SONAR-926 Expose new FileSystem API based on InputFile/InputDir

51 files changed, 559 insertions, 157 deletions

diff --git a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/ignore/scanner/SourceScanner.java b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/ignore/scanner/SourceScanner.java
index f8b3b001453..23a61888fee 100644
--- a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/ignore/scanner/SourceScanner.java
+++ b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/ignore/scanner/SourceScanner.java
@@ -20,13 +20,14 @@
 
 package org.sonar.plugins.core.issue.ignore.scanner;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import org.sonar.api.batch.Phase;
 import org.sonar.api.batch.Sensor;
 import org.sonar.api.batch.SensorContext;
 import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.FileQuery;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.utils.SonarException;
 import org.sonar.batch.scan.filesystem.DefaultModuleFileSystem;
 import org.sonar.plugins.core.issue.ignore.pattern.ExclusionPatternInitializer;
diff --git a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/sensors/FileHashSensor.java b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/sensors/FileHashSensor.java
index 97eecd33f5e..fd14c7b7f06 100644
--- a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/sensors/FileHashSensor.java
+++ b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/sensors/FileHashSensor.java
@@ -19,11 +19,13 @@
  */
 package org.sonar.plugins.core.sensors;
 
+import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
+
+import org.sonar.api.scan.filesystem.InputFile;
 import com.google.common.collect.Maps;
 import org.sonar.api.batch.Sensor;
 import org.sonar.api.batch.SensorContext;
 import org.sonar.api.resources.Project;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.utils.KeyValueFormat;
 import org.sonar.batch.index.ComponentDataCache;
 import org.sonar.batch.scan.filesystem.InputFileCache;
@@ -58,7 +60,7 @@ public final class FileHashSensor implements Sensor {
   public void analyse(Project project, SensorContext context) {
     Map<String, String> map = Maps.newHashMap();
     for (InputFile inputFile : fileCache.byModule(project.key())) {
-      String hash = inputFile.attribute(InputFile.ATTRIBUTE_HASH);
+      String hash = inputFile.attribute(DefaultInputFile.ATTRIBUTE_HASH);
       if (hash != null) {
         map.put(inputFile.path(), hash);
       }
diff --git a/plugins/sonar-core-plugin/src/test/java/org/sonar/plugins/core/sensors/FileHashSensorTest.java b/plugins/sonar-core-plugin/src/test/java/org/sonar/plugins/core/sensors/FileHashSensorTest.java
index e7760be8de4..073db76b693 100644
--- a/plugins/sonar-core-plugin/src/test/java/org/sonar/plugins/core/sensors/FileHashSensorTest.java
+++ b/plugins/sonar-core-plugin/src/test/java/org/sonar/plugins/core/sensors/FileHashSensorTest.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.plugins.core.sensors;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import com.google.common.collect.ImmutableMap;
 import com.google.common.collect.Lists;
@@ -29,7 +31,6 @@ import org.junit.rules.TemporaryFolder;
 import org.sonar.api.batch.SensorContext;
 import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.batch.index.ComponentDataCache;
 import org.sonar.batch.scan.filesystem.InputFileCache;
 import org.sonar.core.source.SnapshotDataTypes;
@@ -58,8 +59,8 @@ public class FileHashSensorTest {
   @Test
   public void store_file_hashes() throws Exception {
     when(fileCache.byModule("struts")).thenReturn(Lists.<InputFile>newArrayList(
-      DefaultInputFile.create(temp.newFile(), Charsets.UTF_8, "src/Foo.java", ImmutableMap.of(InputFile.ATTRIBUTE_HASH, "ABC")),
-      DefaultInputFile.create(temp.newFile(), Charsets.UTF_8, "src/Bar.java", ImmutableMap.of(InputFile.ATTRIBUTE_HASH, "DEF"))
+      DefaultInputFile.create(temp.newFile(), Charsets.UTF_8, "src/Foo.java", ImmutableMap.of(DefaultInputFile.ATTRIBUTE_HASH, "ABC")),
+      DefaultInputFile.create(temp.newFile(), Charsets.UTF_8, "src/Bar.java", ImmutableMap.of(DefaultInputFile.ATTRIBUTE_HASH, "DEF"))
       ));
 
     SensorContext sensorContext = mock(SensorContext.class);
@@ -73,8 +74,8 @@ public class FileHashSensorTest {
   public void store_file_hashes_for_branches() throws Exception {
     project = new Project("struts", "branch-2.x", "Struts 2.x");
     when(fileCache.byModule("struts:branch-2.x")).thenReturn(Lists.<InputFile>newArrayList(
-      DefaultInputFile.create(temp.newFile(), Charsets.UTF_8, "src/Foo.java", ImmutableMap.of(InputFile.ATTRIBUTE_HASH, "ABC")),
-      DefaultInputFile.create(temp.newFile(), Charsets.UTF_8, "src/Bar.java", ImmutableMap.of(InputFile.ATTRIBUTE_HASH, "DEF"))
+      DefaultInputFile.create(temp.newFile(), Charsets.UTF_8, "src/Foo.java", ImmutableMap.of(DefaultInputFile.ATTRIBUTE_HASH, "ABC")),
+      DefaultInputFile.create(temp.newFile(), Charsets.UTF_8, "src/Bar.java", ImmutableMap.of(DefaultInputFile.ATTRIBUTE_HASH, "DEF"))
       ));
 
     SensorContext sensorContext = mock(SensorContext.class);
diff --git a/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/SonarBridgeEngine.java b/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/SonarBridgeEngine.java
index 9750b2fa206..b093558edba 100644
--- a/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/SonarBridgeEngine.java
+++ b/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/SonarBridgeEngine.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.plugins.cpd;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Predicate;
 import com.google.common.collect.Iterables;
@@ -32,7 +34,6 @@ import org.sonar.api.resources.Language;
 import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.FileQuery;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.utils.SonarException;
 import org.sonar.batch.scan.filesystem.DefaultModuleFileSystem;
 import org.sonar.duplications.DuplicationPredicates;
@@ -43,6 +44,7 @@ import org.sonar.plugins.cpd.index.IndexFactory;
 import org.sonar.plugins.cpd.index.SonarDuplicationsIndex;
 
 import javax.annotation.CheckForNull;
+
 import java.util.Collection;
 import java.util.List;
 import java.util.concurrent.ExecutionException;
diff --git a/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/SonarEngine.java b/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/SonarEngine.java
index 832b4e7ab82..62878f1467e 100644
--- a/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/SonarEngine.java
+++ b/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/SonarEngine.java
@@ -20,6 +20,8 @@
 
 package org.sonar.plugins.cpd;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.collect.Iterables;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringEscapeUtils;
@@ -36,7 +38,6 @@ import org.sonar.api.resources.Language;
 import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.FileQuery;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.utils.SonarException;
 import org.sonar.batch.scan.filesystem.DefaultModuleFileSystem;
 import org.sonar.duplications.block.Block;
diff --git a/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/index/DbDuplicationsIndex.java b/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/index/DbDuplicationsIndex.java
index 2ef72e7cae6..83475fbb861 100644
--- a/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/index/DbDuplicationsIndex.java
+++ b/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/index/DbDuplicationsIndex.java
@@ -19,11 +19,12 @@
  */
 package org.sonar.plugins.cpd.index;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.resources.Project;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.batch.index.ResourcePersister;
 import org.sonar.core.duplication.DuplicationDao;
 import org.sonar.core.duplication.DuplicationUnitDto;
diff --git a/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/index/SonarDuplicationsIndex.java b/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/index/SonarDuplicationsIndex.java
index cd554934c04..6a54af3503b 100644
--- a/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/index/SonarDuplicationsIndex.java
+++ b/plugins/sonar-cpd-plugin/src/main/java/org/sonar/plugins/cpd/index/SonarDuplicationsIndex.java
@@ -19,8 +19,9 @@
  */
 package org.sonar.plugins.cpd.index;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.collect.Lists;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.duplications.block.Block;
 import org.sonar.duplications.block.ByteArray;
 import org.sonar.duplications.index.AbstractCloneIndex;
diff --git a/plugins/sonar-cpd-plugin/src/test/java/org/sonar/plugins/cpd/SonarEngineTest.java b/plugins/sonar-cpd-plugin/src/test/java/org/sonar/plugins/cpd/SonarEngineTest.java
index f22eabb3a81..18c80b5dcfc 100644
--- a/plugins/sonar-cpd-plugin/src/test/java/org/sonar/plugins/cpd/SonarEngineTest.java
+++ b/plugins/sonar-cpd-plugin/src/test/java/org/sonar/plugins/cpd/SonarEngineTest.java
@@ -19,12 +19,13 @@
  */
 package org.sonar.plugins.cpd;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import org.junit.Before;
 import org.junit.Test;
 import org.sonar.api.batch.SensorContext;
 import org.sonar.api.measures.CoreMetrics;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.scan.filesystem.internal.InputFileBuilder;
 import org.sonar.api.test.IsMeasure;
 import org.sonar.duplications.index.CloneGroup;
diff --git a/plugins/sonar-maven-batch-plugin/src/main/java/org/sonar/plugins/maven/DefaultMavenPluginExecutor.java b/plugins/sonar-maven-batch-plugin/src/main/java/org/sonar/plugins/maven/DefaultMavenPluginExecutor.java
index 4dea1968071..cab684b55c6 100644
--- a/plugins/sonar-maven-batch-plugin/src/main/java/org/sonar/plugins/maven/DefaultMavenPluginExecutor.java
+++ b/plugins/sonar-maven-batch-plugin/src/main/java/org/sonar/plugins/maven/DefaultMavenPluginExecutor.java
@@ -56,8 +56,8 @@ public class DefaultMavenPluginExecutor implements MavenPluginExecutor {
       }
       MavenPlugin plugin = MavenPlugin.getPlugin(project.getPom(), handler.getGroupId(), handler.getArtifactId());
       execute(project,
-          fs,
-          getGoal(handler.getGroupId(), handler.getArtifactId(), plugin != null && plugin.getPlugin() != null ? plugin.getPlugin().getVersion() : null, goal));
+        fs,
+        getGoal(handler.getGroupId(), handler.getArtifactId(), plugin != null && plugin.getPlugin() != null ? plugin.getPlugin().getVersion() : null, goal));
     }
     return handler;
   }
@@ -76,20 +76,21 @@ public class DefaultMavenPluginExecutor implements MavenPluginExecutor {
         Thread.currentThread().setContextClassLoader(currentClassLoader);
         profiler.stop();
       }
-
-      MavenProjectConverter.synchronizeFileSystem(project.getPom(), fs);
+      if (!fs.isInitialized()) {
+        MavenProjectConverter.synchronizeFileSystem(project.getPom(), fs);
+      }
     }
   }
 
   static String getGoal(String groupId, String artifactId, @Nullable String version, String goal) {
     String defaultVersion = version == null ? "" : version;
     return new StringBuilder()
-        .append(groupId).append(":")
-        .append(artifactId).append(":")
-        .append(defaultVersion)
-        .append(":")
-        .append(goal)
-        .toString();
+      .append(groupId).append(":")
+      .append(artifactId).append(":")
+      .append(defaultVersion)
+      .append(":")
+      .append(goal)
+      .toString();
   }
 
   public void concreteExecute(MavenProject pom, String goal) {
@@ -130,14 +131,14 @@ public class DefaultMavenPluginExecutor implements MavenPluginExecutor {
     try {
       ReactorManager reactor = new ReactorManager(Arrays.asList(pom));
       MavenSession clonedSession = new MavenSession(mavenSession.getContainer(),
-          mavenSession.getSettings(),
-          mavenSession.getLocalRepository(),
-          mavenSession.getEventDispatcher(),
-          reactor,
-          Arrays.asList(goal),
-          mavenSession.getExecutionRootDirectory(),
-          mavenSession.getExecutionProperties(),
-          mavenSession.getStartTime());
+        mavenSession.getSettings(),
+        mavenSession.getLocalRepository(),
+        mavenSession.getEventDispatcher(),
+        reactor,
+        Arrays.asList(goal),
+        mavenSession.getExecutionRootDirectory(),
+        mavenSession.getExecutionProperties(),
+        mavenSession.getStartTime());
       executeMethod.invoke(lifecycleExecutor, clonedSession, reactor, clonedSession.getEventDispatcher());
     } catch (Exception e) {
       throw new SonarException("Unable to execute Maven 2 plugin", e);
diff --git a/sonar-batch/src/main/java/org/sonar/batch/DefaultSensorContext.java b/sonar-batch/src/main/java/org/sonar/batch/DefaultSensorContext.java
index 5fabba61dbc..36e84cea339 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/DefaultSensorContext.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/DefaultSensorContext.java
@@ -19,6 +19,9 @@
  */
 package org.sonar.batch;
 
+import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
+
+import org.sonar.api.scan.filesystem.InputFile;
 import org.apache.commons.lang.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -38,7 +41,6 @@ import org.sonar.api.resources.ProjectLink;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.resources.Scopes;
 import org.sonar.api.rules.Violation;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.utils.SonarException;
 import org.sonar.core.measure.MeasurementFilters;
 
@@ -258,9 +260,9 @@ public class DefaultSensorContext implements SensorContext {
     String languageKey = inputFile.attribute(InputFile.ATTRIBUTE_LANGUAGE);
     boolean unitTest = InputFile.TYPE_TEST.equals(inputFile.attribute(InputFile.ATTRIBUTE_TYPE));
     if (Java.KEY.equals(languageKey)) {
-      return JavaFile.create(inputFile.path(), inputFile.attribute(InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), unitTest);
+      return JavaFile.create(inputFile.path(), inputFile.attribute(DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), unitTest);
     } else {
-      return File.create(inputFile.path(), inputFile.attribute(InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), languages.get(languageKey), unitTest);
+      return File.create(inputFile.path(), inputFile.attribute(DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), languages.get(languageKey), unitTest);
     }
   }
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/DefaultResourcePersister.java b/sonar-batch/src/main/java/org/sonar/batch/index/DefaultResourcePersister.java
index 4931060321c..f387bebe1b6 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/index/DefaultResourcePersister.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/index/DefaultResourcePersister.java
@@ -19,6 +19,9 @@
  */
 package org.sonar.batch.index;
 
+import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
+
+import org.sonar.api.scan.filesystem.InputFile;
 import com.google.common.collect.Maps;
 import org.apache.commons.lang.ObjectUtils;
 import org.apache.commons.lang.StringUtils;
@@ -34,7 +37,6 @@ import org.sonar.api.resources.Qualifiers;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.resources.ResourceUtils;
 import org.sonar.api.resources.Scopes;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.security.ResourcePermissions;
 import org.sonar.api.utils.SonarException;
 
@@ -145,9 +147,9 @@ public final class DefaultResourcePersister implements ResourcePersister {
     String languageKey = inputFile.attribute(InputFile.ATTRIBUTE_LANGUAGE);
     boolean unitTest = InputFile.TYPE_TEST.equals(inputFile.attribute(InputFile.ATTRIBUTE_TYPE));
     if (Java.KEY.equals(languageKey)) {
-      return JavaFile.create(inputFile.path(), inputFile.attribute(InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), unitTest);
+      return JavaFile.create(inputFile.path(), inputFile.attribute(DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), unitTest);
     } else {
-      return File.create(inputFile.path(), inputFile.attribute(InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), null, unitTest);
+      return File.create(inputFile.path(), inputFile.attribute(DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), null, unitTest);
     }
   }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/ResourceKeyMigration.java b/sonar-batch/src/main/java/org/sonar/batch/index/ResourceKeyMigration.java
index ae97d13aa4e..0fe99a889ad 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/index/ResourceKeyMigration.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/index/ResourceKeyMigration.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.index;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang.StringUtils;
 import org.slf4j.Logger;
@@ -34,7 +36,6 @@ import org.sonar.api.resources.Qualifiers;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.resources.Scopes;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.utils.PathUtils;
 
 import java.util.HashMap;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/ResourcePersister.java b/sonar-batch/src/main/java/org/sonar/batch/index/ResourcePersister.java
index 8e41528ba36..100c8b34273 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/index/ResourcePersister.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/index/ResourcePersister.java
@@ -19,10 +19,11 @@
  */
 package org.sonar.batch.index;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 
 public interface ResourcePersister {
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/AttributeFilter.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/AttributeFilter.java
index f7f0ecfa831..1276c11168a 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/AttributeFilter.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/AttributeFilter.java
@@ -19,8 +19,9 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.annotations.VisibleForTesting;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.scan.filesystem.internal.InputFileFilter;
 
 import java.util.Collection;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ComponentIndexer.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ComponentIndexer.java
index c1e97a05f56..ad0064f565c 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ComponentIndexer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ComponentIndexer.java
@@ -19,6 +19,9 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
+
+import org.sonar.api.scan.filesystem.InputFile;
 import com.google.common.base.CharMatcher;
 import com.google.common.io.Files;
 import org.apache.commons.lang.StringUtils;
@@ -34,7 +37,6 @@ import org.sonar.api.resources.Languages;
 import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.scan.filesystem.FileQuery;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.utils.SonarException;
 import org.sonar.batch.index.ResourceKeyMigration;
 import org.sonar.batch.scan.language.DefaultModuleLanguages;
@@ -76,9 +78,9 @@ public class ComponentIndexer implements BatchComponent {
       boolean unitTest = InputFile.TYPE_TEST.equals(inputFile.attribute(InputFile.ATTRIBUTE_TYPE));
       Resource sonarFile;
       if (Java.KEY.equals(languageKey)) {
-        sonarFile = JavaFile.create(inputFile.path(), inputFile.attribute(InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), unitTest);
+        sonarFile = JavaFile.create(inputFile.path(), inputFile.attribute(DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), unitTest);
       } else {
-        sonarFile = File.create(inputFile.path(), inputFile.attribute(InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), languages.get(languageKey), unitTest);
+        sonarFile = File.create(inputFile.path(), inputFile.attribute(DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH), languages.get(languageKey), unitTest);
       }
       if (sonarFile != null) {
         moduleLanguages.addLanguage(languageKey);
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 80bc58ad5eb..7d624ed8b89 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
@@ -27,8 +27,9 @@ import org.sonar.api.CoreProperties;
 import org.sonar.api.config.Settings;
 import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.FileQuery;
+import org.sonar.api.scan.filesystem.InputDir;
+import org.sonar.api.scan.filesystem.InputFile;
 import org.sonar.api.scan.filesystem.ModuleFileSystem;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.scan.filesystem.internal.InputFiles;
 import org.sonar.api.utils.SonarException;
 import org.sonar.batch.bootstrap.AnalysisMode;
@@ -58,7 +59,7 @@ public class DefaultModuleFileSystem implements ModuleFileSystem {
   private List<File> testFiles = Lists.newArrayList();
   private AnalysisMode analysisMode;
   private ComponentIndexer componentIndexer;
-  private boolean indexed;
+  private boolean initialized;
 
   public DefaultModuleFileSystem(Project module, Settings settings, FileIndex index, ModuleFileSystemInitializer initializer, AnalysisMode analysisMode,
     ComponentIndexer componentIndexer) {
@@ -77,6 +78,10 @@ public class DefaultModuleFileSystem implements ModuleFileSystem {
     this.testFiles = initializer.additionalTestFiles();
   }
 
+  public boolean isInitialized() {
+    return initialized;
+  }
+
   public String moduleKey() {
     return moduleKey;
   }
@@ -157,7 +162,11 @@ public class DefaultModuleFileSystem implements ModuleFileSystem {
   /**
    * @since 4.0
    */
+  @Override
   public Iterable<InputFile> inputFiles(FileQuery query) {
+    if (!initialized) {
+      throw new SonarException("Module filesystem is not initialized");
+    }
     List<InputFile> result = Lists.newArrayList();
     FileQueryFilter filter = new FileQueryFilter(analysisMode, query);
     for (InputFile input : index.inputFiles(moduleKey)) {
@@ -169,11 +178,30 @@ public class DefaultModuleFileSystem implements ModuleFileSystem {
   }
 
   @Override
+  public InputFile inputFile(File ioFile) {
+    if (!ioFile.isFile()) {
+      throw new SonarException(ioFile.getAbsolutePath() + "is not a file");
+    }
+    return index.inputFile(this, ioFile);
+  }
+
+  @Override
+  public InputDir inputDir(File ioFile) {
+    if (!ioFile.isDirectory()) {
+      throw new SonarException(ioFile.getAbsolutePath() + "is not a directory");
+    }
+    return index.inputDir(this, ioFile);
+  }
+
+  @Override
   public List<File> files(FileQuery query) {
     return InputFiles.toFiles(inputFiles(query));
   }
 
   public void resetDirs(File basedir, File buildDir, List<File> sourceDirs, List<File> testDirs, List<File> binaryDirs) {
+    if (initialized) {
+      throw new SonarException("Module filesystem is locked");
+    }
     Preconditions.checkNotNull(basedir, "Basedir can't be null");
     this.baseDir = basedir;
     this.buildDir = buildDir;
@@ -183,10 +211,10 @@ public class DefaultModuleFileSystem implements ModuleFileSystem {
   }
 
   public void index() {
-    if (indexed) {
+    if (initialized) {
       throw new SonarException("Module filesystem can only be indexed once");
     }
-    indexed = true;
+    initialized = true;
     index.index(this);
     componentIndexer.execute(this);
   }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DeprecatedFileFilters.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DeprecatedFileFilters.java
index 1c49ec7e85f..5ce26537016 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DeprecatedFileFilters.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DeprecatedFileFilters.java
@@ -19,8 +19,9 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
+
 import org.sonar.api.scan.filesystem.*;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.scan.filesystem.internal.InputFileFilter;
 
 import java.io.File;
@@ -69,13 +70,13 @@ public class DeprecatedFileFilters implements InputFileFilter {
 
     @Override
     public File relativeDir() {
-      String path = inputFile.attribute(InputFile.ATTRIBUTE_SOURCEDIR_PATH);
+      String path = inputFile.attribute(DefaultInputFile.ATTRIBUTE_SOURCEDIR_PATH);
       return path != null ? new File(path) : null;
     }
 
     @Override
     public String relativePath() {
-      return inputFile.attribute(InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH);
+      return inputFile.attribute(DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH);
     }
 
     @Override
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ExclusionFilter.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ExclusionFilter.java
index 4f04f6b41d0..8ce2feff037 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ExclusionFilter.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ExclusionFilter.java
@@ -19,7 +19,8 @@
  */
 package org.sonar.batch.scan.filesystem;
 
-import org.sonar.api.scan.filesystem.internal.InputFile;
+import org.sonar.api.scan.filesystem.InputFile;
+
 import org.sonar.api.scan.filesystem.internal.InputFileFilter;
 
 class ExclusionFilter implements InputFileFilter {
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ExclusionFilters.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ExclusionFilters.java
index 432ba2a695b..f52cd807076 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ExclusionFilters.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ExclusionFilters.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.sonar.api.BatchComponent;
@@ -26,7 +28,6 @@ import org.sonar.api.batch.ResourceFilter;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.resources.ResourceUtils;
 import org.sonar.api.scan.filesystem.FileExclusions;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.scan.filesystem.internal.InputFileFilter;
 
 public class ExclusionFilters implements InputFileFilter, ResourceFilter, BatchComponent {
@@ -58,7 +59,7 @@ public class ExclusionFilters implements InputFileFilter, ResourceFilter, BatchC
     String type = inputFile.attribute(InputFile.ATTRIBUTE_TYPE);
     PathPattern[] inclusionPatterns = null;
     PathPattern[] exclusionPatterns = null;
-    if (InputFile.TYPE_SOURCE.equals(type)) {
+    if (InputFile.TYPE_MAIN.equals(type)) {
       inclusionPatterns = sourceInclusions();
       exclusionPatterns = sourceExclusions();
     } else if (InputFile.TYPE_TEST.equals(type)) {
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndex.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndex.java
index 34d117be2ee..a6d34469019 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndex.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndex.java
@@ -31,10 +31,12 @@ import org.sonar.api.BatchComponent;
 import org.sonar.api.resources.Java;
 import org.sonar.api.resources.JavaFile;
 import org.sonar.api.resources.Project;
+import org.sonar.api.scan.filesystem.InputDir;
+import org.sonar.api.scan.filesystem.InputFile;
 import org.sonar.api.scan.filesystem.ModuleFileSystem;
 import org.sonar.api.scan.filesystem.PathResolver;
+import org.sonar.api.scan.filesystem.internal.DefaultInputDir;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.scan.filesystem.internal.InputFileFilter;
 import org.sonar.api.utils.PathUtils;
 
@@ -73,7 +75,7 @@ public class FileIndex implements BatchComponent {
   private final PathResolver pathResolver;
   private final List<InputFileFilter> filters;
   private final LanguageRecognizer languageRecognizer;
-  private final InputFileCache cache;
+  private final InputFileCache fileCache;
   private final FileHashes fileHashes;
   private final Project project;
 
@@ -81,7 +83,7 @@ public class FileIndex implements BatchComponent {
     InputFileCache cache, FileHashes fileHashes, PathResolver pathResolver, Project project) {
     this.filters = filters;
     this.languageRecognizer = languageRecognizer;
-    this.cache = cache;
+    this.fileCache = cache;
     this.fileHashes = fileHashes;
     this.pathResolver = pathResolver;
     this.project = project;
@@ -92,16 +94,16 @@ public class FileIndex implements BatchComponent {
     logger.info("Index files");
     // TODO log configuration too (replace FileSystemLogger)
 
-    Progress progress = new Progress(cache.fileRelativePaths(fileSystem.moduleKey()));
+    Progress progress = new Progress(fileCache.fileRelativePaths(fileSystem.moduleKey()));
 
     if (fileSystem.sourceFiles().isEmpty()) {
       // index directories
       for (File sourceDir : fileSystem.sourceDirs()) {
-        indexDirectory(fileSystem, progress, sourceDir, InputFile.TYPE_SOURCE);
+        indexDirectory(fileSystem, progress, sourceDir, InputFile.TYPE_MAIN);
       }
     } else {
       // index only given files
-      indexFiles(fileSystem, progress, fileSystem.sourceDirs(), fileSystem.sourceFiles(), InputFile.TYPE_SOURCE);
+      indexFiles(fileSystem, progress, fileSystem.sourceDirs(), fileSystem.sourceFiles(), InputFile.TYPE_MAIN);
     }
 
     if (fileSystem.testFiles().isEmpty()) {
@@ -116,7 +118,7 @@ public class FileIndex implements BatchComponent {
 
     // Remove files that have been removed since previous indexation
     for (String path : progress.removedPaths) {
-      cache.remove(fileSystem.moduleKey(), path);
+      fileCache.remove(fileSystem.moduleKey(), path);
     }
 
     logger.info(String.format("%d files indexed", progress.count));
@@ -137,7 +139,22 @@ public class FileIndex implements BatchComponent {
   }
 
   Iterable<InputFile> inputFiles(String moduleKey) {
-    return cache.byModule(moduleKey);
+    return fileCache.byModule(moduleKey);
+  }
+
+  InputFile inputFile(DefaultModuleFileSystem fileSystem, File ioFile) {
+    String path = computeFilePath(fileSystem, ioFile);
+    return fileCache.byPath(fileSystem.moduleKey(), path);
+  }
+
+  InputDir inputDir(DefaultModuleFileSystem fileSystem, File ioFile) {
+    String path = computeFilePath(fileSystem, ioFile);
+    // TODO no cache for InputDir
+    Map<String, String> attributes = Maps.newHashMap();
+    // paths
+    String resourceKey = PathUtils.sanitize(path);
+    set(attributes, DefaultInputFile.ATTRIBUTE_COMPONENT_KEY, project.getEffectiveKey() + ":" + resourceKey);
+    return DefaultInputDir.create(ioFile, path, attributes);
   }
 
   private void indexDirectory(DefaultModuleFileSystem fileSystem, Progress status, File sourceDir, String type) {
@@ -148,18 +165,23 @@ public class FileIndex implements BatchComponent {
   }
 
   private void indexFile(DefaultModuleFileSystem fileSystem, Progress status, File sourceDir, File file, String type) {
-    String path = pathResolver.relativePath(fileSystem.baseDir(), file);
+    String path = computeFilePath(fileSystem, file);
     if (path == null) {
       LoggerFactory.getLogger(getClass()).warn(String.format("File '%s' is not in basedir '%s'", file.getAbsolutePath(), fileSystem.baseDir()));
     } else {
       InputFile input = newInputFile(fileSystem, sourceDir, type, file, path);
       if (input != null && accept(input)) {
-        cache.put(fileSystem.moduleKey(), input);
+        fileCache.put(fileSystem.moduleKey(), input);
         status.markAsIndexed(path);
       }
     }
   }
 
+  private String computeFilePath(DefaultModuleFileSystem fileSystem, File file) {
+    String path = pathResolver.relativePath(fileSystem.baseDir(), file);
+    return path;
+  }
+
   @CheckForNull
   private InputFile newInputFile(ModuleFileSystem fileSystem, File sourceDir, String type, File file, String path) {
 
@@ -167,9 +189,9 @@ public class FileIndex implements BatchComponent {
     set(attributes, InputFile.ATTRIBUTE_TYPE, type);
 
     // paths
-    set(attributes, InputFile.ATTRIBUTE_SOURCEDIR_PATH, PathUtils.canonicalPath(sourceDir));
+    set(attributes, DefaultInputFile.ATTRIBUTE_SOURCEDIR_PATH, PathUtils.canonicalPath(sourceDir));
     String sourceRelativePath = pathResolver.relativePath(sourceDir, file);
-    set(attributes, InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, sourceRelativePath);
+    set(attributes, DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, sourceRelativePath);
 
     String resourceKey = PathUtils.sanitize(path);
     set(attributes, DefaultInputFile.ATTRIBUTE_COMPONENT_KEY, project.getEffectiveKey() + ":" + resourceKey);
@@ -193,7 +215,7 @@ public class FileIndex implements BatchComponent {
 
   private void initStatus(File file, Charset charset, String baseRelativePath, Map<String, String> attributes) {
     String hash = fileHashes.hash(file, charset);
-    set(attributes, InputFile.ATTRIBUTE_HASH, hash);
+    set(attributes, DefaultInputFile.ATTRIBUTE_HASH, hash);
 
     String remoteHash = fileHashes.remoteHash(baseRelativePath);
     // currently no need to store this remote hash in attributes
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileQueryFilter.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileQueryFilter.java
index 4dad09db531..38affb34c3e 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileQueryFilter.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileQueryFilter.java
@@ -19,10 +19,11 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.Lists;
 import org.sonar.api.scan.filesystem.FileQuery;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.scan.filesystem.internal.InputFileFilter;
 import org.sonar.batch.bootstrap.AnalysisMode;
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InclusionFilter.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InclusionFilter.java
index 4e622372333..c9fe825027c 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InclusionFilter.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InclusionFilter.java
@@ -19,7 +19,8 @@
  */
 package org.sonar.batch.scan.filesystem;
 
-import org.sonar.api.scan.filesystem.internal.InputFile;
+import org.sonar.api.scan.filesystem.InputFile;
+
 import org.sonar.api.scan.filesystem.internal.InputFileFilter;
 
 class InclusionFilter implements InputFileFilter {
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileCache.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileCache.java
index bf360a7e419..7ab06aec59b 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileCache.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileCache.java
@@ -20,10 +20,12 @@
 package org.sonar.batch.scan.filesystem;
 
 import org.sonar.api.BatchComponent;
-import org.sonar.api.scan.filesystem.internal.InputFile;
+import org.sonar.api.scan.filesystem.InputFile;
 import org.sonar.batch.index.Cache;
 import org.sonar.batch.index.Caches;
 
+import javax.annotation.CheckForNull;
+
 import java.util.Set;
 
 /**
@@ -43,6 +45,11 @@ public class InputFileCache implements BatchComponent {
     return cache.values(moduleKey);
   }
 
+  @CheckForNull
+  public InputFile byPath(String moduleKey, String path) {
+    return cache.get(moduleKey, path);
+  }
+
   public InputFileCache removeModule(String moduleKey) {
     cache.clear(moduleKey);
     return this;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageRecognizer.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageRecognizer.java
index 26d898ff2ea..ff4fd3c3006 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageRecognizer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageRecognizer.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.collect.HashMultimap;
 import com.google.common.collect.Maps;
 import com.google.common.collect.SetMultimap;
@@ -32,7 +34,6 @@ import org.sonar.api.CoreProperties;
 import org.sonar.api.config.Settings;
 import org.sonar.api.resources.Language;
 import org.sonar.api.resources.Languages;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.utils.SonarException;
 
 import javax.annotation.CheckForNull;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/PathPattern.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/PathPattern.java
index 650f447e476..4ac66004469 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/PathPattern.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/PathPattern.java
@@ -19,9 +19,10 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import org.apache.commons.lang.StringUtils;
 import org.sonar.api.resources.Resource;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.utils.WildcardPattern;
 
 abstract class PathPattern {
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ProjectFileSystemAdapter.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ProjectFileSystemAdapter.java
index c984d231316..39c139315c5 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ProjectFileSystemAdapter.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ProjectFileSystemAdapter.java
@@ -186,10 +186,10 @@ public class ProjectFileSystemAdapter implements ProjectFileSystem {
 
   public List<InputFile> mainFiles(String... langs) {
     List<InputFile> result = Lists.newArrayList();
-    Iterable<org.sonar.api.scan.filesystem.internal.InputFile> files = target.inputFiles(FileQuery.onSource().onLanguage(langs));
-    for (org.sonar.api.scan.filesystem.internal.InputFile file : files) {
-      String sourceDir = file.attribute(org.sonar.api.scan.filesystem.internal.InputFile.ATTRIBUTE_SOURCEDIR_PATH);
-      String sourceRelativePath = file.attribute(org.sonar.api.scan.filesystem.internal.InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH);
+    Iterable<org.sonar.api.scan.filesystem.InputFile> files = target.inputFiles(FileQuery.onSource().onLanguage(langs));
+    for (org.sonar.api.scan.filesystem.InputFile file : files) {
+      String sourceDir = file.attribute(org.sonar.api.scan.filesystem.internal.DefaultInputFile.ATTRIBUTE_SOURCEDIR_PATH);
+      String sourceRelativePath = file.attribute(org.sonar.api.scan.filesystem.internal.DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH);
       if (sourceDir != null && sourceRelativePath != null) {
         result.add(InputFileUtils.create(new File(sourceDir), sourceRelativePath));
       }
@@ -199,10 +199,10 @@ public class ProjectFileSystemAdapter implements ProjectFileSystem {
 
   public List<InputFile> testFiles(String... langs) {
     List<InputFile> result = Lists.newArrayList();
-    Iterable<org.sonar.api.scan.filesystem.internal.InputFile> files = target.inputFiles(FileQuery.onTest().onLanguage(langs));
-    for (org.sonar.api.scan.filesystem.internal.InputFile file : files) {
-      String sourceDir = file.attribute(org.sonar.api.scan.filesystem.internal.InputFile.ATTRIBUTE_SOURCEDIR_PATH);
-      String sourceRelativePath = file.attribute(org.sonar.api.scan.filesystem.internal.InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH);
+    Iterable<org.sonar.api.scan.filesystem.InputFile> files = target.inputFiles(FileQuery.onTest().onLanguage(langs));
+    for (org.sonar.api.scan.filesystem.InputFile file : files) {
+      String sourceDir = file.attribute(org.sonar.api.scan.filesystem.internal.DefaultInputFile.ATTRIBUTE_SOURCEDIR_PATH);
+      String sourceRelativePath = file.attribute(org.sonar.api.scan.filesystem.internal.DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH);
       if (sourceDir != null && sourceRelativePath != null) {
         result.add(InputFileUtils.create(new File(sourceDir), sourceRelativePath));
       }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/report/IncrementalComponentSelector.java b/sonar-batch/src/main/java/org/sonar/batch/scan/report/IncrementalComponentSelector.java
index 0317edf8b0b..9c18af551fc 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/report/IncrementalComponentSelector.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/report/IncrementalComponentSelector.java
@@ -19,10 +19,11 @@
  */
 package org.sonar.batch.scan.report;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.collect.Sets;
 import org.sonar.api.issue.Issue;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.batch.scan.filesystem.InputFileCache;
 
 import java.util.Set;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/ResourceKeyMigrationTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/ResourceKeyMigrationTest.java
index aad9df2dce5..a03d50f5631 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/index/ResourceKeyMigrationTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/ResourceKeyMigrationTest.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.index;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import org.apache.commons.configuration.PropertiesConfiguration;
 import org.junit.Before;
@@ -29,7 +31,6 @@ import org.junit.rules.TemporaryFolder;
 import org.slf4j.Logger;
 import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.scan.filesystem.internal.InputFileBuilder;
 import org.sonar.jpa.test.AbstractDbUnitTestCase;
 
@@ -94,7 +95,7 @@ public class ResourceKeyMigrationTest extends AbstractDbUnitTestCase {
     return new InputFileBuilder(file, Charsets.UTF_8, path)
       .attribute(DefaultInputFile.ATTRIBUTE_COMPONENT_KEY, effectiveKey)
       .attribute(DefaultInputFile.ATTRIBUTE_COMPONENT_DEPRECATED_KEY, deprecatedEffectiveKey)
-      .attribute(InputFile.ATTRIBUTE_TYPE, isTest ? InputFile.TYPE_TEST : InputFile.TYPE_SOURCE).build();
+      .attribute(InputFile.ATTRIBUTE_TYPE, isTest ? InputFile.TYPE_TEST : InputFile.TYPE_MAIN).build();
   }
 
   @Test
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ComponentIndexerTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ComponentIndexerTest.java
index a64b859cc9d..c0945f0f570 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ComponentIndexerTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ComponentIndexerTest.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang.CharEncoding;
@@ -40,7 +42,6 @@ import org.sonar.api.resources.Qualifiers;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.scan.filesystem.FileQuery;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.scan.filesystem.internal.InputFileBuilder;
 import org.sonar.batch.index.ResourceKeyMigration;
 import org.sonar.batch.scan.language.DefaultModuleLanguages;
@@ -153,9 +154,9 @@ public class ComponentIndexerTest {
     File file = new File(baseDir, path);
     FileUtils.write(file, content);
     return new InputFileBuilder(file, Charsets.UTF_8, path)
-      .attribute(InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, sourceRelativePath)
+      .attribute(DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, sourceRelativePath)
       .attribute(InputFile.ATTRIBUTE_LANGUAGE, languageKey)
-      .attribute(InputFile.ATTRIBUTE_TYPE, unitTest ? InputFile.TYPE_TEST : InputFile.TYPE_SOURCE)
+      .attribute(InputFile.ATTRIBUTE_TYPE, unitTest ? InputFile.TYPE_TEST : InputFile.TYPE_MAIN)
       .build();
   }
 
@@ -188,7 +189,7 @@ public class ComponentIndexerTest {
     FileUtils.write(javaFile1, "\uFEFFpublic class Test", Charsets.UTF_8);
     when(fs.inputFiles(FileQuery.all())).thenReturn((Iterable) Arrays.asList(
       new InputFileBuilder(javaFile1, Charset.forName("UTF-8"), "src/main/java/foo/bar/Foo.java")
-        .attribute(InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "foo/bar/Foo.java")
+        .attribute(DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "foo/bar/Foo.java")
         .attribute(InputFile.ATTRIBUTE_LANGUAGE, "java")
         .build()));
     when(project.getLanguageKey()).thenReturn(Java.KEY);
@@ -217,7 +218,7 @@ public class ComponentIndexerTest {
       .thenReturn(
         (Iterable) Arrays.asList(
           new InputFileBuilder(javaFile1, Charset.forName(encoding), "src/main/java/foo/bar/Foo.java")
-            .attribute(InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "foo/bar/Foo.java")
+            .attribute(DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "foo/bar/Foo.java")
             .attribute(InputFile.ATTRIBUTE_LANGUAGE, "java")
             .build()));
     when(project.getLanguageKey()).thenReturn(Java.KEY);
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 ef1298b4514..4041895dff4 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
@@ -32,8 +32,8 @@ import org.sonar.api.CoreProperties;
 import org.sonar.api.config.Settings;
 import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.FileQuery;
+import org.sonar.api.scan.filesystem.InputFile;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.batch.bootstrap.AnalysisMode;
 
 import java.io.File;
@@ -162,11 +162,12 @@ public class DefaultModuleFileSystemTest {
     DefaultModuleFileSystem fs = new DefaultModuleFileSystem(new Project("foo"), settings, fileIndex, initializer, mode, componentIndexer);
 
     File mainFile = temp.newFile();
-    InputFile mainInput = DefaultInputFile.create(mainFile, Charsets.UTF_8, "Main.java", ImmutableMap.of(InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_SOURCE));
+    InputFile mainInput = DefaultInputFile.create(mainFile, Charsets.UTF_8, "Main.java", ImmutableMap.of(InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_MAIN));
     InputFile testInput = DefaultInputFile.create(temp.newFile(), Charsets.UTF_8, "Test.java", ImmutableMap.of(InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_TEST));
 
     when(fileIndex.inputFiles("foo")).thenReturn(Lists.newArrayList(mainInput, testInput));
 
+    fs.index();
     Iterable<InputFile> inputFiles = fs.inputFiles(FileQuery.onSource());
     assertThat(inputFiles).containsOnly(mainInput);
 
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/DeprecatedFileFiltersTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/DeprecatedFileFiltersTest.java
index 58ba069883d..6fafbb57e20 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/DeprecatedFileFiltersTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/DeprecatedFileFiltersTest.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import com.google.common.collect.ImmutableMap;
 import com.google.common.collect.Maps;
@@ -30,7 +32,6 @@ import org.mockito.ArgumentCaptor;
 import org.sonar.api.scan.filesystem.FileSystemFilter;
 import org.sonar.api.scan.filesystem.FileType;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 
 import java.io.File;
 
@@ -63,8 +64,8 @@ public class DeprecatedFileFiltersTest {
     File basedir = temp.newFolder();
     File file = temp.newFile();
     InputFile inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/Foo.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_SOURCEDIR_PATH, new File(basedir, "src/main/java").getAbsolutePath(),
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "Foo.java",
+      DefaultInputFile.ATTRIBUTE_SOURCEDIR_PATH, new File(basedir, "src/main/java").getAbsolutePath(),
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "Foo.java",
       InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_TEST
 
       ));
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ExclusionFilterTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ExclusionFilterTest.java
index 66c2990ec24..1f2551a119c 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ExclusionFilterTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ExclusionFilterTest.java
@@ -19,13 +19,14 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import com.google.common.collect.ImmutableMap;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 
 import java.io.File;
 
@@ -43,7 +44,7 @@ public class ExclusionFilterTest {
 
     File file = new File(temp.newFolder(), "src/main/java/org/MyFoo.java");
     InputFile inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/org/MyFoo.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "org/MyFoo.java"
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "org/MyFoo.java"
       ));
 
     assertThat(sourceRelativeFilter.accept(inputFile)).isFalse();
@@ -51,7 +52,7 @@ public class ExclusionFilterTest {
 
     file = new File(temp.newFolder(), "src/main/java/org/Other.java");
     inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/org/Other.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "org/Other.java"
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "org/Other.java"
       ));
     assertThat(sourceRelativeFilter.accept(inputFile)).isTrue();
     assertThat(absoluteFilter.accept(inputFile)).isTrue();
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ExclusionFiltersTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ExclusionFiltersTest.java
index 62f844b7aa6..3a8a06a7b6f 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ExclusionFiltersTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ExclusionFiltersTest.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import com.google.common.collect.ImmutableMap;
 import org.junit.Rule;
@@ -31,7 +33,6 @@ import org.sonar.api.resources.JavaFile;
 import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.FileExclusions;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 
 import java.io.IOException;
 
@@ -50,22 +51,22 @@ public class ExclusionFiltersTest {
 
     java.io.File file = temp.newFile();
     InputFile inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/com/mycompany/Foo.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_SOURCE,
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/Foo.java"
+      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_MAIN,
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/Foo.java"
       ));
 
     assertThat(filter.accept(inputFile)).isFalse();
 
     inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/com/mycompany/FooDao.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_SOURCE,
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/FooDao.java"
+      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_MAIN,
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/FooDao.java"
       ));
     assertThat(filter.accept(inputFile)).isTrue();
 
     // source inclusions do not apply to tests
     inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/com/mycompany/Foo.java", ImmutableMap.of(
       InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_TEST,
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/Foo.java"
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/Foo.java"
       ));
     assertThat(filter.accept(inputFile)).isTrue();
   }
@@ -78,15 +79,15 @@ public class ExclusionFiltersTest {
 
     java.io.File file = temp.newFile();
     InputFile inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/com/mycompany/Foo.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_SOURCE,
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/Foo.java"
+      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_MAIN,
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/Foo.java"
       ));
 
     assertThat(filter.accept(inputFile)).isFalse();
 
     inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/com/mycompany/FooDto.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_SOURCE,
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/FooDto.java"
+      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_MAIN,
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/FooDto.java"
       ));
     assertThat(filter.accept(inputFile)).isTrue();
   }
@@ -99,21 +100,21 @@ public class ExclusionFiltersTest {
 
     java.io.File file = temp.newFile();
     InputFile inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/com/mycompany/FooDao.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_SOURCE,
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/FooDao.java"
+      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_MAIN,
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/FooDao.java"
       ));
     assertThat(filter.accept(inputFile)).isFalse();
 
     inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/com/mycompany/Foo.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_SOURCE,
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/Foo.java"
+      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_MAIN,
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/Foo.java"
       ));
     assertThat(filter.accept(inputFile)).isTrue();
 
     // source exclusions do not apply to tests
     inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/com/mycompany/FooDao.java", ImmutableMap.of(
       InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_TEST,
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/FooDao.java"
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "com/mycompany/FooDao.java"
       ));
     assertThat(filter.accept(inputFile)).isTrue();
   }
@@ -128,12 +129,12 @@ public class ExclusionFiltersTest {
     ExclusionFilters filter = new ExclusionFilters(new FileExclusions(settings));
 
     InputFile includedInput = DefaultInputFile.create(includedFile, Charsets.UTF_8, "src/main/java/org/bar/Foo.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_SOURCE
+      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_MAIN
       ));
     assertThat(filter.accept(includedInput)).isTrue();
 
     InputFile excludedInput = DefaultInputFile.create(excludedFile, Charsets.UTF_8, "src/main/java/org/bar/Bar.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_SOURCE
+      InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_MAIN
       ));
     assertThat(filter.accept(excludedInput)).isFalse();
   }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/FileIndexTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/FileIndexTest.java
new file mode 100644
index 00000000000..a72e48f6f7d
--- /dev/null
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/FileIndexTest.java
@@ -0,0 +1,54 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2013 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * SonarQube is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ */
+package org.sonar.batch.scan.filesystem;
+
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import org.sonar.api.resources.Project;
+import org.sonar.api.scan.filesystem.InputDir;
+import org.sonar.api.scan.filesystem.PathResolver;
+import org.sonar.api.scan.filesystem.internal.DefaultInputDir;
+
+import java.io.File;
+
+import static org.fest.assertions.Assertions.assertThat;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+public class FileIndexTest {
+
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
+  @Test
+  public void should_return_inputDir() throws Exception {
+    FileIndex index = new FileIndex(null, null, null, null, new PathResolver(), new Project("myProject"));
+    File baseDir = temp.newFolder();
+    DefaultModuleFileSystem fileSystem = mock(DefaultModuleFileSystem.class);
+    when(fileSystem.baseDir()).thenReturn(baseDir);
+    File ioFile = new File(baseDir, "src/main/java/com/foo");
+    InputDir inputDir = index.inputDir(fileSystem, ioFile);
+
+    assertThat(inputDir.name()).isEqualTo("src/main/java/com/foo");
+    assertThat(inputDir.file()).isEqualTo(ioFile);
+    assertThat(inputDir.attribute(DefaultInputDir.ATTRIBUTE_COMPONENT_KEY)).isEqualTo("myProject:src/main/java/com/foo");
+  }
+}
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/FileQueryFilterTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/FileQueryFilterTest.java
index b7e24b08af6..791ec2f251b 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/FileQueryFilterTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/FileQueryFilterTest.java
@@ -19,13 +19,13 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import org.junit.Before;
 import org.junit.Test;
 import org.sonar.api.scan.filesystem.FileQuery;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.scan.filesystem.internal.InputFileFilter;
 import org.sonar.batch.bootstrap.AnalysisMode;
-
 import static org.fest.assertions.Assertions.assertThat;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
@@ -48,7 +48,7 @@ public class FileQueryFilterTest {
     InputFileFilter typeFilter = filter.filters().get(0);
     assertThat(typeFilter).isInstanceOf(AttributeFilter.class);
     assertThat(((AttributeFilter) typeFilter).key()).isEqualTo(InputFile.ATTRIBUTE_TYPE);
-    assertThat(((AttributeFilter) typeFilter).values()).containsOnly(InputFile.TYPE_SOURCE);
+    assertThat(((AttributeFilter) typeFilter).values()).containsOnly(InputFile.TYPE_MAIN);
   }
 
   @Test
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InclusionFilterTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InclusionFilterTest.java
index cd76e714c66..a8ce2a9194d 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InclusionFilterTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InclusionFilterTest.java
@@ -19,13 +19,14 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import com.google.common.collect.ImmutableMap;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 
 import java.io.File;
 
@@ -42,7 +43,7 @@ public class InclusionFilterTest {
 
     File file = new File(temp.newFolder(), "src/main/java/org/MyFoo.java");
     InputFile inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/org/MyFoo.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "org/MyFoo.java"
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "org/MyFoo.java"
       ));
 
     assertThat(sourceRelativeFilter.accept(inputFile)).isTrue();
@@ -50,7 +51,7 @@ public class InclusionFilterTest {
 
     file = new File(temp.newFolder(), "src/main/java/org/Other.java");
     inputFile = DefaultInputFile.create(file, Charsets.UTF_8, "src/main/java/org/Other.java", ImmutableMap.of(
-      InputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "org/Other.java"
+      DefaultInputFile.ATTRIBUTE_SOURCE_RELATIVE_PATH, "org/Other.java"
       ));
     assertThat(sourceRelativeFilter.accept(inputFile)).isFalse();
     assertThat(absoluteFilter.accept(inputFile)).isFalse();
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileCacheTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileCacheTest.java
index 50635adc091..a829e350f3c 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileCacheTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileCacheTest.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import com.google.common.collect.Maps;
 import org.junit.After;
@@ -27,10 +29,8 @@ import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
 import org.sonar.api.scan.filesystem.internal.DefaultInputFile;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.batch.index.Caches;
 import org.sonar.batch.index.CachesTest;
-
 import static org.fest.assertions.Assertions.assertThat;
 
 public class InputFileCacheTest {
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageRecognizerTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageRecognizerTest.java
index dad6ae8e240..9d4e8e99689 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageRecognizerTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageRecognizerTest.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import org.hamcrest.BaseMatcher;
 import org.hamcrest.Description;
@@ -30,7 +32,6 @@ import org.sonar.api.CoreProperties;
 import org.sonar.api.config.Settings;
 import org.sonar.api.resources.Language;
 import org.sonar.api.resources.Languages;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 import org.sonar.api.scan.filesystem.internal.InputFileBuilder;
 import org.sonar.api.utils.SonarException;
 
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/batch/SensorContext.java b/sonar-plugin-api/src/main/java/org/sonar/api/batch/SensorContext.java
index 23a02fd333a..90a2179dca4 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/batch/SensorContext.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/batch/SensorContext.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.api.batch;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import org.sonar.api.design.Dependency;
 import org.sonar.api.measures.Measure;
 import org.sonar.api.measures.MeasuresFilter;
@@ -26,7 +28,6 @@ import org.sonar.api.measures.Metric;
 import org.sonar.api.resources.ProjectLink;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.rules.Violation;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 
 import java.util.Collection;
 import java.util.Date;
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/FileQuery.java b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/FileQuery.java
index 95dbfb0cf12..c29b31683b6 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/FileQuery.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/FileQuery.java
@@ -25,7 +25,6 @@ import com.google.common.collect.Collections2;
 import com.google.common.collect.ListMultimap;
 import com.google.common.collect.Sets;
 import org.apache.commons.lang.builder.EqualsBuilder;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 
 import javax.annotation.Nullable;
 
@@ -44,6 +43,10 @@ public class FileQuery {
   private final Set<String> inclusions = Sets.newHashSet();
   private final Set<String> exclusions = Sets.newHashSet();
 
+  /**
+   * @deprecated since 4.2 use {@link #onMain()} or {@link #onTest()}
+   */
+  @Deprecated
   public static FileQuery on(FileType... types) {
     FileQuery query = new FileQuery();
     for (FileType type : types) {
@@ -59,12 +62,25 @@ public class FileQuery {
     return on();
   }
 
+  /**
+   * @deprecated since 4.2 use {@link #onMain()}
+   */
+  @Deprecated
   public static FileQuery onSource() {
-    return on(FileType.SOURCE);
+    return onMain();
+  }
+
+  /**
+   * @since 4.2
+   */
+  public static FileQuery onMain() {
+    FileQuery query = new FileQuery();
+    return query.on(InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_MAIN);
   }
 
   public static FileQuery onTest() {
-    return on(FileType.TEST);
+    FileQuery query = new FileQuery();
+    return query.on(InputFile.ATTRIBUTE_TYPE, InputFile.TYPE_TEST);
   }
 
   private FileQuery() {
@@ -81,6 +97,10 @@ public class FileQuery {
     return attributes.asMap();
   }
 
+  /**
+   * @deprecated since 4.2 use {@link #typeAttributes()}
+   */
+  @Deprecated
   public Collection<FileType> types() {
     return Collections2.transform(attributes.get(InputFile.ATTRIBUTE_TYPE), new Function<String, FileType>() {
       @Override
@@ -90,6 +110,10 @@ public class FileQuery {
     });
   }
 
+  public Collection<String> typeAttributes() {
+    return attributes.get(InputFile.ATTRIBUTE_TYPE);
+  }
+
   public Collection<String> languages() {
     return attributes.get(InputFile.ATTRIBUTE_LANGUAGE);
   }
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/FileType.java b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/FileType.java
index 6600ae2099a..31e5581db18 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/FileType.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/FileType.java
@@ -21,7 +21,9 @@ package org.sonar.api.scan.filesystem;
 
 /**
  * @since 3.5
+ * @deprecated since 4.2 use {@link InputFile#TYPE_MAIN} or {@link InputFile#TYPE_TEST}
  */
+@Deprecated
 public enum FileType {
   SOURCE, TEST
 }
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/InputDir.java b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/InputDir.java
new file mode 100644
index 00000000000..ae755fc7ab0
--- /dev/null
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/InputDir.java
@@ -0,0 +1,70 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2013 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.scan.filesystem;
+
+import javax.annotation.CheckForNull;
+
+import java.io.File;
+import java.io.Serializable;
+import java.util.Map;
+
+/**
+ * @since 4.2
+ */
+public interface InputDir extends Serializable {
+
+  /**
+   * Path is relative from module base directory. Path is unique and identifies file
+   * within given <code>{@link org.sonar.api.scan.filesystem.ModuleFileSystem}</code>.
+   * File separator is the forward slash ('/'), even on MSWindows.
+   * <p/>
+   * Returns <code>src/main/java/com</code> if module base dir is
+   * <code>/absolute/path/to/module</code> and if directory is
+   * <code>/absolute/path/to/module/src/main/java/com</code>.
+   * <p/>
+   * Returned path is never null.
+   */
+  String path();
+
+  /**
+   * Not-null canonical path. File separator is forward slash ('/'), even on MSWindows.
+   */
+  String absolutePath();
+
+  File file();
+
+  /**
+   * Not-null directory name
+   */
+  String name();
+
+  /**
+   * Does the given attribute have the given value ?
+   */
+  boolean has(String attribute, String value);
+
+  /**
+   * See list of attribute keys in constants starting with ATTRIBUTE_.
+   */
+  @CheckForNull
+  String attribute(String key);
+
+  Map<String, String> attributes();
+}
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFile.java b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/InputFile.java
index 0503db1dffd..91ed1c144c1 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFile.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/InputFile.java
@@ -17,7 +17,7 @@
  * 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.scan.filesystem.internal;
+package org.sonar.api.scan.filesystem;
 
 import javax.annotation.CheckForNull;
 
@@ -29,31 +29,15 @@ import java.util.Map;
 public interface InputFile extends Serializable {
 
   /**
-   * Canonical path of source directory.
-   * Example: <code>/path/to/module/src/main/java</code> or <code>C:\path\to\module\src\main\java</code>
-   * @deprecated since 4.2 No more sonar.sources
-   */
-  @Deprecated
-  String ATTRIBUTE_SOURCEDIR_PATH = "SRC_DIR_PATH";
-
-  /**
-   * Relative path from source directory. File separator is the forward slash ('/'),
-   * even on MSWindows.
-   * @deprecated since 4.2 No more sonar.sources
-   */
-  @Deprecated
-  String ATTRIBUTE_SOURCE_RELATIVE_PATH = "SRC_REL_PATH";
-
-  /**
    * Detected language
    */
   String ATTRIBUTE_LANGUAGE = "LANG";
 
   /**
-   *
+   * Type of source file. For now only possible values are {@link #TYPE_MAIN} or {@link #TYPE_TEST}
    */
   String ATTRIBUTE_TYPE = "TYPE";
-  String TYPE_SOURCE = "SOURCE";
+  String TYPE_MAIN = "MAIN";
   String TYPE_TEST = "TEST";
 
   String ATTRIBUTE_STATUS = "STATUS";
@@ -61,8 +45,6 @@ public interface InputFile extends Serializable {
   String STATUS_CHANGED = "CHANGED";
   String STATUS_ADDED = "ADDED";
 
-  String ATTRIBUTE_HASH = "HASH";
-
   /**
    * Path is relative from module base directory. Path is unique and identifies file
    * within given <code>{@link org.sonar.api.scan.filesystem.ModuleFileSystem}</code>.
@@ -91,8 +73,8 @@ public interface InputFile extends Serializable {
   String name();
 
   /**
-   * Not-null type (is it a source file or a unit test file?).
-   * See constant values prefixed by <code>TYPE_</code>, for example {@link #TYPE_SOURCE}.
+   * Not-null type (is it a main file or a unit test file?).
+   * See constant values prefixed by <code>TYPE_</code>, for example {@link #TYPE_MAIN}.
    */
   String type();
 
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 3a055f15112..9ab95321f14 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
@@ -22,6 +22,7 @@ package org.sonar.api.scan.filesystem;
 import org.sonar.api.BatchComponent;
 
 import javax.annotation.CheckForNull;
+
 import java.io.File;
 import java.nio.charset.Charset;
 import java.util.List;
@@ -46,13 +47,17 @@ public interface ModuleFileSystem extends BatchComponent {
   /**
    * Source directories. Non-existing directories are excluded.
    * Example in Maven : ${project.basedir}/src/main/java
+   * @deprecated since 4.2 will always return {@link #baseDir()}
    */
+  @Deprecated
   List<File> sourceDirs();
 
   /**
    * Test directories. Non-existing directories are excluded.
    * Example in Maven : ${project.basedir}/src/test/java
+   * @deprecated since 4.2 will always return {@link #baseDir()}
    */
+  @Deprecated
   List<File> testDirs();
 
   /**
@@ -63,17 +68,42 @@ public interface ModuleFileSystem extends BatchComponent {
    * <li>Binary directories can be empty</li>
    * <li>Test binary directories are not supported yet.</li>
    * </ul>
+   * @deprecated since 4.2 sonar.binaries should be converted to language specific property
    */
+  @Deprecated
   List<File> binaryDirs();
 
   /**
    * Search for files. Never return null.
+   * @deprecated since 4.2 use {@link #inputFiles(FileQuery)}
    */
+  @Deprecated
   List<File> files(FileQuery query);
 
   /**
-   * Charset of source and test files. If it's not defined, then
-   * return the platform default charset.
+   * Search for input files. Never return null.
+   * @since 4.2
+   */
+  Iterable<InputFile> inputFiles(FileQuery query);
+
+  /**
+   * Search for input file corresponding to the given java.io.File.
+   * @since 4.2
+   */
+  @CheckForNull
+  InputFile inputFile(File ioFile);
+
+  /**
+   * Search for input directory corresponding to the given java.io.File.
+   * @since 4.2
+   */
+  @CheckForNull
+  InputDir inputDir(File ioFile);
+
+  /**
+   * Default charset for files of the module. If it's not defined, then
+   * return the platform default charset. When trying to read an input file it is better to rely on
+   * {@link InputFile#encoding()} as encoding may be different for each file.
    */
   Charset sourceCharset();
 
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/DefaultInputDir.java b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/DefaultInputDir.java
new file mode 100644
index 00000000000..2e83b122d02
--- /dev/null
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/DefaultInputDir.java
@@ -0,0 +1,119 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2013 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.scan.filesystem.internal;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.lang.StringUtils;
+import org.sonar.api.scan.filesystem.InputDir;
+import org.sonar.api.utils.PathUtils;
+
+import javax.annotation.CheckForNull;
+
+import java.io.File;
+import java.util.Map;
+
+/**
+ * PLUGINS MUST NOT USE THIS CLASS, EVEN FOR UNIT TESTING.
+ *
+ * @since 4.2
+ */
+public class DefaultInputDir implements InputDir {
+
+  /**
+   * We're not sure that this is the correct way, so not in API yet.
+   */
+  public static final String ATTRIBUTE_COMPONENT_KEY = "CMP_KEY";
+
+  private final String absolutePath;
+  private final String path;
+  private final Map<String, String> attributes;
+
+  private DefaultInputDir(File file, String path, Map<String, String> attributes) {
+    this.absolutePath = PathUtils.canonicalPath(file);
+    this.path = FilenameUtils.separatorsToUnix(path);
+    this.attributes = attributes;
+  }
+
+  /**
+   * Plugins must not build their own instances of {@link InputDir}.
+   * {@link org.sonar.api.scan.filesystem.ModuleFileSystem} must be used to search for inputDir.
+   */
+  public static DefaultInputDir create(File file, String path, Map<String, String> attributes) {
+    return new DefaultInputDir(file, path, attributes);
+  }
+
+  @Override
+  public String path() {
+    return path;
+  }
+
+  @Override
+  public String absolutePath() {
+    return absolutePath;
+  }
+
+  @Override
+  public File file() {
+    return new File(absolutePath);
+  }
+
+  @Override
+  public String name() {
+    return path();
+  }
+
+  @Override
+  public boolean has(String attribute, String value) {
+    return StringUtils.equals(attributes.get(attribute), value);
+  }
+
+  @Override
+  @CheckForNull
+  public String attribute(String key) {
+    return attributes.get(key);
+  }
+
+  @Override
+  public Map<String, String> attributes() {
+    return attributes;
+  }
+
+  @Override
+  public boolean equals(Object o) {
+    if (this == o) {
+      return true;
+    }
+    if (o == null || getClass() != o.getClass()) {
+      return false;
+    }
+    DefaultInputDir other = (DefaultInputDir) o;
+    return absolutePath.equals(other.absolutePath);
+  }
+
+  @Override
+  public int hashCode() {
+    return absolutePath.hashCode();
+  }
+
+  @Override
+  public String toString() {
+    return String.format("[%s]", path);
+  }
+}
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/DefaultInputFile.java b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/DefaultInputFile.java
index 43024fdf860..e8ea24e1715 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/DefaultInputFile.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/DefaultInputFile.java
@@ -22,6 +22,7 @@ package org.sonar.api.scan.filesystem.internal;
 import org.apache.commons.codec.Charsets;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.lang.StringUtils;
+import org.sonar.api.scan.filesystem.InputFile;
 import org.sonar.api.utils.PathUtils;
 
 import javax.annotation.CheckForNull;
@@ -44,6 +45,24 @@ public class DefaultInputFile implements InputFile {
 
   public static final String ATTRIBUTE_COMPONENT_DEPRECATED_KEY = "CMP_DEPRECATED_KEY";
 
+  public static final String ATTRIBUTE_HASH = "HASH";
+
+  /**
+   * Relative path from source directory. File separator is the forward slash ('/'),
+   * even on MSWindows.
+   * @deprecated since 4.2 No more sonar.sources
+   */
+  @Deprecated
+  public static final String ATTRIBUTE_SOURCE_RELATIVE_PATH = "SRC_REL_PATH";
+
+  /**
+   * Canonical path of source directory.
+   * Example: <code>/path/to/module/src/main/java</code> or <code>C:\path\to\module\src\main\java</code>
+   * @deprecated since 4.2 No more sonar.sources
+   */
+  @Deprecated
+  public static final String ATTRIBUTE_SOURCEDIR_PATH = "SRC_DIR_PATH";
+
   private final String absolutePath;
   private final String path;
   private final Map<String, String> attributes;
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFileBuilder.java b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFileBuilder.java
index 0c57f806285..d7e2d730fbe 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFileBuilder.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFileBuilder.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.api.scan.filesystem.internal;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import org.sonar.api.utils.PathUtils;
 
 import javax.annotation.Nullable;
@@ -66,7 +68,7 @@ public class InputFileBuilder {
   }
 
   public InputFileBuilder hash(@Nullable String hash) {
-    return attribute(InputFile.ATTRIBUTE_HASH, hash);
+    return attribute(DefaultInputFile.ATTRIBUTE_HASH, hash);
   }
 
   public InputFileBuilder status(@Nullable String status) {
@@ -74,11 +76,11 @@ public class InputFileBuilder {
   }
 
   public InputFileBuilder sourceDir(File dir) {
-    return attribute(InputFile.ATTRIBUTE_SOURCEDIR_PATH, PathUtils.canonicalPath(dir));
+    return attribute(DefaultInputFile.ATTRIBUTE_SOURCEDIR_PATH, PathUtils.canonicalPath(dir));
   }
 
   public InputFileBuilder sourceDir(@Nullable String path) {
-    return attribute(InputFile.ATTRIBUTE_SOURCEDIR_PATH, PathUtils.sanitize(path));
+    return attribute(DefaultInputFile.ATTRIBUTE_SOURCEDIR_PATH, PathUtils.sanitize(path));
   }
 
   public DefaultInputFile build() {
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFileFilter.java b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFileFilter.java
index e48880d58d5..d9c9adc8374 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFileFilter.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFileFilter.java
@@ -19,8 +19,9 @@
  */
 package org.sonar.api.scan.filesystem.internal;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import org.sonar.api.BatchExtension;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 
 /**
  * TODO document lifecycle -> executed when initializing project
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFiles.java b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFiles.java
index f6272e24a99..923cd32b133 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFiles.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/scan/filesystem/internal/InputFiles.java
@@ -19,8 +19,9 @@
  */
 package org.sonar.api.scan.filesystem.internal;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.collect.Lists;
-import org.sonar.api.scan.filesystem.internal.InputFile;
 
 import java.io.File;
 import java.util.List;
diff --git a/sonar-plugin-api/src/test/java/org/sonar/api/scan/filesystem/internal/DefaultInputFileTest.java b/sonar-plugin-api/src/test/java/org/sonar/api/scan/filesystem/internal/DefaultInputFileTest.java
index d62a24aab72..a8346a0ccd3 100644
--- a/sonar-plugin-api/src/test/java/org/sonar/api/scan/filesystem/internal/DefaultInputFileTest.java
+++ b/sonar-plugin-api/src/test/java/org/sonar/api/scan/filesystem/internal/DefaultInputFileTest.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.api.scan.filesystem.internal;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import org.apache.commons.io.FilenameUtils;
 import org.junit.Rule;
@@ -51,7 +53,7 @@ public class DefaultInputFileTest {
     assertThat(input.attribute("unknown")).isNull();
     assertThat(input.attribute("foo")).isEqualTo("bar");
     assertThat(input.attribute(InputFile.ATTRIBUTE_TYPE)).isEqualTo(InputFile.TYPE_TEST);
-    assertThat(input.attribute(InputFile.ATTRIBUTE_HASH)).isEqualTo("ABC");
+    assertThat(input.attribute(DefaultInputFile.ATTRIBUTE_HASH)).isEqualTo("ABC");
     assertThat(input.attribute(InputFile.ATTRIBUTE_LANGUAGE)).isEqualTo("java");
     assertThat(input.attribute(InputFile.ATTRIBUTE_STATUS)).isEqualTo(InputFile.STATUS_ADDED);
 
@@ -70,7 +72,7 @@ public class DefaultInputFileTest {
 
     assertThat(input.name()).isEqualTo("Foo.java");
     assertThat(input.file()).isEqualTo(file);
-    assertThat(input.attribute(InputFile.ATTRIBUTE_SOURCEDIR_PATH)).isEqualTo(FilenameUtils.separatorsToUnix(sourceDir.getAbsolutePath()));
+    assertThat(input.attribute(DefaultInputFile.ATTRIBUTE_SOURCEDIR_PATH)).isEqualTo(FilenameUtils.separatorsToUnix(sourceDir.getAbsolutePath()));
     assertThat(input.path()).isEqualTo("src/main/java/Foo.java");
     assertThat(input.absolutePath()).isEqualTo(PathUtils.canonicalPath(file));
   }
diff --git a/sonar-plugin-api/src/test/java/org/sonar/api/scan/filesystem/internal/InputFilesTest.java b/sonar-plugin-api/src/test/java/org/sonar/api/scan/filesystem/internal/InputFilesTest.java
index c56dc617721..f0b522be7c5 100644
--- a/sonar-plugin-api/src/test/java/org/sonar/api/scan/filesystem/internal/InputFilesTest.java
+++ b/sonar-plugin-api/src/test/java/org/sonar/api/scan/filesystem/internal/InputFilesTest.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.api.scan.filesystem.internal;
 
+import org.sonar.api.scan.filesystem.InputFile;
+
 import com.google.common.base.Charsets;
 import com.google.common.collect.Lists;
 import org.junit.Rule;