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

24 files changed, 87 insertions, 650 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 1363134d449..beeec9e389f 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
@@ -22,7 +22,6 @@ 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;
@@ -134,7 +133,6 @@ 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 670bf714eef..ad67711a857 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
@@ -81,8 +81,6 @@ 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.
@@ -344,22 +342,9 @@ 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);
     }
   }
 
@@ -384,16 +369,6 @@ 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
@@ -414,8 +389,6 @@ 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 24e26f5eb94..cb67cf534eb 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
@@ -19,19 +19,26 @@
  */
 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;
@@ -46,6 +53,7 @@ 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;
@@ -54,7 +62,6 @@ 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;
 
@@ -69,7 +76,6 @@ public class DefaultModuleFileSystem extends DefaultFileSystem implements Module
     this.buildDir = initializer.buildDir();
     this.sourceDirsOrFiles = initializer.sources();
     this.testDirsOrFiles = initializer.tests();
-    this.binaryDirs = initializer.binaryDirs();
   }
 
   @VisibleForTesting
@@ -84,7 +90,6 @@ 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() {
@@ -131,7 +136,8 @@ public class DefaultModuleFileSystem extends DefaultFileSystem implements Module
 
   @Override
   public List<File> binaryDirs() {
-    return binaryDirs;
+    LOG.warn("ModuleFileSystem#binaryDirs() is deprecated and will always return an empty list");
+    return new LinkedList<>();
   }
 
   @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 fd2e8a9226a..aa8e20813e1 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
@@ -42,13 +42,11 @@ 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);
   }
@@ -84,13 +82,6 @@ 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;
   }
@@ -111,12 +102,4 @@ 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 0aaf6e2dfd2..f42cdc208d5 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
@@ -52,12 +52,11 @@ 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.getSourceDirs().contains("sources")).isFalse();
-    assertThat(rootProject.getTestDirs().contains("tests")).isFalse();
-    assertThat(rootProject.getBinaries().contains("target/classes")).isFalse();
+    assertThat(rootProject.sources().contains("sources")).isFalse();
+    assertThat(rootProject.tests().contains("tests")).isFalse();
     // and module properties must have been cleaned
-    assertThat(rootProject.getProperties().getProperty("module1.sonar.projectKey")).isNull();
-    assertThat(rootProject.getProperties().getProperty("module2.sonar.projectKey")).isNull();
+    assertThat(rootProject.properties().get("module1.sonar.projectKey")).isNull();
+    assertThat(rootProject.properties().get("module2.sonar.projectKey")).isNull();
 
     // CHECK MODULES
     List<ProjectDefinition> modules = rootProject.getSubProjects();
@@ -71,12 +70,11 @@ 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.getSourceDirs()).contains("sources");
-    assertThat(module1.getTestDirs()).contains("tests");
-    assertThat(module1.getBinaries()).contains("target/classes");
+    assertThat(module1.sources()).contains("sources");
+    assertThat(module1.tests()).contains("tests");
     // and module properties must have been cleaned
-    assertThat(module1.getProperties().getProperty("module1.sonar.projectKey")).isNull();
-    assertThat(module1.getProperties().getProperty("module2.sonar.projectKey")).isNull();
+    assertThat(module1.properties().get("module1.sonar.projectKey")).isNull();
+    assertThat(module1.properties().get("module2.sonar.projectKey")).isNull();
 
     // Module 2
     ProjectDefinition module2 = modules.get(1);
@@ -85,12 +83,11 @@ 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.getSourceDirs()).contains("src");
-    assertThat(module2.getTestDirs()).contains("tests");
-    assertThat(module2.getBinaries()).contains("target/classes");
+    assertThat(module2.sources()).contains("src");
+    assertThat(module2.tests()).contains("tests");
     // and module properties must have been cleaned
-    assertThat(module2.getProperties().getProperty("module1.sonar.projectKey")).isNull();
-    assertThat(module2.getProperties().getProperty("module2.sonar.projectKey")).isNull();
+    assertThat(module2.properties().get("module1.sonar.projectKey")).isNull();
+    assertThat(module2.properties().get("module2.sonar.projectKey")).isNull();
   }
 
   @Test
@@ -103,12 +100,11 @@ 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.getSourceDirs().contains("sources")).isFalse();
-    assertThat(rootProject.getTestDirs().contains("tests")).isFalse();
-    assertThat(rootProject.getBinaries().contains("target/classes")).isFalse();
+    assertThat(rootProject.sources().contains("sources")).isFalse();
+    assertThat(rootProject.tests().contains("tests")).isFalse();
     // and module properties must have been cleaned
-    assertThat(rootProject.getProperties().getProperty("module1.sonar.projectKey")).isNull();
-    assertThat(rootProject.getProperties().getProperty("module2.sonar.projectKey")).isNull();
+    assertThat(rootProject.properties().get("module1.sonar.projectKey")).isNull();
+    assertThat(rootProject.properties().get("module2.sonar.projectKey")).isNull();
 
     // CHECK MODULES
     List<ProjectDefinition> modules = rootProject.getSubProjects();
@@ -122,12 +118,11 @@ 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.getSourceDirs()).contains("sources");
-    assertThat(module1.getTestDirs()).contains("tests");
-    assertThat(module1.getBinaries()).contains("target/classes");
+    assertThat(module1.sources()).contains("sources");
+    assertThat(module1.tests()).contains("tests");
     // and module properties must have been cleaned
-    assertThat(module1.getProperties().getProperty("module1.sonar.projectKey")).isNull();
-    assertThat(module1.getProperties().getProperty("module2.sonar.projectKey")).isNull();
+    assertThat(module1.properties().get("module1.sonar.projectKey")).isNull();
+    assertThat(module1.properties().get("module2.sonar.projectKey")).isNull();
 
     // Module 2
     ProjectDefinition module2 = modules.get(1);
@@ -136,12 +131,11 @@ 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.getSourceDirs()).contains("src");
-    assertThat(module2.getTestDirs()).contains("tests");
-    assertThat(module2.getBinaries()).contains("target/classes");
+    assertThat(module2.sources()).contains("src");
+    assertThat(module2.tests()).contains("tests");
     // and module properties must have been cleaned
-    assertThat(module2.getProperties().getProperty("module1.sonar.projectKey")).isNull();
-    assertThat(module2.getProperties().getProperty("module2.sonar.projectKey")).isNull();
+    assertThat(module2.properties().get("module1.sonar.projectKey")).isNull();
+    assertThat(module2.properties().get("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 b4bdeb07877..8db640586d8 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
@@ -52,9 +52,7 @@ 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.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());
+    assertThat(projectDefinition.sources()).contains("sources");
   }
 
   @Test
@@ -96,9 +94,8 @@ 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.getSourceDirs().contains("sources")).isFalse();
-    assertThat(rootProject.getTestDirs().contains("tests")).isFalse();
-    assertThat(rootProject.getBinaries().contains("target/classes")).isFalse();
+    assertThat(rootProject.sources().contains("sources")).isFalse();
+    assertThat(rootProject.tests().contains("tests")).isFalse();
     // and module properties must have been cleaned
     assertThat(rootProject.getProperties().getProperty("module1.sonar.projectKey")).isNull();
     assertThat(rootProject.getProperties().getProperty("module2.sonar.projectKey")).isNull();
@@ -120,9 +117,8 @@ 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.getSourceDirs()).contains("sources");
-    assertThat(module1.getTestDirs()).contains("tests");
-    assertThat(module1.getBinaries()).contains("target/classes");
+    assertThat(module1.sources()).contains("sources");
+    assertThat(module1.tests()).contains("tests");
     // and module properties must have been cleaned
     assertThat(module1.getProperties().getProperty("module1.sonar.projectKey")).isNull();
     assertThat(module1.getProperties().getProperty("module2.sonar.projectKey")).isNull();
@@ -139,9 +135,8 @@ 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.getSourceDirs()).contains("src");
-    assertThat(module2.getTestDirs()).contains("tests");
-    assertThat(module2.getBinaries()).contains("target/classes");
+    assertThat(module2.sources()).contains("src");
+    assertThat(module2.tests()).contains("tests");
     // and module properties must have been cleaned
     assertThat(module2.getProperties().getProperty("module1.sonar.projectKey")).isNull();
     assertThat(module2.getProperties().getProperty("module2.sonar.projectKey")).isNull();
@@ -188,7 +183,7 @@ 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.getSourceDirs()).contains("src/main/java");
+    assertThat(module1.sources()).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"));
@@ -196,7 +191,7 @@ 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.getSourceDirs()).contains("src/main/groovy");
+    assertThat(module2.sources()).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"));
@@ -243,33 +238,6 @@ 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 = "
@@ -279,24 +247,6 @@ 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");
 
@@ -583,9 +533,8 @@ 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.getSourceDirs().contains("sources")).isFalse();
-    assertThat(rootProject.getTestDirs().contains("tests")).isFalse();
-    assertThat(rootProject.getBinaries().contains("target/classes")).isFalse();
+    assertThat(rootProject.sources().contains("sources")).isFalse();
+    assertThat(rootProject.tests().contains("tests")).isFalse();
     // and module properties must have been cleaned
     assertThat(rootProject.getProperties().getProperty("module1.sonar.projectKey")).isNull();
     assertThat(rootProject.getProperties().getProperty("module2.sonar.projectKey")).isNull();
@@ -607,9 +556,8 @@ 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.getSourceDirs()).contains("sources");
-    assertThat(module1.getTestDirs()).contains("tests");
-    assertThat(module1.getBinaries()).contains("target/classes");
+    assertThat(module1.sources()).contains("sources");
+    assertThat(module1.tests()).contains("tests");
     // and module properties must have been cleaned
     assertThat(module1.getProperties().getProperty("module1.sonar.projectKey")).isNull();
     assertThat(module1.getProperties().getProperty("module2.sonar.projectKey")).isNull();
@@ -626,9 +574,8 @@ 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.getSourceDirs()).contains("src");
-    assertThat(module1Feature.getTestDirs()).contains("tests");
-    assertThat(module1Feature.getBinaries()).contains("target/classes");
+    assertThat(module1Feature.sources()).contains("src");
+    assertThat(module1Feature.tests()).contains("tests");
     // 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 4a5e04b4a8e..1486b1b5482 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.sourceCharset()).isEqualTo(Charset.defaultCharset());
+    assertThat(fs.encoding()).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.sourceCharset()).isEqualTo(Charset.forName("Cp1124"));
+    assertThat(fs.encoding()).isEqualTo(Charset.forName("Cp1124"));
 
     // This test fails when default Java encoding is "IBM AIX Ukraine". Sorry for that.
     assertThat(fs.isDefaultJvmEncoding()).isFalse();
@@ -109,7 +109,6 @@ 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");
@@ -127,7 +126,7 @@ public class DefaultModuleFileSystemTest {
     assertThat(fs.buildDir().getCanonicalPath()).isEqualTo(buildDir.getCanonicalPath());
     assertThat(fs.sourceDirs()).hasSize(2);
     assertThat(fs.testDirs()).hasSize(1);
-    assertThat(fs.binaryDirs()).hasSize(1);
+    assertThat(fs.binaryDirs()).hasSize(0);
   }
 
   @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 53ee455adfb..815ead7e5bd 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
@@ -69,9 +69,8 @@ public class ModuleFileSystemInitializerTest {
     ProjectDefinition project = ProjectDefinition.create()
       .setBaseDir(baseDir)
       .setBuildDir(buildDir)
-      .addSourceDirs("src/main/java", "src/main/unknown")
-      .addTestDirs("src/test/java", "src/test/unknown")
-      .addBinaryDir("target/classes");
+      .addSources("src/main/java", "src/main/unknown")
+      .addTests("src/test/java", "src/test/unknown");
 
     ModuleFileSystemInitializer initializer = new ModuleFileSystemInitializer(project, mock(TempFolder.class), pathResolver);
 
@@ -81,8 +80,6 @@ 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
deleted file mode 100644
index 8b137891791..00000000000
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-binary-dir/module1/src/Fake.java
+++ /dev/null
@@ -1 +0,0 @@
-
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
deleted file mode 100644
index 8007363a9c4..00000000000
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-binary-dir/sonar-project.properties
+++ /dev/null
@@ -1,9 +0,0 @@
-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
deleted file mode 100644
index 8b137891791..00000000000
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-lib/module1/src/Fake.java
+++ /dev/null
@@ -1 +0,0 @@
-
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
deleted file mode 100644
index d97a18bb16d..00000000000
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/multi-module-with-explicit-unexisting-lib/sonar-project.properties
+++ /dev/null
@@ -1,9 +0,0 @@
-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
deleted file mode 100644
index bf2c3a09e07..00000000000
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/lib/Fake.class
+++ /dev/null
@@ -1,3 +0,0 @@
-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
deleted file mode 100644
index 0cada50b51f..00000000000
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/sonar-project.properties
+++ /dev/null
@@ -1,7 +0,0 @@
-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
deleted file mode 100644
index aee03e60b4a..00000000000
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-lib-dir/sources/Fake.java
+++ /dev/null
@@ -1,3 +0,0 @@
-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
deleted file mode 100644
index 55d1ddf0242..00000000000
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-binary/sonar-project.properties
+++ /dev/null
@@ -1,7 +0,0 @@
-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
deleted file mode 100644
index e67004defc5..00000000000
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-binary/sources/Fake.java
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 69ccd8d1411..00000000000
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-lib/sonar-project.properties
+++ /dev/null
@@ -1,7 +0,0 @@
-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
deleted file mode 100644
index e67004defc5..00000000000
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/ProjectReactorBuilderTest/simple-project-with-unexisting-lib/sources/Fake.java
+++ /dev/null
@@ -1 +0,0 @@
-class Fake {}
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
deleted file mode 100644
index e9f71cc17d1..00000000000
--- a/sonar-plugin-api/src/main/java/org/sonar/api/batch/ProjectClasspath.java
+++ /dev/null
@@ -1,90 +0,0 @@
-/*
- * SonarQube, open source software quality management tool.
- * Copyright (C) 2008-2014 SonarSource
- * mailto:contact AT sonarsource DOT com
- *
- * SonarQube is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
- * version 3 of the License, or (at your option) any later version.
- *
- * SonarQube is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
- */
-package org.sonar.api.batch;
-
-import com.google.common.collect.Lists;
-import java.io.File;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLClassLoader;
-import java.util.List;
-import org.sonar.api.BatchComponent;
-import org.sonar.api.batch.bootstrap.ProjectDefinition;
-import org.sonar.api.resources.ProjectFileSystem;
-import org.sonar.api.utils.SonarException;
-
-/**
- * @since 2.2
- * @deprecated since 4.5 this is some Java specific stuff that should by handled by SQ Java plugin
- */
-@Deprecated
-public class ProjectClasspath implements BatchComponent {
-
-  private final ProjectDefinition def;
-  private final ProjectFileSystem projectFileSystem;
-  private List<File> elements;
-  private URLClassLoader classloader;
-
-  public ProjectClasspath(ProjectDefinition def, ProjectFileSystem projectFileSystem) {
-    this.def = def;
-    this.projectFileSystem = projectFileSystem;
-  }
-
-  public URLClassLoader getClassloader() {
-    if (classloader == null) {
-      classloader = createClassLoader();
-    }
-    return classloader;
-  }
-
-  /**
-   * bytecode directory + JARs (dependencies)
-   */
-  public List<File> getElements() {
-    if (elements == null) {
-      elements = createElements();
-    }
-    return elements;
-  }
-
-  protected URLClassLoader createClassLoader() {
-    try {
-      List<URL> urls = Lists.newArrayList();
-      for (File file : getElements()) {
-        urls.add(file.toURI().toURL());
-      }
-      return new URLClassLoader(urls.toArray(new URL[urls.size()]), null);
-
-    } catch (MalformedURLException e) {
-      throw new SonarException("Fail to create the project classloader. Classpath element is unvalid.", e);
-    }
-  }
-
-  protected List<File> createElements() {
-    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-plugin-api/src/main/java/org/sonar/api/batch/bootstrap/ProjectDefinition.java b/sonar-plugin-api/src/main/java/org/sonar/api/batch/bootstrap/ProjectDefinition.java
index 88f80180cc9..49ec7b68fd0 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/batch/bootstrap/ProjectDefinition.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/batch/bootstrap/ProjectDefinition.java
@@ -42,38 +42,8 @@ import org.sonar.api.CoreProperties;
 public class ProjectDefinition {
 
   public static final String SOURCES_PROPERTY = "sonar.sources";
-  /**
-   * @deprecated since 4.5 use {@link #SOURCES_PROPERTY}
-   */
-  @Deprecated
-  public static final String SOURCE_DIRS_PROPERTY = SOURCES_PROPERTY;
-  /**
-   * @deprecated since 4.5 use {@link #SOURCES_PROPERTY}
-   */
-  @Deprecated
-  public static final String SOURCE_FILES_PROPERTY = "sonar.sourceFiles";
 
   public static final String TESTS_PROPERTY = "sonar.tests";
-  /**
-   * @deprecated since 4.5 use {@link #TESTS_PROPERTY}
-   */
-  @Deprecated
-  public static final String TEST_DIRS_PROPERTY = TESTS_PROPERTY;
-  /**
-   * @deprecated since 4.5 use {@link #TESTS_PROPERTY}
-   */
-  @Deprecated
-  public static final String TEST_FILES_PROPERTY = "sonar.testFiles";
-  /**
-   * @deprecated since 4.5.1 use SonarQube Java specific API
-   */
-  @Deprecated
-  public static final String BINARIES_PROPERTY = "sonar.binaries";
-  /**
-   * @deprecated since 4.5.1 use SonarQube Java specific API
-   */
-  @Deprecated
-  public static final String LIBRARIES_PROPERTY = "sonar.libraries";
   public static final String BUILD_DIR_PROPERTY = "sonar.buildDir";
 
   private static final char SEPARATOR = ',';
@@ -257,14 +227,6 @@ public class ProjectDefinition {
   }
 
   /**
-   * @deprecated since 4.5 use {@link #sources()}
-   */
-  @Deprecated
-  public List<String> getSourceDirs() {
-    return sources();
-  }
-
-  /**
    * @param paths paths to file or directory with main sources.
    *              They can be absolute or relative to project base directory.
    */
@@ -275,14 +237,6 @@ public class ProjectDefinition {
     return this;
   }
 
-  /**
-   * @deprecated since 4.5 use {@link #addSources(String...)}
-   */
-  @Deprecated
-  public ProjectDefinition addSourceDirs(String... paths) {
-    return addSources(paths);
-  }
-
   public ProjectDefinition addSources(File... fileOrDirs) {
     for (File fileOrDir : fileOrDirs) {
       addSources(fileOrDir.getAbsolutePath());
@@ -290,40 +244,16 @@ public class ProjectDefinition {
     return this;
   }
 
-  /**
-   * @deprecated since 4.5 use {@link #addSources(File...)}
-   */
-  @Deprecated
-  public ProjectDefinition addSourceDirs(File... dirs) {
-    return addSources(dirs);
-  }
-
   public ProjectDefinition resetSources() {
     properties.remove(SOURCES_PROPERTY);
     return this;
   }
 
-  /**
-   * @deprecated since 4.5 use {@link #resetSources()}
-   */
-  @Deprecated
-  public ProjectDefinition resetSourceDirs() {
-    return resetSources();
-  }
-
   public ProjectDefinition setSources(String... paths) {
     resetSources();
     return addSources(paths);
   }
 
-  /**
-   * @deprecated since 4.5 use {@link #setSources(String...)}
-   */
-  @Deprecated
-  public ProjectDefinition setSourceDirs(String... paths) {
-    return setSources(paths);
-  }
-
   public ProjectDefinition setSources(File... filesOrDirs) {
     resetSources();
     for (File fileOrDir : filesOrDirs) {
@@ -332,66 +262,12 @@ public class ProjectDefinition {
     return this;
   }
 
-  /**
-   * @deprecated since 4.5 use {@link #setSources(File...)}
-   */
-  @Deprecated
-  public ProjectDefinition setSourceDirs(File... dirs) {
-    resetSourceDirs();
-    for (File dir : dirs) {
-      addSourceDirs(dir.getAbsolutePath());
-    }
-    return this;
-  }
-
-  /**
-   * @deprecated since 4.5 use {@link #addSources(File...)}
-   */
-  @Deprecated
-  public ProjectDefinition addSourceFiles(String... paths) {
-    // Hack for visual studio project builder that used to add baseDir first as source dir
-    List<String> sourceDirs = getSourceDirs();
-    if (sourceDirs.size() == 1 && isDirectory(sourceDirs.get(0))) {
-      resetSources();
-    }
-    return addSources(paths);
-  }
-
-  /**
-   * @deprecated since 4.5 use {@link #addSources(File...)}
-   */
-  @Deprecated
-  public ProjectDefinition addSourceFiles(File... files) {
-    // Hack for visual studio project builder that used to add baseDir first as source dir
-    List<String> sourceDirs = getSourceDirs();
-    if (sourceDirs.size() == 1 && isDirectory(sourceDirs.get(0))) {
-      resetSources();
-    }
-    return addSources(files);
-  }
-
-  /**
-   * @deprecated since 4.5 use {@link #sources()}
-   */
-  @Deprecated
-  public List<String> getSourceFiles() {
-    return sources();
-  }
-
   public List<String> tests() {
     String sources = (String) ObjectUtils.defaultIfNull(properties.get(TESTS_PROPERTY), "");
     return trim(StringUtils.split(sources, SEPARATOR));
   }
 
   /**
-   * @deprecated since 4.5 use {@link #tests()}
-   */
-  @Deprecated
-  public List<String> getTestDirs() {
-    return tests();
-  }
-
-  /**
    * @param paths path to files or directories with test sources.
    *              It can be absolute or relative to project directory.
    */
@@ -402,14 +278,6 @@ public class ProjectDefinition {
     return this;
   }
 
-  /**
-   * @deprecated since 4.5 use {@link #addTests(String...)}
-   */
-  @Deprecated
-  public ProjectDefinition addTestDirs(String... paths) {
-    return addTests(paths);
-  }
-
   public ProjectDefinition addTests(File... fileOrDirs) {
     for (File fileOrDir : fileOrDirs) {
       addTests(fileOrDir.getAbsolutePath());
@@ -417,27 +285,11 @@ public class ProjectDefinition {
     return this;
   }
 
-  /**
-   * @deprecated since 4.5 use {@link #addTests(File...)}
-   */
-  @Deprecated
-  public ProjectDefinition addTestDirs(File... dirs) {
-    return addTests(dirs);
-  }
-
   public ProjectDefinition setTests(String... paths) {
     resetTests();
     return addTests(paths);
   }
 
-  /**
-   * @deprecated since 4.5 use {@link #setTests(String...)}
-   */
-  @Deprecated
-  public ProjectDefinition setTestDirs(String... paths) {
-    return setTests(paths);
-  }
-
   public ProjectDefinition setTests(File... fileOrDirs) {
     resetTests();
     for (File dir : fileOrDirs) {
@@ -460,103 +312,6 @@ public class ProjectDefinition {
   }
 
   /**
-   * @deprecated since 4.5 use {@link #resetTests()}
-   */
-  @Deprecated
-  public ProjectDefinition resetTestDirs() {
-    return resetTests();
-  }
-
-  /**
-   * @deprecated since 4.5 use {@link #addTests(String...)}
-   */
-  @Deprecated
-  public ProjectDefinition addTestFiles(String... paths) {
-    // Hack for visual studio project builder that used to add baseDir first as test dir
-    List<String> testDirs = getTestDirs();
-    if (testDirs.size() == 1 && isDirectory(testDirs.get(0))) {
-      resetTests();
-    }
-    return addTests(paths);
-  }
-
-  private boolean isDirectory(String relativeOrAbsoluteDir) {
-    File file = new File(relativeOrAbsoluteDir);
-    if (!file.isAbsolute()) {
-      file = new File(baseDir, relativeOrAbsoluteDir);
-    }
-    return file.isDirectory();
-  }
-
-  /**
-   * @deprecated since 4.5 use {@link #addTests(File...)}
-   */
-  @Deprecated
-  public ProjectDefinition addTestFiles(File... files) {
-    // Hack for visual studio project builder that used to add baseDir first as test dir
-    List<String> testDirs = getTestDirs();
-    if (testDirs.size() == 1 && isDirectory(testDirs.get(0))) {
-      resetTests();
-    }
-    return addTests(files);
-  }
-
-  /**
-   * @deprecated since 4.5 use {@link #tests()}
-   */
-  @Deprecated
-  public List<String> getTestFiles() {
-    return tests();
-  }
-
-  /**
-   * @deprecated since 4.5.1 use SonarQube Java specific API
-   */
-  @Deprecated
-  public List<String> getBinaries() {
-    String sources = (String) ObjectUtils.defaultIfNull(properties.get(BINARIES_PROPERTY), "");
-    return trim(StringUtils.split(sources, SEPARATOR));
-  }
-
-  /**
-   * @param path path to directory with compiled source. In case of Java this is directory with class files.
-   *             It can be absolute or relative to project directory.
-   * @deprecated since 4.5.1 use SonarQube Java specific API
-   */
-  @Deprecated
-  public ProjectDefinition addBinaryDir(String path) {
-    appendProperty(BINARIES_PROPERTY, path);
-    return this;
-  }
-
-  /**
-   * @deprecated since 4.5.1 use SonarQube Java specific API
-   */
-  @Deprecated
-  public ProjectDefinition addBinaryDir(File f) {
-    return addBinaryDir(f.getAbsolutePath());
-  }
-
-  /**
-   * @deprecated since 4.5.1 use SonarQube Java specific API
-   */
-  @Deprecated
-  public List<String> getLibraries() {
-    String sources = (String) ObjectUtils.defaultIfNull(properties.get(LIBRARIES_PROPERTY), "");
-    return trim(StringUtils.split(sources, SEPARATOR));
-  }
-
-  /**
-   * @param path path to file with third-party library. In case of Java this is path to jar file.
-   *             It can be absolute or relative to project directory.
-   * @deprecated since 4.5.1 use SonarQube Java specific API
-   */
-  @Deprecated
-  public void addLibrary(String path) {
-    appendProperty(LIBRARIES_PROPERTY, path);
-  }
-
-  /**
    * Adds an extension, which would be available in PicoContainer during analysis of this project.
    *
    * @since 2.8
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/ModuleFileSystem.java b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/ModuleFileSystem.java
index 8979f73b7c1..dd88f5b9bfd 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/ModuleFileSystem.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/ModuleFileSystem.java
@@ -63,14 +63,7 @@ public interface ModuleFileSystem {
   List<File> testDirs();
 
   /**
-   * Optional directories that contain the compiled sources, for example java bytecode.
-   * Note that :
-   * <ul>
-   * <li>Maven projects have only a single binary directory, which is generally ${project.basedir}/target/classes</li>
-   * <li>Binary directories can be empty</li>
-   * <li>Test binary directories are not supported yet.</li>
-   * </ul>
-   * @deprecated since 4.2 sonar.binaries will be converted to java specific property
+   * @deprecated since 4.2 - returns always empty list
    */
   List<File> binaryDirs();
 
diff --git a/sonar-plugin-api/src/test/java/org/sonar/api/batch/bootstrap/ProjectBuilderTest.java b/sonar-plugin-api/src/test/java/org/sonar/api/batch/bootstrap/ProjectBuilderTest.java
index 7a13e851401..14280131018 100644
--- a/sonar-plugin-api/src/test/java/org/sonar/api/batch/bootstrap/ProjectBuilderTest.java
+++ b/sonar-plugin-api/src/test/java/org/sonar/api/batch/bootstrap/ProjectBuilderTest.java
@@ -43,7 +43,7 @@ public class ProjectBuilderTest {
     ProjectDefinition root = projectReactor.getRoot();
     assertThat(root.getName(), is("Name changed by plugin"));
     assertThat(root.getSubProjects().size(), is(1));
-    assertThat(root.getSubProjects().get(0).getSourceDirs(), hasItem("src"));
+    assertThat(root.getSubProjects().get(0).sources(), hasItem("src"));
   }
 
   final static class ProjectBuilderSample extends ProjectBuilder {
@@ -68,7 +68,7 @@ public class ProjectBuilderTest {
       subProject.setKey("groupId:parentProjectId");
       subProject.setVersion(root.getVersion());
       subProject.setName("Sub Project");
-      subProject.setSourceDirs("src");
+      subProject.setSources("src");
       root.addSubProject(subProject);
     }
   }
diff --git a/sonar-plugin-api/src/test/java/org/sonar/api/batch/bootstrap/ProjectDefinitionTest.java b/sonar-plugin-api/src/test/java/org/sonar/api/batch/bootstrap/ProjectDefinitionTest.java
index 14faa2ec0a0..db99a5f3fbf 100644
--- a/sonar-plugin-api/src/test/java/org/sonar/api/batch/bootstrap/ProjectDefinitionTest.java
+++ b/sonar-plugin-api/src/test/java/org/sonar/api/batch/bootstrap/ProjectDefinitionTest.java
@@ -25,11 +25,9 @@ import org.junit.rules.TemporaryFolder;
 import org.sonar.api.CoreProperties;
 
 import java.io.File;
-import java.io.IOException;
 import java.util.List;
 import java.util.Properties;
 
-import static org.assertj.core.api.Assertions.assertThat;
 import static org.hamcrest.Matchers.is;
 import static org.hamcrest.Matchers.nullValue;
 import static org.junit.Assert.assertThat;
@@ -81,10 +79,8 @@ public class ProjectDefinitionTest {
   @Test
   public void testDefaultValues() {
     ProjectDefinition def = ProjectDefinition.create();
-    assertThat(def.getSourceDirs().size(), is(0));
-    assertThat(def.getTestDirs().size(), is(0));
-    assertThat(def.getBinaries().size(), is(0));
-    assertThat(def.getLibraries().size(), is(0));
+    assertThat(def.sources().size(), is(0));
+    assertThat(def.tests().size(), is(0));
   }
 
   /**
@@ -93,54 +89,43 @@ public class ProjectDefinitionTest {
   @Test
   public void shouldTrimPaths() {
     ProjectDefinition def = ProjectDefinition.create();
-    def.setProperty(ProjectDefinition.SOURCE_DIRS_PROPERTY, "src1, src2 , with whitespace");
-    def.setProperty(ProjectDefinition.TEST_DIRS_PROPERTY, "test1, test2 , with whitespace");
-    def.setProperty(ProjectDefinition.BINARIES_PROPERTY, "bin1, bin2 , with whitespace");
-    def.setProperty(ProjectDefinition.LIBRARIES_PROPERTY, "lib1, lib2 , with whitespace");
-
-    assertFiles(def.getSourceDirs(), "src1", "src2", "with whitespace");
-    assertFiles(def.getTestDirs(), "test1", "test2", "with whitespace");
-    assertFiles(def.getBinaries(), "bin1", "bin2", "with whitespace");
-    assertFiles(def.getLibraries(), "lib1", "lib2", "with whitespace");
+    def.setProperty(ProjectDefinition.SOURCES_PROPERTY, "src1, src2 , with whitespace");
+    def.setProperty(ProjectDefinition.TESTS_PROPERTY, "test1, test2 , with whitespace");
+
+
+    assertFiles(def.sources(), "src1", "src2", "with whitespace");
+    assertFiles(def.tests(), "test1", "test2", "with whitespace");
   }
 
   @Test
   public void shouldAddDirectoriesAsPath() {
     ProjectDefinition def = ProjectDefinition.create();
-    def.addSourceDirs("src/main/java", "src/main/java2");
-    def.addTestDirs("src/test/java");
-    def.addTestDirs("src/test/java2");
-    def.addBinaryDir("target/classes");
-    def.addBinaryDir("target/classes2");
-    def.addLibrary("junit.jar");
-    def.addLibrary("mockito.jar");
-
-    assertFiles(def.getSourceDirs(), "src/main/java", "src/main/java2");
-    assertFiles(def.getTestDirs(), "src/test/java", "src/test/java2");
-    assertFiles(def.getBinaries(), "target/classes", "target/classes2");
-    assertFiles(def.getLibraries(), "junit.jar", "mockito.jar");
+    def.addSources("src/main/java", "src/main/java2");
+    def.addTests("src/test/java");
+    def.addTests("src/test/java2");
+
+    assertFiles(def.sources(), "src/main/java", "src/main/java2");
+    assertFiles(def.tests(), "src/test/java", "src/test/java2");
   }
 
   @Test
   public void shouldAddDirectories() {
     ProjectDefinition def = ProjectDefinition.create();
-    def.addSourceDirs(new File("src/main/java"), new File("src/main/java2"));
-    def.addTestDirs(new File("src/test/java"), new File("src/test/java2"));
-    def.addBinaryDir(new File("target/classes"));
+    def.addSources(new File("src/main/java"), new File("src/main/java2"));
+    def.addTests(new File("src/test/java"), new File("src/test/java2"));
 
-    assertThat(def.getSourceDirs().size(), is(2));
-    assertThat(def.getTestDirs().size(), is(2));
-    assertThat(def.getBinaries().size(), is(1));
+    assertThat(def.sources().size(), is(2));
+    assertThat(def.tests().size(), is(2));
   }
 
   @Test
   public void shouldAddFiles() {
     ProjectDefinition def = ProjectDefinition.create();
-    def.addSourceFiles("src/main/java/foo/Bar.java", "src/main/java/hello/World.java");
-    def.addTestFiles("src/test/java/foo/BarTest.java", "src/test/java/hello/WorldTest.java");
+    def.addSources("src/main/java/foo/Bar.java", "src/main/java/hello/World.java");
+    def.addTests("src/test/java/foo/BarTest.java", "src/test/java/hello/WorldTest.java");
 
-    assertFiles(def.getSourceFiles(), "src/main/java/foo/Bar.java", "src/main/java/hello/World.java");
-    assertFiles(def.getTestFiles(), "src/test/java/foo/BarTest.java", "src/test/java/hello/WorldTest.java");
+    assertFiles(def.sources(), "src/main/java/foo/Bar.java", "src/main/java/hello/World.java");
+    assertFiles(def.tests(), "src/test/java/foo/BarTest.java", "src/test/java/hello/WorldTest.java");
   }
 
   @Test
@@ -159,75 +144,21 @@ public class ProjectDefinitionTest {
   @Test
   public void shouldResetSourceDirs() {
     ProjectDefinition root = ProjectDefinition.create();
-    root.addSourceDirs("src", "src2/main");
-    assertThat(root.getSourceDirs().size(), is(2));
+    root.addSources("src", "src2/main");
+    assertThat(root.sources().size(), is(2));
 
-    root.resetSourceDirs();
-    assertThat(root.getSourceDirs().size(), is(0));
+    root.resetSources();
+    assertThat(root.sources().size(), is(0));
   }
 
   @Test
   public void shouldResetTestDirs() {
     ProjectDefinition root = ProjectDefinition.create();
-    root.addTestDirs("src", "src2/test");
-    assertThat(root.getTestDirs().size(), is(2));
-
-    root.resetTestDirs();
-    assertThat(root.getTestDirs().size(), is(0));
-  }
-
-  @Test
-  public void shouldResetSourceDirsWhenUsindDeprecatedMethod() throws IOException {
-    File baseDir = temp.newFolder();
-    ProjectDefinition root = ProjectDefinition.create().setBaseDir(baseDir);
-    File src = new File(baseDir, "src");
-    src.mkdir();
-    root.addSourceDirs("src");
-    assertThat(root.getSourceDirs()).containsOnly("src");
-
-    root.addSourceFiles("foo.java");
-    assertThat(root.getSourceDirs()).containsOnly("foo.java");
-  }
+    root.addTests("src", "src2/test");
+    assertThat(root.tests().size(), is(2));
 
-  @Test
-  public void shouldResetTestDirsWhenUsindDeprecatedMethod() throws IOException {
-    File baseDir = temp.newFolder();
-    ProjectDefinition root = ProjectDefinition.create().setBaseDir(baseDir);
-    File test = new File(baseDir, "test");
-    test.mkdir();
-    root.addTestDirs("test");
-    assertThat(root.getTestDirs()).containsOnly("test");
-
-    root.addTestFiles("fooTest.java");
-    assertThat(root.getTestDirs()).containsOnly("fooTest.java");
-  }
-
-  @Test
-  public void shouldResetSourceDirsWhenUsindDeprecatedFileMethod() throws IOException {
-    File baseDir = temp.newFolder();
-    ProjectDefinition root = ProjectDefinition.create().setBaseDir(baseDir);
-    File src = new File(baseDir, "src");
-    src.mkdir();
-    root.addSourceDirs("src");
-    assertThat(root.getSourceDirs()).containsOnly("src");
-
-    File file = new File(src, "foo.java");
-    root.addSourceFiles(file);
-    assertThat(root.getSourceDirs()).containsOnly(file.getAbsolutePath());
-  }
-
-  @Test
-  public void shouldResetTestDirsWhenUsindDeprecatedFileMethod() throws IOException {
-    File baseDir = temp.newFolder();
-    ProjectDefinition root = ProjectDefinition.create().setBaseDir(baseDir);
-    File test = new File(baseDir, "test");
-    test.mkdir();
-    root.addTestDirs("test");
-    assertThat(root.getTestDirs()).containsOnly("test");
-
-    File file = new File(test, "fooTest.java");
-    root.addTestFiles(file);
-    assertThat(root.getTestDirs()).containsOnly(file.getAbsolutePath());
+    root.resetTests();
+    assertThat(root.tests().size(), is(0));
   }
 
   private static void assertFiles(List<String> paths, String... values) {