Revert "SONAR-6658 Drop validation on sonar.libraries and sonar.binaries"

This reverts commit 1dd1cd5c6517ffe91ae9b0b003d65c126d54b4b4.

19 files changed, 206 insertions, 54 deletions

diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java b/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java
index beeec9e389f..1363134d449 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java
@@ -22,6 +22,7 @@ package org.sonar.batch.scan;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.sonar.api.batch.InstantiationStrategy;
+import org.sonar.api.batch.ProjectClasspath;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.fs.internal.FileMetadata;
 import org.sonar.api.batch.rule.CheckFactory;
@@ -133,6 +134,7 @@ public class ModuleScanContainer extends ComponentContainer {
       DefaultModuleFileSystem.class,
       ModuleFileSystemInitializer.class,
       ProjectFileSystemAdapter.class,
+      ProjectClasspath.class,
       QProfileVerifier.class,
 
     SensorOptimizer.class,
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectReactorBuilder.java b/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectReactorBuilder.java
index ad67711a857..670bf714eef 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectReactorBuilder.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectReactorBuilder.java
@@ -81,6 +81,8 @@ public class ProjectReactorBuilder {
    */
   private static final String PROPERTY_SOURCES = "sonar.sources";
   private static final String PROPERTY_TESTS = "sonar.tests";
+  private static final String PROPERTY_BINARIES = "sonar.binaries";
+  private static final String PROPERTY_LIBRARIES = "sonar.libraries";
 
   /**
    * Array of all mandatory properties required for a project without child.
@@ -342,9 +344,22 @@ public class ProjectReactorBuilder {
     if (!props.containsKey(PROPERTY_MODULES)) {
       // SONARPLUGINS-2285 Not an aggregator project so we can validate that paths are correct if defined
 
+      // We need to resolve patterns that may have been used in "sonar.libraries"
+      for (String pattern : getListFromProperty(props, PROPERTY_LIBRARIES)) {
+        File[] files = getLibraries(baseDir, pattern);
+        if (files == null || files.length == 0) {
+          LOG.error(MessageFormat.format(INVALID_VALUE_OF_X_FOR_Y, PROPERTY_LIBRARIES, projectId));
+          throw new IllegalStateException("No files nor directories matching '" + pattern + "' in directory " + baseDir);
+        }
+      }
+
       // Check sonar.tests
       String[] testPaths = getListFromProperty(props, PROPERTY_TESTS);
       checkExistenceOfPaths(projectId, baseDir, testPaths, PROPERTY_TESTS);
+
+      // Check sonar.binaries
+      String[] binDirs = getListFromProperty(props, PROPERTY_BINARIES);
+      checkExistenceOfDirectories(projectId, baseDir, binDirs, PROPERTY_BINARIES);
     }
   }
 
@@ -369,6 +384,16 @@ public class ProjectReactorBuilder {
     // We need to check the existence of source directories
     String[] sourcePaths = getListFromProperty(properties, PROPERTY_SOURCES);
     checkExistenceOfPaths(project.getKey(), project.getBaseDir(), sourcePaths, PROPERTY_SOURCES);
+
+    // And we need to resolve patterns that may have been used in "sonar.libraries"
+    List<String> libPaths = Lists.newArrayList();
+    for (String pattern : getListFromProperty(properties, PROPERTY_LIBRARIES)) {
+      for (File file : getLibraries(project.getBaseDir(), pattern)) {
+        libPaths.add(file.getAbsolutePath());
+      }
+    }
+    properties.remove(PROPERTY_LIBRARIES);
+    properties.put(PROPERTY_LIBRARIES, StringUtils.join(libPaths, ","));
   }
 
   @VisibleForTesting
@@ -389,6 +414,8 @@ public class ProjectReactorBuilder {
     // "aggregator" project must not have the following properties:
     properties.remove(PROPERTY_SOURCES);
     properties.remove(PROPERTY_TESTS);
+    properties.remove(PROPERTY_BINARIES);
+    properties.remove(PROPERTY_LIBRARIES);
   }
 
   @VisibleForTesting
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystem.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystem.java
index cb67cf534eb..24e26f5eb94 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystem.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystem.java
@@ -19,26 +19,19 @@
  */
 package org.sonar.batch.scan.filesystem;
 
-import org.sonar.api.utils.log.Logger;
-import org.sonar.api.utils.log.Loggers;
-
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Function;
 import com.google.common.collect.Collections2;
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Lists;
-
 import java.io.File;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
-
 import javax.annotation.CheckForNull;
 import javax.annotation.Nullable;
-
 import org.apache.commons.lang.StringUtils;
 import org.sonar.api.CoreProperties;
 import org.sonar.api.batch.fs.FilePredicate;
@@ -53,7 +46,6 @@ import org.sonar.api.utils.MessageException;
  * @since 3.5
  */
 public class DefaultModuleFileSystem extends DefaultFileSystem implements ModuleFileSystem {
-  private static final Logger LOG = Loggers.get(DefaultModuleFileSystem.class);
 
   private final String moduleKey;
   private final FileIndexer indexer;
@@ -62,6 +54,7 @@ public class DefaultModuleFileSystem extends DefaultFileSystem implements Module
   private File buildDir;
   private List<File> sourceDirsOrFiles = Lists.newArrayList();
   private List<File> testDirsOrFiles = Lists.newArrayList();
+  private List<File> binaryDirs = Lists.newArrayList();
   private ComponentIndexer componentIndexer;
   private boolean initialized;
 
@@ -76,6 +69,7 @@ public class DefaultModuleFileSystem extends DefaultFileSystem implements Module
     this.buildDir = initializer.buildDir();
     this.sourceDirsOrFiles = initializer.sources();
     this.testDirsOrFiles = initializer.tests();
+    this.binaryDirs = initializer.binaryDirs();
   }
 
   @VisibleForTesting
@@ -90,6 +84,7 @@ public class DefaultModuleFileSystem extends DefaultFileSystem implements Module
     this.buildDir = initializer.buildDir();
     this.sourceDirsOrFiles = initializer.sources();
     this.testDirsOrFiles = initializer.tests();
+    this.binaryDirs = initializer.binaryDirs();
   }
 
   public boolean isInitialized() {
@@ -136,8 +131,7 @@ public class DefaultModuleFileSystem extends DefaultFileSystem implements Module
 
   @Override
   public List<File> binaryDirs() {
-    LOG.warn("ModuleFileSystem#binaryDirs() is deprecated and will always return an empty list");
-    return new LinkedList<>();
+    return binaryDirs;
   }
 
   @Override
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleFileSystemInitializer.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleFileSystemInitializer.java
index aa8e20813e1..fd2e8a9226a 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleFileSystemInitializer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleFileSystemInitializer.java
@@ -42,11 +42,13 @@ public class ModuleFileSystemInitializer {
   private File buildDir;
   private List<File> sourceDirsOrFiles = Lists.newArrayList();
   private List<File> testDirsOrFiles = Lists.newArrayList();
+  private List<File> binaryDirs = Lists.newArrayList();
 
   public ModuleFileSystemInitializer(ProjectDefinition module, TempFolder tempUtils, PathResolver pathResolver) {
     baseDir = module.getBaseDir();
     buildDir = module.getBuildDir();
     initWorkingDir(module, tempUtils);
+    initBinaryDirs(module, pathResolver);
     initSources(module, pathResolver);
     initTests(module, pathResolver);
   }
@@ -82,6 +84,13 @@ public class ModuleFileSystemInitializer {
     }
   }
 
+  private void initBinaryDirs(ProjectDefinition module, PathResolver pathResolver) {
+    for (String path : module.getBinaries()) {
+      File dir = pathResolver.relativeFile(module.getBaseDir(), path);
+      binaryDirs.add(dir);
+    }
+  }
+
   File baseDir() {
     return baseDir;
   }
@@ -102,4 +111,12 @@ public class ModuleFileSystemInitializer {
   List<File> tests() {
     return testDirsOrFiles;
   }
+
+  /**
+   * @deprecated since 4.5.1 use SonarQube Java specific API
+   */
+  @Deprecated
+  List<File> binaryDirs() {
+    return binaryDirs;
+  }
 }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/DeprecatedProjectReactorBuilderTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/DeprecatedProjectReactorBuilderTest.java
index f42cdc208d5..0aaf6e2dfd2 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/DeprecatedProjectReactorBuilderTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/DeprecatedProjectReactorBuilderTest.java
@@ -52,11 +52,12 @@ public class DeprecatedProjectReactorBuilderTest {
     assertThat(rootProject.getVersion()).isEqualTo("1.0-SNAPSHOT");
     assertThat(rootProject.getDescription()).isEqualTo("Description of Foo Project");
     // root project must not contain some properties - even if they are defined in the root properties file
-    assertThat(rootProject.sources().contains("sources")).isFalse();
-    assertThat(rootProject.tests().contains("tests")).isFalse();
+    assertThat(rootProject.getSourceDirs().contains("sources")).isFalse();
+    assertThat(rootProject.getTestDirs().contains("tests")).isFalse();
+    assertThat(rootProject.getBinaries().contains("target/classes")).isFalse();
     // and module properties must have been cleaned
-    assertThat(rootProject.properties().get("module1.sonar.projectKey")).isNull();
-    assertThat(rootProject.properties().get("module2.sonar.projectKey")).isNull();
+    assertThat(rootProject.getProperties().getProperty("module1.sonar.projectKey")).isNull();
+    assertThat(rootProject.getProperties().getProperty("module2.sonar.projectKey")).isNull();
 
     // CHECK MODULES
     List<ProjectDefinition> modules = rootProject.getSubProjects();
@@ -70,11 +71,12 @@ public class DeprecatedProjectReactorBuilderTest {
     assertThat(module1.getVersion()).isEqualTo("1.0-SNAPSHOT");
     // Description should not be inherited from parent if not set
     assertThat(module1.getDescription()).isEqualTo("Description of Module 1");
-    assertThat(module1.sources()).contains("sources");
-    assertThat(module1.tests()).contains("tests");
+    assertThat(module1.getSourceDirs()).contains("sources");
+    assertThat(module1.getTestDirs()).contains("tests");
+    assertThat(module1.getBinaries()).contains("target/classes");
     // and module properties must have been cleaned
-    assertThat(module1.properties().get("module1.sonar.projectKey")).isNull();
-    assertThat(module1.properties().get("module2.sonar.projectKey")).isNull();
+    assertThat(module1.getProperties().getProperty("module1.sonar.projectKey")).isNull();
+    assertThat(module1.getProperties().getProperty("module2.sonar.projectKey")).isNull();
 
     // Module 2
     ProjectDefinition module2 = modules.get(1);
@@ -83,11 +85,12 @@ public class DeprecatedProjectReactorBuilderTest {
     assertThat(module2.getName()).isEqualTo("Foo Module 2");
     assertThat(module2.getVersion()).isEqualTo("1.0-SNAPSHOT");
     assertThat(module2.getDescription()).isEqualTo("Description of Module 2");
-    assertThat(module2.sources()).contains("src");
-    assertThat(module2.tests()).contains("tests");
+    assertThat(module2.getSourceDirs()).contains("src");
+    assertThat(module2.getTestDirs()).contains("tests");
+    assertThat(module2.getBinaries()).contains("target/classes");
     // and module properties must have been cleaned
-    assertThat(module2.properties().get("module1.sonar.projectKey")).isNull();
-    assertThat(module2.properties().get("module2.sonar.projectKey")).isNull();
+    assertThat(module2.getProperties().getProperty("module1.sonar.projectKey")).isNull();
+    assertThat(module2.getProperties().getProperty("module2.sonar.projectKey")).isNull();
   }
 
   @Test
@@ -100,11 +103,12 @@ public class DeprecatedProjectReactorBuilderTest {
     assertThat(rootProject.getVersion()).isEqualTo("1.0-SNAPSHOT");
     assertThat(rootProject.getDescription()).isEqualTo("Description of Foo Project");
     // root project must not contain some properties - even if they are defined in the root properties file
-    assertThat(rootProject.sources().contains("sources")).isFalse();
-    assertThat(rootProject.tests().contains("tests")).isFalse();
+    assertThat(rootProject.getSourceDirs().contains("sources")).isFalse();
+    assertThat(rootProject.getTestDirs().contains("tests")).isFalse();
+    assertThat(rootProject.getBinaries().contains("target/classes")).isFalse();
     // and module properties must have been cleaned
-    assertThat(rootProject.properties().get("module1.sonar.projectKey")).isNull();
-    assertThat(rootProject.properties().get("module2.sonar.projectKey")).isNull();
+    assertThat(rootProject.getProperties().getProperty("module1.sonar.projectKey")).isNull();
+    assertThat(rootProject.getProperties().getProperty("module2.sonar.projectKey")).isNull();
 
     // CHECK MODULES
     List<ProjectDefinition> modules = rootProject.getSubProjects();
@@ -118,11 +122,12 @@ public class DeprecatedProjectReactorBuilderTest {
     assertThat(module1.getVersion()).isEqualTo("1.0-SNAPSHOT");
     // Description should not be inherited from parent if not set
     assertThat(module1.getDescription()).isNull();
-    assertThat(module1.sources()).contains("sources");
-    assertThat(module1.tests()).contains("tests");
+    assertThat(module1.getSourceDirs()).contains("sources");
+    assertThat(module1.getTestDirs()).contains("tests");
+    assertThat(module1.getBinaries()).contains("target/classes");
     // and module properties must have been cleaned
-    assertThat(module1.properties().get("module1.sonar.projectKey")).isNull();
-    assertThat(module1.properties().get("module2.sonar.projectKey")).isNull();
+    assertThat(module1.getProperties().getProperty("module1.sonar.projectKey")).isNull();
+    assertThat(module1.getProperties().getProperty("module2.sonar.projectKey")).isNull();
 
     // Module 2
     ProjectDefinition module2 = modules.get(1);
@@ -131,11 +136,12 @@ public class DeprecatedProjectReactorBuilderTest {
     assertThat(module2.getName()).isEqualTo("Foo Module 2");
     assertThat(module2.getVersion()).isEqualTo("1.0-SNAPSHOT");
     assertThat(module2.getDescription()).isEqualTo("Description of Module 2");
-    assertThat(module2.sources()).contains("src");
-    assertThat(module2.tests()).contains("tests");
+    assertThat(module2.getSourceDirs()).contains("src");
+    assertThat(module2.getTestDirs()).contains("tests");
+    assertThat(module2.getBinaries()).contains("target/classes");
     // and module properties must have been cleaned
-    assertThat(module2.properties().get("module1.sonar.projectKey")).isNull();
-    assertThat(module2.properties().get("module2.sonar.projectKey")).isNull();
+    assertThat(module2.getProperties().getProperty("module1.sonar.projectKey")).isNull();
+    assertThat(module2.getProperties().getProperty("module2.sonar.projectKey")).isNull();
   }
 
   @Test
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/ProjectReactorBuilderTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/ProjectReactorBuilderTest.java
index 8db640586d8..b4bdeb07877 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/ProjectReactorBuilderTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/ProjectReactorBuilderTest.java
@@ -52,7 +52,9 @@ public class ProjectReactorBuilderTest {
     assertThat(projectDefinition.getName()).isEqualTo("Foo Project");
     assertThat(projectDefinition.getVersion()).isEqualTo("1.0-SNAPSHOT");
     assertThat(projectDefinition.getDescription()).isEqualTo("Description of Foo Project");
-    assertThat(projectDefinition.sources()).contains("sources");
+    assertThat(projectDefinition.getSourceDirs()).contains("sources");
+    assertThat(projectDefinition.getLibraries()).contains(TestUtils.getResource(this.getClass(), "simple-project/libs/lib2.txt").getAbsolutePath(),
+      TestUtils.getResource(this.getClass(), "simple-project/libs/lib2.txt").getAbsolutePath());
   }
 
   @Test
@@ -94,8 +96,9 @@ public class ProjectReactorBuilderTest {
     assertThat(rootProject.getVersion()).isEqualTo("1.0-SNAPSHOT");
     assertThat(rootProject.getDescription()).isEqualTo("Description of Foo Project");
     // root project must not contain some properties - even if they are defined in the root properties file
-    assertThat(rootProject.sources().contains("sources")).isFalse();
-    assertThat(rootProject.tests().contains("tests")).isFalse();
+    assertThat(rootProject.getSourceDirs().contains("sources")).isFalse();
+    assertThat(rootProject.getTestDirs().contains("tests")).isFalse();
+    assertThat(rootProject.getBinaries().contains("target/classes")).isFalse();
     // and module properties must have been cleaned
     assertThat(rootProject.getProperties().getProperty("module1.sonar.projectKey")).isNull();
     assertThat(rootProject.getProperties().getProperty("module2.sonar.projectKey")).isNull();
@@ -117,8 +120,9 @@ public class ProjectReactorBuilderTest {
     assertThat(module1.getVersion()).isEqualTo("1.0-SNAPSHOT");
     // Description should not be inherited from parent if not set
     assertThat(module1.getDescription()).isNull();
-    assertThat(module1.sources()).contains("sources");
-    assertThat(module1.tests()).contains("tests");
+    assertThat(module1.getSourceDirs()).contains("sources");
+    assertThat(module1.getTestDirs()).contains("tests");
+    assertThat(module1.getBinaries()).contains("target/classes");
     // and module properties must have been cleaned
     assertThat(module1.getProperties().getProperty("module1.sonar.projectKey")).isNull();
     assertThat(module1.getProperties().getProperty("module2.sonar.projectKey")).isNull();
@@ -135,8 +139,9 @@ public class ProjectReactorBuilderTest {
     assertThat(module2.getName()).isEqualTo("Foo Module 2");
     assertThat(module2.getVersion()).isEqualTo("1.0-SNAPSHOT");
     assertThat(module2.getDescription()).isEqualTo("Description of Module 2");
-    assertThat(module2.sources()).contains("src");
-    assertThat(module2.tests()).contains("tests");
+    assertThat(module2.getSourceDirs()).contains("src");
+    assertThat(module2.getTestDirs()).contains("tests");
+    assertThat(module2.getBinaries()).contains("target/classes");
     // and module properties must have been cleaned
     assertThat(module2.getProperties().getProperty("module1.sonar.projectKey")).isNull();
     assertThat(module2.getProperties().getProperty("module2.sonar.projectKey")).isNull();
@@ -183,7 +188,7 @@ public class ProjectReactorBuilderTest {
     // Module 1
     ProjectDefinition module1 = modules.get(0);
     assertThat(module1.getBaseDir().getCanonicalFile()).isEqualTo(TestUtils.getResource(this.getClass(), "multi-language-definitions-all-in-root"));
-    assertThat(module1.sources()).contains("src/main/java");
+    assertThat(module1.getSourceDirs()).contains("src/main/java");
     // and module properties must have been cleaned
     assertThat(module1.getWorkDir().getCanonicalFile())
       .isEqualTo(new File(TestUtils.getResource(this.getClass(), "multi-language-definitions-all-in-root"), ".sonar/example_java-module"));
@@ -191,7 +196,7 @@ public class ProjectReactorBuilderTest {
     // Module 2
     ProjectDefinition module2 = modules.get(1);
     assertThat(module2.getBaseDir().getCanonicalFile()).isEqualTo(TestUtils.getResource(this.getClass(), "multi-language-definitions-all-in-root"));
-    assertThat(module2.sources()).contains("src/main/groovy");
+    assertThat(module2.getSourceDirs()).contains("src/main/groovy");
     // and module properties must have been cleaned
     assertThat(module2.getWorkDir().getCanonicalFile())
       .isEqualTo(new File(TestUtils.getResource(this.getClass(), "multi-language-definitions-all-in-root"), ".sonar/example_groovy-module"));
@@ -238,6 +243,33 @@ public class ProjectReactorBuilderTest {
   }
 
   @Test
+  public void shouldFailIfExplicitUnexistingBinaryFolder() {
+    thrown.expect(IllegalStateException.class);
+    thrown.expectMessage("The folder 'bin' does not exist for 'com.foo.project' (base directory = "
+      + TestUtils.getResource(this.getClass(), "simple-project-with-unexisting-binary").getAbsolutePath());
+
+    loadProjectDefinition("simple-project-with-unexisting-binary");
+  }
+
+  @Test
+  public void shouldFailIfExplicitUnmatchingLibFolder() {
+    thrown.expect(IllegalStateException.class);
+    thrown.expectMessage("No files nor directories matching 'libs/*.txt' in directory "
+      + TestUtils.getResource(this.getClass(), "simple-project-with-unexisting-lib").getAbsolutePath());
+
+    loadProjectDefinition("simple-project-with-unexisting-lib");
+  }
+
+  @Test
+  public void shouldGetLibDirectory() {
+    ProjectDefinition def = loadProjectDefinition("simple-project-with-lib-dir");
+    assertThat(def.getLibraries()).hasSize(1);
+    File libDir = new File(def.getLibraries().get(0));
+    assertThat(libDir).isDirectory().exists();
+    assertThat(libDir.getName()).isEqualTo("lib");
+  }
+
+  @Test
   public void shouldFailIfExplicitUnexistingTestFolderOnModule() {
     thrown.expect(IllegalStateException.class);
     thrown.expectMessage("The folder 'tests' does not exist for 'module1' (base directory = "
@@ -247,6 +279,24 @@ public class ProjectReactorBuilderTest {
   }
 
   @Test
+  public void shouldFailIfExplicitUnexistingBinaryFolderOnModule() {
+    thrown.expect(IllegalStateException.class);
+    thrown.expectMessage("The folder 'bin' does not exist for 'module1' (base directory = "
+      + TestUtils.getResource(this.getClass(), "multi-module-with-explicit-unexisting-binary-dir").getAbsolutePath() + File.separator + "module1)");
+
+    loadProjectDefinition("multi-module-with-explicit-unexisting-binary-dir");
+  }
+
+  @Test
+  public void shouldFailIfExplicitUnmatchingLibFolderOnModule() {
+    thrown.expect(IllegalStateException.class);
+    thrown.expectMessage("No files nor directories matching 'lib/*.jar' in directory "
+      + TestUtils.getResource(this.getClass(), "multi-module-with-explicit-unexisting-lib").getAbsolutePath() + File.separator + "module1");
+
+    loadProjectDefinition("multi-module-with-explicit-unexisting-lib");
+  }
+
+  @Test
   public void multiModuleProperties() {
     ProjectDefinition projectDefinition = loadProjectDefinition("big-multi-module-definitions-all-in-root");
 
@@ -533,8 +583,9 @@ public class ProjectReactorBuilderTest {
     assertThat(rootProject.getVersion()).isEqualTo("1.0-SNAPSHOT");
     assertThat(rootProject.getDescription()).isEqualTo("Description of Foo Project");
     // root project must not contain some properties - even if they are defined in the root properties file
-    assertThat(rootProject.sources().contains("sources")).isFalse();
-    assertThat(rootProject.tests().contains("tests")).isFalse();
+    assertThat(rootProject.getSourceDirs().contains("sources")).isFalse();
+    assertThat(rootProject.getTestDirs().contains("tests")).isFalse();
+    assertThat(rootProject.getBinaries().contains("target/classes")).isFalse();
     // and module properties must have been cleaned
     assertThat(rootProject.getProperties().getProperty("module1.sonar.projectKey")).isNull();
     assertThat(rootProject.getProperties().getProperty("module2.sonar.projectKey")).isNull();
@@ -556,8 +607,9 @@ public class ProjectReactorBuilderTest {
     assertThat(module1.getVersion()).isEqualTo("1.0-SNAPSHOT");
     // Description should not be inherited from parent if not set
     assertThat(module1.getDescription()).isNull();
-    assertThat(module1.sources()).contains("sources");
-    assertThat(module1.tests()).contains("tests");
+    assertThat(module1.getSourceDirs()).contains("sources");
+    assertThat(module1.getTestDirs()).contains("tests");
+    assertThat(module1.getBinaries()).contains("target/classes");
     // and module properties must have been cleaned
     assertThat(module1.getProperties().getProperty("module1.sonar.projectKey")).isNull();
     assertThat(module1.getProperties().getProperty("module2.sonar.projectKey")).isNull();
@@ -574,8 +626,9 @@ public class ProjectReactorBuilderTest {
     assertThat(module1Feature.getName()).isEqualTo("Foo Module 1 Feature");
     assertThat(module1Feature.getVersion()).isEqualTo("1.0-SNAPSHOT");
     assertThat(module1Feature.getDescription()).isEqualTo("Description of Module 1 Feature");
-    assertThat(module1Feature.sources()).contains("src");
-    assertThat(module1Feature.tests()).contains("tests");
+    assertThat(module1Feature.getSourceDirs()).contains("src");
+    assertThat(module1Feature.getTestDirs()).contains("tests");
+    assertThat(module1Feature.getBinaries()).contains("target/classes");
     // and module properties must have been cleaned
     assertThat(module1Feature.getProperties().getProperty("module1.sonar.projectKey")).isNull();
     assertThat(module1Feature.getProperties().getProperty("module2.sonar.projectKey")).isNull();
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystemTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystemTest.java
index 1486b1b5482..4a5e04b4a8e 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystemTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystemTest.java
@@ -82,7 +82,7 @@ public class DefaultModuleFileSystemTest {
     DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache,
       new Project("foo"), settings, fileIndexer, initializer, componentIndexer);
 
-    assertThat(fs.encoding()).isEqualTo(Charset.defaultCharset());
+    assertThat(fs.sourceCharset()).isEqualTo(Charset.defaultCharset());
     assertThat(fs.isDefaultJvmEncoding()).isTrue();
   }
 
@@ -93,7 +93,7 @@ public class DefaultModuleFileSystemTest {
       new Project("foo"), settings, fileIndexer, initializer, componentIndexer);
 
     assertThat(fs.encoding()).isEqualTo(Charset.forName("Cp1124"));
-    assertThat(fs.encoding()).isEqualTo(Charset.forName("Cp1124"));
+    assertThat(fs.sourceCharset()).isEqualTo(Charset.forName("Cp1124"));
 
     // This test fails when default Java encoding is "IBM AIX Ukraine". Sorry for that.
     assertThat(fs.isDefaultJvmEncoding()).isFalse();
@@ -109,6 +109,7 @@ public class DefaultModuleFileSystemTest {
     when(initializer.baseDir()).thenReturn(basedir);
     when(initializer.buildDir()).thenReturn(buildDir);
     when(initializer.workingDir()).thenReturn(workingDir);
+    when(initializer.binaryDirs()).thenReturn(Arrays.asList(new File(basedir, "target/classes")));
     File javaSrc = new File(basedir, "src/main/java");
     javaSrc.mkdirs();
     File groovySrc = new File(basedir, "src/main/groovy");
@@ -126,7 +127,7 @@ public class DefaultModuleFileSystemTest {
     assertThat(fs.buildDir().getCanonicalPath()).isEqualTo(buildDir.getCanonicalPath());
     assertThat(fs.sourceDirs()).hasSize(2);
     assertThat(fs.testDirs()).hasSize(1);
-    assertThat(fs.binaryDirs()).hasSize(0);
+    assertThat(fs.binaryDirs()).hasSize(1);
   }
 
   @Test
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ModuleFileSystemInitializerTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ModuleFileSystemInitializerTest.java
index 815ead7e5bd..53ee455adfb 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ModuleFileSystemInitializerTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ModuleFileSystemInitializerTest.java
@@ -69,8 +69,9 @@ public class ModuleFileSystemInitializerTest {
     ProjectDefinition project = ProjectDefinition.create()
       .setBaseDir(baseDir)
       .setBuildDir(buildDir)
-      .addSources("src/main/java", "src/main/unknown")
-      .addTests("src/test/java", "src/test/unknown");
+      .addSourceDirs("src/main/java", "src/main/unknown")
+      .addTestDirs("src/test/java", "src/test/unknown")
+      .addBinaryDir("target/classes");
 
     ModuleFileSystemInitializer initializer = new ModuleFileSystemInitializer(project, mock(TempFolder.class), pathResolver);
 
@@ -80,6 +81,8 @@ public class ModuleFileSystemInitializerTest {
     assertThat(path(initializer.sources().get(0))).endsWith("src/main/java");
     assertThat(initializer.tests()).hasSize(1);
     assertThat(path(initializer.tests().get(0))).endsWith("src/test/java");
+    assertThat(initializer.binaryDirs()).hasSize(1);
+    assertThat(path(initializer.binaryDirs().get(0))).endsWith("target/classes");
   }
 
   private String path(File f) throws IOException {
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-binary-dir/module1/src/Fake.java b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-binary-dir/module1/src/Fake.java
new file mode 100644
index 00000000000..8b137891791
--- /dev/null
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-binary-dir/module1/src/Fake.java
@@ -0,0 +1 @@
+
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-binary-dir/sonar-project.properties b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-binary-dir/sonar-project.properties
new file mode 100644
index 00000000000..8007363a9c4
--- /dev/null
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-binary-dir/sonar-project.properties
@@ -0,0 +1,9 @@
+sonar.projectKey=com.foo.project
+sonar.projectName=Foo Project
+sonar.projectVersion=1.0-SNAPSHOT
+sonar.projectDescription=Description of Foo Project
+
+sonar.sources=src
+
+sonar.modules=module1
+module1.sonar.binaries=bin
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-lib/module1/src/Fake.java b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-lib/module1/src/Fake.java
new file mode 100644
index 00000000000..8b137891791
--- /dev/null
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-lib/module1/src/Fake.java
@@ -0,0 +1 @@
+
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-lib/sonar-project.properties b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-lib/sonar-project.properties
new file mode 100644
index 00000000000..d97a18bb16d
--- /dev/null
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-lib/sonar-project.properties
@@ -0,0 +1,9 @@
+sonar.projectKey=com.foo.project
+sonar.projectName=Foo Project
+sonar.projectVersion=1.0-SNAPSHOT
+sonar.projectDescription=Description of Foo Project
+
+sonar.sources=src
+
+sonar.modules=module1
+module1.sonar.libraries=lib/*.jar
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/lib/Fake.class b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/lib/Fake.class
new file mode 100644
index 00000000000..bf2c3a09e07
--- /dev/null
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/lib/Fake.class
@@ -0,0 +1,3 @@
+package org.sonar.runner.batch.ProjectReactorBuilderTest.simple
+
+Fake
\ No newline at end of file
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/sonar-project.properties b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/sonar-project.properties
new file mode 100644
index 00000000000..0cada50b51f
--- /dev/null
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/sonar-project.properties
@@ -0,0 +1,7 @@
+sonar.projectKey=com.foo.project
+sonar.projectName=Foo Project
+sonar.projectVersion=1.0-SNAPSHOT
+sonar.projectDescription=Description of Foo Project
+
+sonar.sources=sources
+sonar.libraries=lib
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/sources/Fake.java b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/sources/Fake.java
new file mode 100644
index 00000000000..aee03e60b4a
--- /dev/null
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/sources/Fake.java
@@ -0,0 +1,3 @@
+package org.sonar.runner.batch.ProjectReactorBuilderTest.simple;
+
+class Fake {}
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-binary/sonar-project.properties b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-binary/sonar-project.properties
new file mode 100644
index 00000000000..55d1ddf0242
--- /dev/null
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-binary/sonar-project.properties
@@ -0,0 +1,7 @@
+sonar.projectKey=com.foo.project
+sonar.projectName=Foo Project
+sonar.projectVersion=1.0-SNAPSHOT
+sonar.projectDescription=Description of Foo Project
+
+sonar.sources=sources
+sonar.binaries=bin
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-binary/sources/Fake.java b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-binary/sources/Fake.java
new file mode 100644
index 00000000000..e67004defc5
--- /dev/null
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-binary/sources/Fake.java
@@ -0,0 +1 @@
+class Fake {}
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-lib/sonar-project.properties b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-lib/sonar-project.properties
new file mode 100644
index 00000000000..69ccd8d1411
--- /dev/null
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-lib/sonar-project.properties
@@ -0,0 +1,7 @@
+sonar.projectKey=com.foo.project
+sonar.projectName=Foo Project
+sonar.projectVersion=1.0-SNAPSHOT
+sonar.projectDescription=Description of Foo Project
+
+sonar.sources=sources
+sonar.libraries=libs/*.txt
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-lib/sources/Fake.java b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-lib/sources/Fake.java
new file mode 100644
index 00000000000..e67004defc5
--- /dev/null
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-lib/sources/Fake.java
@@ -0,0 +1 @@
+class Fake {}