldAddDirectories() {
+    def.addSourceDir("src/main/java");
+    def.addSourceDir("src/main/java2");
+    def.addTestDir("src/test/java");
+    def.addTestDir("src/test/java2");
+    def.addBinaryDir("target/classes");
+    def.addBinaryDir("target/classes2");
+    def.addLibrary("junit.jar");
+    def.addLibrary("mockito.jar");
+
+    assertDirs(def.getSourceDirs(), "src/main/java", "src/main/java2");
+    assertDirs(def.getTestDirs(), "src/test/java", "src/test/java2");
+    assertDirs(def.getBinaries(), "target/classes", "target/classes2");
+    assertDirs(def.getLibraries(), "junit.jar", "mockito.jar");
+  }
+
+  private static void assertDirs(List<String> dirs, String... values) {
+    assertThat(dirs.size(), is(values.length));
+    for (int i = 0; i < values.length; i++) {
+      assertThat(dirs.get(i), is(values[i]));
+    }
+  }
+}
diff --git a/sonar-core-maven-plugin/src/main/java/org/sonar/maven2/BatchMojo.java b/sonar-core-maven-plugin/src/main/java/org/sonar/maven2/BatchMojo.java
index 075dfe9110a..f979a24944d 100644
--- a/sonar-core-maven-plugin/src/main/java/org/sonar/maven2/BatchMojo.java
+++ b/sonar-core-maven-plugin/src/main/java/org/sonar/maven2/BatchMojo.java
@@ -19,8 +19,6 @@
  */
 package org.sonar.maven2;
 
-import java.io.InputStream;
-
 import ch.qos.logback.classic.LoggerContext;
 import ch.qos.logback.classic.joran.JoranConfigurator;
 import ch.qos.logback.core.joran.spi.JoranException;
@@ -42,8 +40,12 @@ import org.apache.maven.project.MavenProjectBuilder;
 import org.apache.maven.shared.dependency.tree.DependencyTreeBuilder;
 import org.slf4j.LoggerFactory;
 import org.sonar.batch.Batch;
-import org.sonar.batch.MavenReactor;
+import org.sonar.batch.MavenProjectConverter;
 import org.sonar.batch.bootstrapper.EnvironmentInformation;
+import org.sonar.batch.bootstrapper.ProjectDefinition;
+import org.sonar.batch.bootstrapper.Reactor;
+
+import java.io.InputStream;
 
 /**
  * @goal internal
@@ -143,7 +145,9 @@ public final class BatchMojo extends AbstractMojo {
   }
 
   private void executeBatch() throws MojoExecutionException {
-    MavenReactor reactor = new MavenReactor(session);
+    ProjectDefinition def = MavenProjectConverter.convert(session.getSortedProjects());
+    Reactor reactor = new Reactor(def);
+
     Batch batch = new Batch(getInitialConfiguration(), reactor, session, project,
         getLog(), lifecycleExecutor, pluginManager, artifactFactory,
         localRepository, artifactMetadataSource, artifactCollector,
diff --git a/sonar-maven-plugin/src/main/java/org/sonar/maven/SonarMojo.java b/sonar-maven-plugin/src/main/java/org/sonar/maven/SonarMojo.java
index ab0123210f5..eb57053ba8a 100644
--- a/sonar-maven-plugin/src/main/java/org/sonar/maven/SonarMojo.java
+++ b/sonar-maven-plugin/src/main/java/org/sonar/maven/SonarMojo.java
@@ -19,8 +19,6 @@
  */
 package org.sonar.maven;
 
-import java.io.InputStream;
-
 import ch.qos.logback.classic.LoggerContext;
 import ch.qos.logback.classic.joran.JoranConfigurator;
 import ch.qos.logback.core.joran.spi.JoranException;
@@ -42,8 +40,12 @@ import org.apache.maven.project.MavenProjectBuilder;
 import org.apache.maven.shared.dependency.tree.DependencyTreeBuilder;
 import org.slf4j.LoggerFactory;
 import org.sonar.batch.Batch;
-import org.sonar.batch.MavenReactor;
+import org.sonar.batch.MavenProjectConverter;
 import org.sonar.batch.bootstrapper.EnvironmentInformation;
+import org.sonar.batch.bootstrapper.ProjectDefinition;
+import org.sonar.batch.bootstrapper.Reactor;
+
+import java.io.InputStream;
 
 /**
  * @goal sonar
@@ -143,7 +145,9 @@ public final class SonarMojo extends AbstractMojo {
   }
 
   private void executeBatch() throws MojoExecutionException {
-    MavenReactor reactor = new MavenReactor(session);
+    ProjectDefinition def = MavenProjectConverter.convert(session.getSortedProjects());
+    Reactor reactor = new Reactor(def);
+
     Batch batch = new Batch(getInitialConfiguration(),
         reactor, session, project, getLog(), lifecycleExecutor, pluginManager, artifactFactory,
         localRepository, artifactMetadataSource, artifactCollector, dependencyTreeBuilder,
diff --git a/sonar-maven3-plugin/src/main/java/org/sonar/maven3/SonarMojo.java b/sonar-maven3-plugin/src/main/java/org/sonar/maven3/SonarMojo.java
index baca606b874..7bb5e3e5f69 100644
--- a/sonar-maven3-plugin/src/main/java/org/sonar/maven3/SonarMojo.java
+++ b/sonar-maven3-plugin/src/main/java/org/sonar/maven3/SonarMojo.java
@@ -19,8 +19,6 @@
  */
 package org.sonar.maven3;
 
-import java.io.InputStream;
-
 import ch.qos.logback.classic.LoggerContext;
 import ch.qos.logback.classic.joran.JoranConfigurator;
 import ch.qos.logback.core.joran.spi.JoranException;
@@ -41,8 +39,12 @@ import org.apache.maven.project.MavenProjectBuilder;
 import org.apache.maven.shared.dependency.tree.DependencyTreeBuilder;
 import org.slf4j.LoggerFactory;
 import org.sonar.batch.Batch;
-import org.sonar.batch.MavenReactor;
+import org.sonar.batch.MavenProjectConverter;
 import org.sonar.batch.bootstrapper.EnvironmentInformation;
+import org.sonar.batch.bootstrapper.ProjectDefinition;
+import org.sonar.batch.bootstrapper.Reactor;
+
+import java.io.InputStream;
 
 /**
  * @goal sonar
@@ -136,7 +138,9 @@ public final class SonarMojo extends AbstractMojo {
   }
 
   private void executeBatch() throws MojoExecutionException {
-    MavenReactor reactor = new MavenReactor(session);
+    ProjectDefinition def = MavenProjectConverter.convert(session.getSortedProjects());
+    Reactor reactor = new Reactor(def);
+
     Batch batch = new Batch(getInitialConfiguration(),
         reactor, session, project, getLog(), lifecycleExecutor, artifactFactory,
         localRepository, artifactMetadataSource, artifactCollector, dependencyTreeBuilder,
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/batch/ProjectClasspath.java b/sonar-plugin-api/src/main/java/org/sonar/api/batch/ProjectClasspath.java
index 9fffa244dbf..130ad3c29fe 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/batch/ProjectClasspath.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/batch/ProjectClasspath.java
@@ -36,7 +36,7 @@ import java.util.List;
  */
 public class ProjectClasspath implements BatchComponent {
 
-  private MavenProject pom;
+  protected MavenProject pom;
   private List<File> elements;
   private URLClassLoader classloader;
 
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/resources/DefaultProjectFileSystem.java b/sonar-plugin-api/src/main/java/org/sonar/api/resources/DefaultProjectFileSystem.java
index 9670a437af9..6b3737ac39d 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/resources/DefaultProjectFileSystem.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/resources/DefaultProjectFileSystem.java
@@ -43,8 +43,9 @@ import java.util.List;
  * For internal use only.
  * 
  * @since 1.10
- * @TODO in fact this class should not be located in sonar-plugin-api
+ * @deprecated in 2.8. In fact this class should not be located in sonar-plugin-api and most of the methods were overridden by a component in sonar-batch.
  */
+@Deprecated
 public class DefaultProjectFileSystem implements ProjectFileSystem {
 
   private Project project;