SONAR-6134, SONAR-6048 Improve performance of FS indexation

74 files changed, 362 insertions, 421 deletions

diff --git a/sonar-batch/src/test/java/org/sonar/batch/DefaultFileLinesContextTest.java b/sonar-batch/src/test/java/org/sonar/batch/DefaultFileLinesContextTest.java
index 9bf9dc201d4..e85e6003c2f 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/DefaultFileLinesContextTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/DefaultFileLinesContextTest.java
@@ -57,7 +57,7 @@ public class DefaultFileLinesContextTest {
 
   @Test(expected = IllegalArgumentException.class)
   public void shouldNotAllowCreationForDirectory() {
-    new DefaultFileLinesContext(index, new Directory("key"));
+    new DefaultFileLinesContext(index, Directory.create("key"));
   }
 
   @Test
diff --git a/sonar-batch/src/test/java/org/sonar/batch/components/PastMeasuresLoaderTest.java b/sonar-batch/src/test/java/org/sonar/batch/components/PastMeasuresLoaderTest.java
index 4be6293c27a..d032e2b1cd1 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/components/PastMeasuresLoaderTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/components/PastMeasuresLoaderTest.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.components;
 
+import org.sonar.batch.components.PastMeasuresLoader;
+
 import org.junit.Test;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.measures.Metric;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderTest.java b/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderTest.java
index c335d3b87d6..f712b04dbc4 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderTest.java
@@ -19,6 +19,12 @@
  */
 package org.sonar.batch.components;
 
+import org.sonar.batch.components.PastSnapshotFinder;
+import org.sonar.batch.deprecated.components.PastSnapshotFinderByDate;
+import org.sonar.batch.deprecated.components.PastSnapshotFinderByDays;
+import org.sonar.batch.deprecated.components.PastSnapshotFinderByPreviousAnalysis;
+import org.sonar.batch.deprecated.components.PastSnapshotFinderByPreviousVersion;
+import org.sonar.batch.deprecated.components.PastSnapshotFinderByVersion;
 import org.junit.Before;
 import org.junit.Test;
 import org.mockito.ArgumentMatcher;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotTest.java b/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotTest.java
index 3d38431f780..201155b1188 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotTest.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.components;
 
+import org.sonar.batch.components.PastSnapshot;
+
 import org.junit.Test;
 import org.sonar.api.CoreProperties;
 import org.sonar.api.database.model.Snapshot;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/components/TimeMachineConfigurationTest.java b/sonar-batch/src/test/java/org/sonar/batch/components/TimeMachineConfigurationTest.java
index 023690acdbd..eae7b0f8377 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/components/TimeMachineConfigurationTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/components/TimeMachineConfigurationTest.java
@@ -19,6 +19,10 @@
  */
 package org.sonar.batch.components;
 
+import org.sonar.batch.components.TimeMachineConfiguration;
+
+import org.sonar.batch.components.PastSnapshot;
+import org.sonar.batch.deprecated.components.PeriodsDefinition;
 import org.junit.Before;
 import org.junit.Test;
 import org.sonar.api.database.model.Snapshot;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/debt/DebtDecoratorTest.java b/sonar-batch/src/test/java/org/sonar/batch/debt/DebtDecoratorTest.java
index 945a3d7614b..7cb4b47c1c5 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/debt/DebtDecoratorTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/debt/DebtDecoratorTest.java
@@ -247,7 +247,7 @@ public class DebtDecoratorTest {
 
     // or for a file
     context = mock(DecoratorContext.class);
-    when(context.getResource()).thenReturn(new File("foo"));
+    when(context.getResource()).thenReturn(File.create("foo"));
     decorator.saveCharacteristicMeasure(context, (Characteristic) null, 12.0, false);
     verify(context, times(1)).saveMeasure(new Measure(CoreMetrics.TECHNICAL_DEBT));
   }
@@ -282,7 +282,7 @@ public class DebtDecoratorTest {
   @Test
   public void not_save_technical_debt_for_file_if_zero() throws Exception {
     DecoratorContext context = mock(DecoratorContext.class);
-    when(context.getResource()).thenReturn(new File("foo"));
+    when(context.getResource()).thenReturn(File.create("foo"));
 
     decorator.saveCharacteristicMeasure(context, null, 0.0, true);
     verify(context, never()).saveMeasure(new Measure(CoreMetrics.TECHNICAL_DEBT));
diff --git a/sonar-batch/src/test/java/org/sonar/batch/debt/NewDebtDecoratorTest.java b/sonar-batch/src/test/java/org/sonar/batch/debt/NewDebtDecoratorTest.java
index 0bb25ad1d82..c930eb1075e 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/debt/NewDebtDecoratorTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/debt/NewDebtDecoratorTest.java
@@ -20,6 +20,9 @@
 
 package org.sonar.batch.debt;
 
+import org.sonar.batch.components.TimeMachineConfiguration;
+
+import org.sonar.batch.deprecated.components.Period;
 import org.apache.commons.lang.ObjectUtils;
 import org.apache.commons.lang.time.DateUtils;
 import org.junit.Before;
@@ -42,8 +45,6 @@ import org.sonar.api.measures.Metric;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.test.IsMeasure;
 import org.sonar.api.utils.Duration;
-import org.sonar.batch.components.Period;
-import org.sonar.batch.components.TimeMachineConfiguration;
 import org.sonar.batch.debt.IssueChangelogDebtCalculator;
 import org.sonar.batch.debt.NewDebtDecorator;
 
diff --git a/sonar-batch/src/test/java/org/sonar/batch/debt/SqaleRatingDecoratorTest.java b/sonar-batch/src/test/java/org/sonar/batch/debt/SqaleRatingDecoratorTest.java
index 0caa8cf219e..79ce075a097 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/debt/SqaleRatingDecoratorTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/debt/SqaleRatingDecoratorTest.java
@@ -73,10 +73,9 @@ public class SqaleRatingDecoratorTest {
   public void setUp() throws Exception {
     settings = new Settings();
 
-    fs = new DefaultFileSystem(temp.newFolder());
+    fs = new DefaultFileSystem(temp.newFolder().toPath());
     fs.add(new DefaultInputFile("foo", file.getPath())
-      .setLanguage("java")
-      .setFile(temp.newFile("Foo.java")));
+      .setLanguage("java"));
 
     decorator = new SqaleRatingDecorator(new SqaleRatingSettings(settings), metrics, fs);
   }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/ResourceFiltersTest.java b/sonar-batch/src/test/java/org/sonar/batch/deprecated/ResourceFiltersTest.java
index 602b6c7dd42..c93334474b2 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/ResourceFiltersTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/deprecated/ResourceFiltersTest.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.batch;
+package org.sonar.batch.deprecated;
 
 import org.junit.Test;
 import org.slf4j.Logger;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderByDateTest.java b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByDateTest.java
index 7abd043f62b..2cf8b317531 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderByDateTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByDateTest.java
@@ -17,8 +17,11 @@
  * 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.components;
+package org.sonar.batch.deprecated.components;
 
+import org.sonar.batch.components.PastSnapshot;
+
+import org.sonar.batch.deprecated.components.PastSnapshotFinderByDate;
 import org.junit.Test;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.jpa.test.AbstractDbUnitTestCase;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderByDaysTest.java b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByDaysTest.java
index 1b136e9ae72..0515b30673d 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderByDaysTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByDaysTest.java
@@ -17,7 +17,9 @@
  * 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.components;
+package org.sonar.batch.deprecated.components;
+
+import org.sonar.batch.deprecated.components.PastSnapshotFinderByDays;
 
 import org.hamcrest.core.IsNull;
 import org.junit.Test;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderByPreviousAnalysisTest.java b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousAnalysisTest.java
index a2c0d82e301..9ec2024b7d4 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderByPreviousAnalysisTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousAnalysisTest.java
@@ -17,12 +17,14 @@
  * 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.components;
+package org.sonar.batch.deprecated.components;
 
+import org.sonar.batch.components.PastSnapshot;
+
+import org.sonar.batch.deprecated.components.PastSnapshotFinderByPreviousAnalysis;
 import org.junit.Test;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.jpa.test.AbstractDbUnitTestCase;
-
 import static org.hamcrest.Matchers.is;
 import static org.hamcrest.core.IsNull.nullValue;
 import static org.junit.Assert.assertThat;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderByPreviousVersionTest.java b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousVersionTest.java
index da160c87a4f..d932060914a 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderByPreviousVersionTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousVersionTest.java
@@ -17,13 +17,15 @@
  * 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.components;
+package org.sonar.batch.deprecated.components;
 
+import org.sonar.batch.components.PastSnapshot;
+
+import org.sonar.batch.deprecated.components.PastSnapshotFinderByPreviousVersion;
 import org.junit.Test;
 import org.sonar.api.CoreProperties;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.jpa.test.AbstractDbUnitTestCase;
-
 import static org.assertj.core.api.Assertions.assertThat;
 
 public class PastSnapshotFinderByPreviousVersionTest extends AbstractDbUnitTestCase {
diff --git a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderByVersionTest.java b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByVersionTest.java
index b35f4b8990b..5d8c87ad7f0 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/components/PastSnapshotFinderByVersionTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByVersionTest.java
@@ -17,13 +17,15 @@
  * 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.components;
+package org.sonar.batch.deprecated.components;
 
+import org.sonar.batch.components.PastSnapshot;
+
+import org.sonar.batch.deprecated.components.PastSnapshotFinderByVersion;
 import org.junit.Test;
 import org.sonar.api.CoreProperties;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.jpa.test.AbstractDbUnitTestCase;
-
 import static org.assertj.core.api.Assertions.assertThat;
 
 public class PastSnapshotFinderByVersionTest extends AbstractDbUnitTestCase {
diff --git a/sonar-batch/src/test/java/org/sonar/batch/components/PeriodsDefinitionTest.java b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PeriodsDefinitionTest.java
index 7483d54cf23..425ce9e4e89 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/components/PeriodsDefinitionTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/deprecated/components/PeriodsDefinitionTest.java
@@ -18,8 +18,11 @@
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
 
-package org.sonar.batch.components;
+package org.sonar.batch.deprecated.components;
 
+import org.sonar.batch.components.PastSnapshotFinder;
+
+import org.sonar.batch.deprecated.components.PeriodsDefinition;
 import org.junit.Before;
 import org.junit.Test;
 import org.mockito.ArgumentMatcher;
@@ -28,7 +31,6 @@ import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.resources.Project;
 import org.sonar.batch.ProjectTree;
 import org.sonar.jpa.test.AbstractDbUnitTestCase;
-
 import static org.mockito.Matchers.anyString;
 import static org.mockito.Matchers.argThat;
 import static org.mockito.Matchers.eq;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/DecoratorsSelectorTest.java b/sonar-batch/src/test/java/org/sonar/batch/deprecated/decorator/DecoratorsSelectorTest.java
index 8a0e9a24764..f469d6b52e9 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/DecoratorsSelectorTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/deprecated/decorator/DecoratorsSelectorTest.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.batch;
+package org.sonar.batch.deprecated.decorator;
 
 import com.google.common.collect.Iterables;
 import org.junit.Test;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/FormulaDecoratorTest.java b/sonar-batch/src/test/java/org/sonar/batch/deprecated/decorator/FormulaDecoratorTest.java
index ff5fdc5d159..4507ab8cbc0 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/FormulaDecoratorTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/deprecated/decorator/FormulaDecoratorTest.java
@@ -17,7 +17,9 @@
  * 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;
+package org.sonar.batch.deprecated.decorator;
+
+import org.sonar.batch.deprecated.decorator.FormulaDecorator;
 
 import org.junit.Test;
 import org.sonar.api.batch.DecoratorContext;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/tasks/ListTaskTest.java b/sonar-batch/src/test/java/org/sonar/batch/deprecated/tasks/ListTaskTest.java
index 923af5177e5..2812b4d28cf 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/tasks/ListTaskTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/deprecated/tasks/ListTaskTest.java
@@ -17,7 +17,10 @@
  * 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.tasks;
+package org.sonar.batch.deprecated.tasks;
+
+import org.sonar.batch.deprecated.tasks.ListTask;
+import org.sonar.batch.deprecated.tasks.Tasks;
 
 import org.junit.Test;
 import org.sonar.api.task.Task;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/tasks/TasksTest.java b/sonar-batch/src/test/java/org/sonar/batch/deprecated/tasks/TasksTest.java
index 5c4315890c2..51f6eb1c53b 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/tasks/TasksTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/deprecated/tasks/TasksTest.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.batch.tasks;
+package org.sonar.batch.deprecated.tasks;
 
 import org.junit.Rule;
 import org.junit.Test;
@@ -36,20 +36,20 @@ public class TasksTest {
 
   @Test
   public void should_get_definitions() {
-    Tasks tasks = new Tasks(new TaskDefinition[]{ScanTask.DEFINITION, ListTask.DEFINITION});
+    Tasks tasks = new Tasks(new TaskDefinition[] {ScanTask.DEFINITION, ListTask.DEFINITION});
     assertThat(tasks.definitions()).hasSize(2);
   }
 
   @Test
   public void should_get_definition_by_key() {
-    Tasks tasks = new Tasks(new TaskDefinition[]{ScanTask.DEFINITION, ListTask.DEFINITION});
+    Tasks tasks = new Tasks(new TaskDefinition[] {ScanTask.DEFINITION, ListTask.DEFINITION});
     tasks.start();
     assertThat(tasks.definition(ListTask.DEFINITION.key())).isEqualTo(ListTask.DEFINITION);
   }
 
   @Test
   public void should_return_null_if_task_not_found() {
-    Tasks tasks = new Tasks(new TaskDefinition[]{ScanTask.DEFINITION, ListTask.DEFINITION});
+    Tasks tasks = new Tasks(new TaskDefinition[] {ScanTask.DEFINITION, ListTask.DEFINITION});
 
     assertThat(tasks.definition("not-exists")).isNull();
   }
@@ -59,7 +59,7 @@ public class TasksTest {
     thrown.expect(SonarException.class);
     thrown.expectMessage("Task 'foo' is declared twice");
 
-    new Tasks(new TaskDefinition[]{
+    new Tasks(new TaskDefinition[] {
       TaskDefinition.builder().key("foo").taskClass(FakeTask1.class).description("foo1").build(),
       TaskDefinition.builder().key("foo").taskClass(FakeTask2.class).description("foo2").build()
     });
@@ -67,13 +67,13 @@ public class TasksTest {
 
   @Test
   public void should_fail_on_duplicated_class() {
-    Tasks tasks = new Tasks(new TaskDefinition[]{
+    Tasks tasks = new Tasks(new TaskDefinition[] {
       TaskDefinition.builder().key("foo1").taskClass(FakeTask1.class).description("foo1").build(),
       TaskDefinition.builder().key("foo2").taskClass(FakeTask1.class).description("foo1").build()
     });
 
     thrown.expect(SonarException.class);
-    thrown.expectMessage("Task 'org.sonar.batch.tasks.TasksTest$FakeTask1' is defined twice: first by 'foo1' and then by 'foo2'");
+    thrown.expectMessage("Task 'org.sonar.batch.deprecated.tasks.TasksTest$FakeTask1' is defined twice: first by 'foo1' and then by 'foo2'");
 
     tasks.start();
   }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/design/DirectoryDsmDecoratorTest.java b/sonar-batch/src/test/java/org/sonar/batch/design/DirectoryDsmDecoratorTest.java
index 598bf4d6f88..fa3ceecc3a5 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/design/DirectoryDsmDecoratorTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/design/DirectoryDsmDecoratorTest.java
@@ -65,9 +65,9 @@ public class DirectoryDsmDecoratorTest {
     dir = Directory.create("src");
     dirContext = mock(DecoratorContext.class);
 
-    file1 = File.create("src/Foo1.java", "Foo1.java", null, false);
+    file1 = File.create("src/Foo1.java", null, false);
     file1.setId(1);
-    file2 = File.create("src/Foo2.java", "Foo2.java", null, false);
+    file2 = File.create("src/Foo2.java", null, false);
     file2.setId(2);
 
     file1Context = mock(DecoratorContext.class);
diff --git a/sonar-batch/src/test/java/org/sonar/batch/design/DsmSerializerTest.java b/sonar-batch/src/test/java/org/sonar/batch/design/DsmSerializerTest.java
index 24d949d000c..5d9b0b508ef 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/design/DsmSerializerTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/design/DsmSerializerTest.java
@@ -43,8 +43,8 @@ public class DsmSerializerTest {
 
   @Test
   public void serialize() throws IOException {
-    Resource foo = Directory.create("src/org/foo", "org/foo").setId(7);
-    Resource bar = Directory.create("src/org/bar", "org/bar").setId(8);
+    Resource foo = Directory.create("src/org/foo").setId(7);
+    Resource bar = Directory.create("src/org/bar").setId(8);
     Dependency dep = new Dependency(foo, bar).setId(30l).setWeight(1);
 
     DirectedGraph<Resource, Dependency> graph = new DirectedGraph<Resource, Dependency>();
diff --git a/sonar-batch/src/test/java/org/sonar/batch/design/SubProjectDsmDecoratorTest.java b/sonar-batch/src/test/java/org/sonar/batch/design/SubProjectDsmDecoratorTest.java
index 94d7d621108..a9a41264adf 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/design/SubProjectDsmDecoratorTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/design/SubProjectDsmDecoratorTest.java
@@ -60,9 +60,9 @@ public class SubProjectDsmDecoratorTest {
     module = new Project("foo");
     moduleContext = mock(DecoratorContext.class);
 
-    dir1 = Directory.create("src/foo1", "foo1");
+    dir1 = Directory.create("src/foo1");
     dir1.setId(1);
-    dir2 = Directory.create("src/foo2", "foo2");
+    dir2 = Directory.create("src/foo2");
     dir2.setId(2);
 
     DecoratorContext dir1Context = mock(DecoratorContext.class);
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/BucketTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/BucketTest.java
index 51a9c0269c9..97bdb61d75e 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/index/BucketTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/BucketTest.java
@@ -24,17 +24,17 @@ import org.sonar.api.measures.Metric;
 import org.sonar.api.resources.Directory;
 import org.sonar.api.resources.File;
 
+import static org.hamcrest.Matchers.hasItem;
 import static org.hamcrest.Matchers.is;
 import static org.hamcrest.core.IsNot.not;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertThat;
-import static org.hamcrest.Matchers.hasItem;
 
 public class BucketTest {
 
-  Directory directory = new Directory("org/foo");
-  File javaFile = new File("org/foo/Bar.java");
+  Directory directory = Directory.create("org/foo");
+  File javaFile = File.create("org/foo/Bar.java");
   Metric ncloc = new Metric("ncloc");
 
   @Test
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/DefaultIndexTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/DefaultIndexTest.java
index ca7a86e791c..fe541281e05 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/index/DefaultIndexTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/DefaultIndexTest.java
@@ -95,10 +95,10 @@ public class DefaultIndexTest {
 
   @Test
   public void shouldIndexParentOfDeprecatedFiles() {
-    File file = File.create("src/org/foo/Bar.java", "org/foo/Bar.java", null, false);
+    File file = File.create("src/org/foo/Bar.java", null, false);
     assertThat(index.index(file)).isTrue();
 
-    Directory reference = Directory.create("src/org/foo", "org/foo");
+    Directory reference = Directory.create("src/org/foo");
     assertThat(index.getResource(reference).getName()).isEqualTo("src/org/foo");
     assertThat(index.isIndexed(reference, true)).isTrue();
     assertThat(index.isExcluded(reference)).isFalse();
@@ -108,15 +108,14 @@ public class DefaultIndexTest {
 
   @Test
   public void shouldIndexTreeOfResources() {
-    Directory directory = Directory.create("src/org/foo", "org/foo");
-    File file = File.create("src/org/foo/Bar.java", "org/foo/Bar.java", Java.INSTANCE, false);
+    Directory directory = Directory.create("src/org/foo");
+    File file = File.create("src/org/foo/Bar.java", Java.INSTANCE, false);
 
     assertThat(index.index(directory)).isTrue();
     assertThat(index.index(file, directory)).isTrue();
 
-    File fileRef = File.create("src/org/foo/Bar.java", "org/foo/Bar.java", null, false);
+    File fileRef = File.create("src/org/foo/Bar.java", null, false);
     assertThat(index.getResource(fileRef).getKey()).isEqualTo("src/org/foo/Bar.java");
-    assertThat(index.getResource(fileRef).getDeprecatedKey()).isEqualTo("org/foo/Bar.java");
     assertThat(index.getResource(fileRef).getLanguage().getKey()).isEqualTo("java");
     assertThat(index.isIndexed(fileRef, true)).isTrue();
     assertThat(index.isExcluded(fileRef)).isFalse();
@@ -126,14 +125,14 @@ public class DefaultIndexTest {
 
   @Test
   public void shouldGetSource() throws Exception {
-    Directory directory = Directory.create("src/org/foo", "org/foo");
-    File file = File.create("src/org/foo/Bar.java", "org/foo/Bar.java", Java.INSTANCE, false);
+    Directory directory = Directory.create("src/org/foo");
+    File file = File.create("src/org/foo/Bar.java", Java.INSTANCE, false);
     FileUtils.write(new java.io.File(baseDir, "src/org/foo/Bar.java"), "Foo bar");
 
     assertThat(index.index(directory)).isTrue();
     assertThat(index.index(file, directory)).isTrue();
 
-    File fileRef = File.create("src/org/foo/Bar.java", "org/foo/Bar.java", null, false);
+    File fileRef = File.create("src/org/foo/Bar.java", null, false);
     assertThat(index.getSource(fileRef)).isEqualTo("Foo bar");
   }
 
@@ -150,12 +149,12 @@ public class DefaultIndexTest {
 
   @Test
   public void shouldNotIndexResourceIfParentNotIndexed() {
-    Directory directory = Directory.create("src/org/other", "org/other");
-    File file = File.create("src/org/foo/Bar.java", "org/foo/Bar.java", null, false);
+    Directory directory = Directory.create("src/org/other");
+    File file = File.create("src/org/foo/Bar.java", null, false);
 
     assertThat(index.index(file, directory)).isFalse();
 
-    File fileRef = File.create("src/org/foo/Bar.java", "org/foo/Bar.java", null, false);
+    File fileRef = File.create("src/org/foo/Bar.java", null, false);
     assertThat(index.isIndexed(directory, true)).isFalse();
     assertThat(index.isIndexed(fileRef, true)).isFalse();
     assertThat(index.isExcluded(fileRef)).isFalse();
@@ -165,7 +164,7 @@ public class DefaultIndexTest {
 
   @Test
   public void shouldNotIndexResourceWhenAddingMeasure() {
-    Resource dir = Directory.create("src/org/foo", "org/foo");
+    Resource dir = Directory.create("src/org/foo");
     index.addMeasure(dir, new Measure("ncloc").setValue(50.0));
 
     assertThat(index.isIndexed(dir, true)).isFalse();
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/DuplicationPersisterTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/DuplicationPersisterTest.java
index 3517b28789f..a62dd075bb5 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/index/DuplicationPersisterTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/DuplicationPersisterTest.java
@@ -46,7 +46,7 @@ public class DuplicationPersisterTest extends AbstractDaoTestCase {
 
   DuplicationPersister duplicationPersister;
   RuleFinder ruleFinder = mock(RuleFinder.class);
-  File aFile = new File("org/foo/Bar.java");
+  File aFile = File.create("org/foo/Bar.java");
   Snapshot fileSnapshot = snapshot(FILE_SNAPSHOT_ID);
 
   private DuplicationCache duplicationCache;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/MeasurePersisterTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/MeasurePersisterTest.java
index b5cfb38c063..fb59aa4d0a5 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/index/MeasurePersisterTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/MeasurePersisterTest.java
@@ -61,8 +61,8 @@ public class MeasurePersisterTest extends AbstractDaoTestCase {
   MeasurePersister measurePersister;
   RuleFinder ruleFinder = mock(RuleFinder.class);
   Project project = new Project("foo");
-  Directory aDirectory = new Directory("org/foo");
-  File aFile = new File("org/foo/Bar.java");
+  Directory aDirectory = Directory.create("org/foo");
+  File aFile = File.create("org/foo/Bar.java");
   BatchResource projectResource = batchResource(project, PROJECT_SNAPSHOT_ID);
   BatchResource dirResource = batchResource(aDirectory, PACKAGE_SNAPSHOT_ID);
   BatchResource fileResource = batchResource(aFile, FILE_SNAPSHOT_ID);
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/ResourceCacheTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/ResourceCacheTest.java
index 33eb06086d0..bd250b544dd 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/index/ResourceCacheTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/ResourceCacheTest.java
@@ -31,7 +31,7 @@ public class ResourceCacheTest {
   public void should_cache_resource() throws Exception {
     ResourceCache cache = new ResourceCache();
     String componentKey = "struts:src/org/struts/Action.java";
-    Resource resource = new File("org/struts/Action.java").setEffectiveKey(componentKey);
+    Resource resource = File.create("org/struts/Action.java").setEffectiveKey(componentKey);
     cache.add(resource, null);
 
     assertThat(cache.get(componentKey).resource()).isSameAs(resource);
@@ -41,7 +41,7 @@ public class ResourceCacheTest {
   @Test
   public void should_fail_if_missing_component_key() throws Exception {
     ResourceCache cache = new ResourceCache();
-    Resource resource = new File("org/struts/Action.java").setEffectiveKey(null);
+    Resource resource = File.create("org/struts/Action.java").setEffectiveKey(null);
     try {
       cache.add(resource, null);
       fail();
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 e91b5596101..1d3d227a4d4 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
@@ -31,6 +31,8 @@ import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
 import org.sonar.api.config.Settings;
 import org.sonar.api.resources.Project;
+import org.sonar.api.scan.filesystem.PathResolver;
+import org.sonar.batch.scan.filesystem.DefaultModuleFileSystem;
 import org.sonar.jpa.test.AbstractDbUnitTestCase;
 
 import java.io.File;
@@ -39,6 +41,7 @@ import java.util.Arrays;
 
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
 
 public class ResourceKeyMigrationTest extends AbstractDbUnitTestCase {
 
@@ -73,23 +76,21 @@ public class ResourceKeyMigrationTest extends AbstractDbUnitTestCase {
     baseDir = temp.newFolder();
 
     javaInputFiles = (Iterable) Arrays.asList(
-      newInputFile(javaModule, "src/main/java/org/foo/Bar.java", "org.foo.Bar", false),
-      newInputFile(javaModule, "src/main/java/RootBar.java", "[default].RootBar", false),
-      newInputFile(javaModule, "src/test/java/org/foo/BarTest.java", "org.foo.BarTest", true));
+      newInputFile(javaModule, "src/main/java/org/foo/Bar.java", false, "java"),
+      newInputFile(javaModule, "src/main/java/RootBar.java", false, "java"),
+      newInputFile(javaModule, "src/test/java/org/foo/BarTest.java", true, "java"));
 
     phpInputFiles = (Iterable) Arrays.asList(
-      newInputFile(phpModule, "org/foo/Bar.php", "org/foo/Bar.php", false),
-      newInputFile(phpModule, "RootBar.php", "RootBar.php", false),
-      newInputFile(phpModule, "test/org/foo/BarTest.php", "org/foo/BarTest.php", true));
+      newInputFile(phpModule, "org/foo/Bar.php", false, "php"),
+      newInputFile(phpModule, "RootBar.php", false, "php"),
+      newInputFile(phpModule, "test/org/foo/BarTest.php", true, "php"));
 
   }
 
-  private DefaultInputFile newInputFile(Project module, String path, String deprecatedKey, boolean isTest) {
-    File file = new File(baseDir, path);
-    String deprecatedEffectiveKey = module.getKey() + ":" + deprecatedKey;
+  private DefaultInputFile newInputFile(Project module, String path, boolean isTest, String language) {
     return new DeprecatedDefaultInputFile(module.getKey(), path)
-      .setDeprecatedKey(deprecatedEffectiveKey)
-      .setFile(file)
+      .setModuleBaseDir(baseDir.toPath())
+      .setLanguage(language)
       .setType(isTest ? InputFile.Type.TEST : InputFile.Type.MAIN);
   }
 
@@ -98,11 +99,17 @@ public class ResourceKeyMigrationTest extends AbstractDbUnitTestCase {
     setupData("shouldMigrateResourceKeys");
 
     Logger logger = mock(Logger.class);
-    ResourceKeyMigration migration = new ResourceKeyMigration(getSession(), logger);
+    ResourceKeyMigration migration = new ResourceKeyMigration(getSession(), new PathResolver(), logger);
     migration.checkIfMigrationNeeded(multiModuleProject);
 
-    migration.migrateIfNeeded(javaModule, javaInputFiles);
-    migration.migrateIfNeeded(phpModule, phpInputFiles);
+    DefaultModuleFileSystem fs = mock(DefaultModuleFileSystem.class);
+    when(fs.sourceDirs()).thenReturn(Arrays.asList(new File(baseDir, "src/main/java")));
+    when(fs.testDirs()).thenReturn(Arrays.asList(new File(baseDir, "src/test/java")));
+    migration.migrateIfNeeded(javaModule, javaInputFiles, fs);
+
+    when(fs.sourceDirs()).thenReturn(Arrays.asList(new File(baseDir, ".")));
+    when(fs.testDirs()).thenReturn(Arrays.asList(new File(baseDir, "test")));
+    migration.migrateIfNeeded(phpModule, phpInputFiles, fs);
 
     verify(logger).info("Component {} changed to {}", "b:org.foo.Bar", "b:src/main/java/org/foo/Bar.java");
     verify(logger).warn("Directory with key b:org/foo matches both b:src/main/java/org/foo and b:src/test/java/org/foo. First match is arbitrary chosen.");
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/ResourcePersisterTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/ResourcePersisterTest.java
index 6ec57439787..6a4506273b4 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/index/ResourcePersisterTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/ResourcePersisterTest.java
@@ -290,7 +290,7 @@ public class ResourcePersisterTest extends AbstractDbUnitTestCase {
     setupData("shared");
 
     resourceCache.add(singleProject, null).setSnapshot(persister.persist(null, singleProject, null));
-    persister.persist(singleProject, Directory.create("src/main/java/org/foo", "org.foo").setEffectiveKey("foo:src/main/java/org/foo"), null);
+    persister.persist(singleProject, Directory.create("src/main/java/org/foo").setEffectiveKey("foo:src/main/java/org/foo"), null);
     // check that the directory is attached to the project
     checkTables("shouldSaveNewDirectory", new String[] {"build_date", "created_at", "authorization_updated_at", "uuid", "project_uuid", "module_uuid", "module_uuid_path"},
       "projects", "snapshots");
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/SourceDataFactoryTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/SourceDataFactoryTest.java
index 821cb735756..2c510d62aac 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/index/SourceDataFactoryTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/SourceDataFactoryTest.java
@@ -26,6 +26,7 @@ import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
+import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.sensor.duplication.DuplicationGroup;
 import org.sonar.api.batch.sensor.highlighting.TypeOfText;
@@ -35,6 +36,7 @@ import org.sonar.api.measures.Metric;
 import org.sonar.batch.duplication.DuplicationCache;
 import org.sonar.batch.highlighting.SyntaxHighlightingData;
 import org.sonar.batch.highlighting.SyntaxHighlightingDataBuilder;
+import org.sonar.batch.scan.filesystem.InputFileMetadata;
 import org.sonar.batch.scan.measure.MeasureCache;
 import org.sonar.batch.source.CodeColorizers;
 import org.sonar.batch.symbol.DefaultSymbolTableBuilder;
@@ -58,18 +60,21 @@ public class SourceDataFactoryTest {
   DuplicationCache duplicationCache = mock(DuplicationCache.class);
   CodeColorizers colorizers = mock(CodeColorizers.class);
   DefaultInputFile inputFile;
+  InputFileMetadata metadata;
   SourceDataFactory sut = new SourceDataFactory(measureCache, componentDataCache, duplicationCache, colorizers);
   FileSourceDb.Data.Builder output;
 
   @Before
   public void setUp() throws Exception {
     // generate a file with 3 lines
-    File file = temp.newFile();
+    File baseDir = temp.newFolder();
+    DefaultFileSystem fs = new DefaultFileSystem(baseDir.toPath());
     inputFile = new DefaultInputFile("module_key", "src/Foo.java")
       .setLines(3)
-      .setEncoding(Charsets.UTF_8.name())
-      .setFile(file);
-    FileUtils.write(file, "one\ntwo\nthree\n");
+      .setCharset(Charsets.UTF_8);
+    fs.add(inputFile);
+    metadata = new InputFileMetadata();
+    FileUtils.write(inputFile.file(), "one\ntwo\nthree\n");
     output = sut.createForSource(inputFile);
   }
 
@@ -84,7 +89,7 @@ public class SourceDataFactoryTest {
 
   @Test
   public void consolidateData() throws Exception {
-    byte[] bytes = sut.consolidateData(inputFile);
+    byte[] bytes = sut.consolidateData(inputFile, metadata);
     assertThat(bytes).isNotEmpty();
   }
 
@@ -145,7 +150,6 @@ public class SourceDataFactoryTest {
       Arrays.asList(new Measure().setData(dataPerLine).setMetric(metric)));
   }
 
-
   @Test
   public void applyDuplications() throws Exception {
     DuplicationGroup group1 = new DuplicationGroup(new DuplicationGroup.Block(inputFile.key(), 1, 1))
@@ -169,7 +173,7 @@ public class SourceDataFactoryTest {
   public void applyHighlighting_missing() throws Exception {
     when(componentDataCache.getData(inputFile.key(), SnapshotDataTypes.SYNTAX_HIGHLIGHTING)).thenReturn(null);
 
-    sut.applyHighlighting(inputFile, output);
+    sut.applyHighlighting(inputFile, metadata, output);
 
     FileSourceDb.Data data = output.build();
     assertThat(data.getLines(0).hasHighlighting()).isFalse();
@@ -185,9 +189,9 @@ public class SourceDataFactoryTest {
       .registerHighlightingRule(7, 16, TypeOfText.CONSTANT)
       .build();
     when(componentDataCache.getData(inputFile.key(), SnapshotDataTypes.SYNTAX_HIGHLIGHTING)).thenReturn(highlighting);
-    inputFile.setOriginalLineOffsets(new long[] {0, 4, 7});
+    metadata.setOriginalLineOffsets(new int[] {0, 4, 7});
 
-    sut.applyHighlighting(inputFile, output);
+    sut.applyHighlighting(inputFile, metadata, output);
 
     FileSourceDb.Data data = output.build();
     assertThat(data.getLines(0).getHighlighting()).isEqualTo("0,4,a");
@@ -203,9 +207,9 @@ public class SourceDataFactoryTest {
       .registerHighlightingRule(10, 16, TypeOfText.CONSTANT)
       .build();
     when(componentDataCache.getData(inputFile.key(), SnapshotDataTypes.SYNTAX_HIGHLIGHTING)).thenReturn(highlighting);
-    inputFile.setOriginalLineOffsets(new long[] {0, 4, 7});
+    metadata.setOriginalLineOffsets(new int[] {0, 4, 7});
 
-    sut.applyHighlighting(inputFile, output);
+    sut.applyHighlighting(inputFile, metadata, output);
 
     FileSourceDb.Data data = output.build();
     assertThat(data.getLines(0).getHighlighting()).isEqualTo("0,3,a");
@@ -222,9 +226,9 @@ public class SourceDataFactoryTest {
       .registerHighlightingRule(8, 15, TypeOfText.KEYWORD)
       .build();
     when(componentDataCache.getData(inputFile.key(), SnapshotDataTypes.SYNTAX_HIGHLIGHTING)).thenReturn(highlighting);
-    inputFile.setOriginalLineOffsets(new long[] {0, 4, 7});
+    metadata.setOriginalLineOffsets(new int[] {0, 4, 7});
 
-    sut.applyHighlighting(inputFile, output);
+    sut.applyHighlighting(inputFile, metadata, output);
 
     FileSourceDb.Data data = output.build();
     assertThat(data.getLines(0).getHighlighting()).isEqualTo("0,3,a");
@@ -241,9 +245,9 @@ public class SourceDataFactoryTest {
       .registerHighlightingRule(8, 15, TypeOfText.KEYWORD)
       .build();
     when(componentDataCache.getData(inputFile.key(), SnapshotDataTypes.SYNTAX_HIGHLIGHTING)).thenReturn(highlighting);
-    inputFile.setOriginalLineOffsets(new long[] {0, 4, 7});
+    metadata.setOriginalLineOffsets(new int[] {0, 4, 7});
 
-    sut.applyHighlighting(inputFile, output);
+    sut.applyHighlighting(inputFile, metadata, output);
 
     FileSourceDb.Data data = output.build();
     assertThat(data.getLines(0).getHighlighting()).isEqualTo("0,3,a");
@@ -255,7 +259,7 @@ public class SourceDataFactoryTest {
   public void applySymbolReferences_missing() throws Exception {
     when(componentDataCache.getData(inputFile.key(), SnapshotDataTypes.SYMBOL_HIGHLIGHTING)).thenReturn(null);
 
-    sut.applySymbolReferences(inputFile, output);
+    sut.applySymbolReferences(inputFile, metadata, output);
 
     FileSourceDb.Data data = output.build();
     assertThat(data.getLines(0).hasSymbols()).isFalse();
@@ -273,9 +277,9 @@ public class SourceDataFactoryTest {
     symbolBuilder.newReference(s2, 0);
     symbolBuilder.newReference(s2, 7);
     when(componentDataCache.getData(inputFile.key(), SnapshotDataTypes.SYMBOL_HIGHLIGHTING)).thenReturn(symbolBuilder.build());
-    inputFile.setOriginalLineOffsets(new long[] {0, 4, 7});
+    metadata.setOriginalLineOffsets(new int[] {0, 4, 7});
 
-    sut.applySymbolReferences(inputFile, output);
+    sut.applySymbolReferences(inputFile, metadata, output);
 
     FileSourceDb.Data data = output.build();
     assertThat(data.getLines(0).getSymbols()).isEqualTo("1,2,1;0,2,2");
@@ -293,9 +297,9 @@ public class SourceDataFactoryTest {
     symbolBuilder.newReference(s1, 11);
     symbolBuilder.newReference(s1, 4);
     when(componentDataCache.getData(inputFile.key(), SnapshotDataTypes.SYMBOL_HIGHLIGHTING)).thenReturn(symbolBuilder.build());
-    inputFile.setOriginalLineOffsets(new long[] {0, 4, 7});
+    metadata.setOriginalLineOffsets(new int[] {0, 4, 7});
 
-    sut.applySymbolReferences(inputFile, output);
+    sut.applySymbolReferences(inputFile, metadata, output);
 
     FileSourceDb.Data data = output.build();
     assertThat(data.getLines(0).getSymbols()).isEqualTo("1,2,1;0,2,2");
diff --git a/sonar-batch/src/test/java/org/sonar/batch/issue/IssuableFactoryTest.java b/sonar-batch/src/test/java/org/sonar/batch/issue/IssuableFactoryTest.java
index c24e04a1ded..514a6d05a1b 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/issue/IssuableFactoryTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/issue/IssuableFactoryTest.java
@@ -40,7 +40,7 @@ public class IssuableFactoryTest {
   @Test
   public void file_should_be_issuable() throws Exception {
     IssuableFactory factory = new IssuableFactory(moduleIssues, cache, projectTree);
-    Component component = new ResourceComponent(new File("foo/bar.c").setEffectiveKey("foo/bar.c"));
+    Component component = new ResourceComponent(File.create("foo/bar.c").setEffectiveKey("foo/bar.c"));
     Issuable issuable = factory.loadPerspective(Issuable.class, component);
 
     assertThat(issuable).isNotNull();
diff --git a/sonar-batch/src/test/java/org/sonar/batch/issue/ModuleIssuesTest.java b/sonar-batch/src/test/java/org/sonar/batch/issue/ModuleIssuesTest.java
index 0594cb16234..7ffa9905721 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/issue/ModuleIssuesTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/issue/ModuleIssuesTest.java
@@ -207,7 +207,7 @@ public class ModuleIssuesTest {
     initModuleIssues();
 
     org.sonar.api.rules.Rule rule = org.sonar.api.rules.Rule.create("squid", "AvoidCycle", "Avoid Cycle");
-    Resource resource = new File("org/struts/Action.java").setEffectiveKey("struts:src/org/struts/Action.java");
+    Resource resource = File.create("org/struts/Action.java").setEffectiveKey("struts:src/org/struts/Action.java");
     Violation violation = new Violation(rule, resource);
     violation.setLineId(42);
     violation.setSeverity(RulePriority.CRITICAL);
diff --git a/sonar-batch/src/test/java/org/sonar/batch/issue/ignore/scanner/IssueExclusionsLoaderTest.java b/sonar-batch/src/test/java/org/sonar/batch/issue/ignore/scanner/IssueExclusionsLoaderTest.java
index 9fd36ece0b7..3cca58ac2b2 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/issue/ignore/scanner/IssueExclusionsLoaderTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/issue/ignore/scanner/IssueExclusionsLoaderTest.java
@@ -72,7 +72,7 @@ public class IssueExclusionsLoaderTest {
   @Before
   public void before() throws Exception {
     baseDir = temp.newFolder();
-    fs = new DefaultFileSystem(baseDir).setEncoding(UTF_8);
+    fs = new DefaultFileSystem(baseDir.toPath()).setEncoding(UTF_8);
     MockitoAnnotations.initMocks(this);
     scanner = new IssueExclusionsLoader(regexpScanner, exclusionPatternInitializer, inclusionPatternInitializer, fs);
   }
@@ -106,11 +106,9 @@ public class IssueExclusionsLoaderTest {
   public void shouldAnalyzeProject() throws IOException {
     File javaFile1 = new File(baseDir, "src/main/java/Foo.java");
     fs.add(new DeprecatedDefaultInputFile("polop", "src/main/java/Foo.java")
-      .setFile(javaFile1)
       .setType(InputFile.Type.MAIN));
     File javaTestFile1 = new File(baseDir, "src/test/java/FooTest.java");
     fs.add(new DeprecatedDefaultInputFile("polop", "src/test/java/FooTest.java")
-      .setFile(javaTestFile1)
       .setType(InputFile.Type.TEST));
 
     when(exclusionPatternInitializer.hasFileContentPattern()).thenReturn(true);
@@ -129,11 +127,9 @@ public class IssueExclusionsLoaderTest {
   public void shouldAnalyseFilesOnlyWhenRegexConfigured() throws IOException {
     File javaFile1 = new File(baseDir, "src/main/java/Foo.java");
     fs.add(new DeprecatedDefaultInputFile("polop", "src/main/java/Foo.java")
-      .setFile(javaFile1)
       .setType(InputFile.Type.MAIN));
     File javaTestFile1 = new File(baseDir, "src/test/java/FooTest.java");
     fs.add(new DeprecatedDefaultInputFile("polop", "src/test/java/FooTest.java")
-      .setFile(javaTestFile1)
       .setType(InputFile.Type.TEST));
     when(exclusionPatternInitializer.hasFileContentPattern()).thenReturn(false);
 
@@ -150,7 +146,6 @@ public class IssueExclusionsLoaderTest {
   public void shouldReportFailure() throws IOException {
     File phpFile1 = new File(baseDir, "src/Foo.php");
     fs.add(new DeprecatedDefaultInputFile("polop", "src/Foo.php")
-      .setFile(phpFile1)
       .setType(InputFile.Type.MAIN));
 
     when(exclusionPatternInitializer.hasFileContentPattern()).thenReturn(true);
diff --git a/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/IssueTrackingDecoratorTest.java b/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/IssueTrackingDecoratorTest.java
index 7691dbf6538..1c5e080cd06 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/IssueTrackingDecoratorTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/IssueTrackingDecoratorTest.java
@@ -19,9 +19,12 @@
  */
 package org.sonar.batch.issue.tracking;
 
+import com.google.common.base.Charsets;
 import org.apache.commons.codec.digest.DigestUtils;
+import org.apache.commons.io.FileUtils;
 import org.junit.Before;
 import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
 import org.mockito.ArgumentCaptor;
 import org.mockito.ArgumentMatcher;
 import org.sonar.api.batch.DecoratorContext;
@@ -41,6 +44,7 @@ import org.sonar.api.utils.Duration;
 import org.sonar.api.utils.System2;
 import org.sonar.batch.issue.IssueCache;
 import org.sonar.batch.scan.LastLineHashes;
+import org.sonar.batch.scan.filesystem.InputFileMetadata;
 import org.sonar.batch.scan.filesystem.InputPathCache;
 import org.sonar.core.issue.IssueUpdater;
 import org.sonar.core.issue.db.IssueChangeDto;
@@ -48,6 +52,7 @@ import org.sonar.core.issue.db.IssueDto;
 import org.sonar.core.issue.workflow.IssueWorkflow;
 import org.sonar.java.api.JavaClass;
 
+import java.io.IOException;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
@@ -71,6 +76,9 @@ import static org.mockito.Mockito.when;
 
 public class IssueTrackingDecoratorTest {
 
+  @org.junit.Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
   IssueTrackingDecorator decorator;
   IssueCache issueCache = mock(IssueCache.class, RETURNS_MOCKS);
   InitialOpenIssuesStack initialOpenIssues = mock(InitialOpenIssuesStack.class);
@@ -124,6 +132,7 @@ public class IssueTrackingDecoratorTest {
     List<PreviousIssue> dbIssues = Collections.emptyList();
     when(initialOpenIssues.selectAndRemoveIssues("struts:Action.java")).thenReturn(dbIssues);
     when(inputPathCache.getFile("foo", "Action.java")).thenReturn(mock(DefaultInputFile.class));
+    when(inputPathCache.getFileMetadata("foo", "Action.java")).thenReturn(new InputFileMetadata());
     decorator.doDecorate(file);
 
     // Apply filters, track, apply transitions, notify extensions then update cache
@@ -152,6 +161,7 @@ public class IssueTrackingDecoratorTest {
 
     when(tracking.track(isA(SourceHashHolder.class), anyCollection(), anyCollection())).thenReturn(trackingResult);
     when(inputPathCache.getFile("foo", "Action.java")).thenReturn(mock(DefaultInputFile.class));
+    when(inputPathCache.getFileMetadata("foo", "Action.java")).thenReturn(new InputFileMetadata());
 
     decorator.doDecorate(file);
 
@@ -210,10 +220,13 @@ public class IssueTrackingDecoratorTest {
     assertThat(issue.isOnDisabledRule()).isFalse();
   }
 
-  private Resource mockHashes(String originalSource, String newSource) {
+  private Resource mockHashes(String originalSource, String newSource) throws IOException {
     DefaultInputFile inputFile = mock(DefaultInputFile.class);
-    byte[][] hashes = computeHashes(newSource);
-    when(inputFile.lineHashes()).thenReturn(hashes);
+    java.io.File f = temp.newFile();
+    when(inputFile.path()).thenReturn(f.toPath());
+    when(inputFile.charset()).thenReturn(Charsets.UTF_8);
+    when(inputFile.lines()).thenReturn(newSource.split("\n").length);
+    FileUtils.write(f, newSource, Charsets.UTF_8);
     when(inputFile.key()).thenReturn("foo:Action.java");
     when(inputPathCache.getFile("foo", "Action.java")).thenReturn(inputFile);
     when(lastSnapshots.getLineHashes("foo:Action.java")).thenReturn(computeHexHashes(originalSource));
@@ -561,15 +574,6 @@ public class IssueTrackingDecoratorTest {
     assertThat(issue.changes()).hasSize(1);
   }
 
-  private byte[][] computeHashes(String source) {
-    String[] lines = source.split("\n");
-    byte[][] hashes = new byte[lines.length][];
-    for (int i = 0; i < lines.length; i++) {
-      hashes[i] = DigestUtils.md5(lines[i].replaceAll("[\t ]", ""));
-    }
-    return hashes;
-  }
-
   private String[] computeHexHashes(String source) {
     String[] lines = source.split("\n");
     String[] hashes = new String[lines.length];
diff --git a/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/IssueTrackingTest.java b/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/IssueTrackingTest.java
index 2efb24c13eb..bcc25ac598c 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/IssueTrackingTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/IssueTrackingTest.java
@@ -24,8 +24,11 @@ import com.google.common.base.Charsets;
 import com.google.common.collect.Lists;
 import com.google.common.io.Resources;
 import org.apache.commons.codec.digest.DigestUtils;
+import org.apache.commons.io.FileUtils;
 import org.junit.Before;
+import org.junit.Rule;
 import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.issue.Issue;
 import org.sonar.api.issue.internal.DefaultIssue;
@@ -35,6 +38,7 @@ import org.sonar.api.rule.RuleKey;
 import org.sonar.batch.scan.LastLineHashes;
 import org.sonar.core.issue.db.IssueDto;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.Collections;
@@ -47,6 +51,9 @@ import static org.mockito.Mockito.when;
 
 public class IssueTrackingTest {
 
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
   IssueTracking tracking;
   Resource project;
   SourceHashHolder sourceHashHolder;
@@ -345,22 +352,17 @@ public class IssueTrackingTest {
 
   private void initLastHashes(String reference, String newSource) throws IOException {
     DefaultInputFile inputFile = mock(DefaultInputFile.class);
-    byte[][] hashes = computeHashes(load(newSource));
-    when(inputFile.lineHashes()).thenReturn(hashes);
+    File f = temp.newFile();
+    when(inputFile.path()).thenReturn(f.toPath());
+    when(inputFile.charset()).thenReturn(Charsets.UTF_8);
+    String data = load(newSource);
+    when(inputFile.lines()).thenReturn(data.split("\n").length);
+    FileUtils.write(f, data, Charsets.UTF_8);
     when(inputFile.key()).thenReturn("foo:Action.java");
     when(lastSnapshots.getLineHashes("foo:Action.java")).thenReturn(computeHexHashes(load(reference)));
     sourceHashHolder = new SourceHashHolder(inputFile, lastSnapshots);
   }
 
-  private byte[][] computeHashes(String source) {
-    String[] lines = source.split("\n");
-    byte[][] hashes = new byte[lines.length][];
-    for (int i = 0; i < lines.length; i++) {
-      hashes[i] = DigestUtils.md5(lines[i].replaceAll("[\t ]", ""));
-    }
-    return hashes;
-  }
-
   private String[] computeHexHashes(String source) {
     String[] lines = source.split("\n");
     String[] hashes = new String[lines.length];
diff --git a/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/SourceHashHolderTest.java b/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/SourceHashHolderTest.java
index 6ac6645bbae..59371ca4947 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/SourceHashHolderTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/issue/tracking/SourceHashHolderTest.java
@@ -19,14 +19,19 @@
  */
 package org.sonar.batch.issue.tracking;
 
+import com.google.common.base.Charsets;
+import org.apache.commons.io.FileUtils;
 import org.junit.Before;
+import org.junit.Rule;
 import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
 import org.mockito.Mockito;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.batch.scan.LastLineHashes;
 
-import static org.apache.commons.codec.digest.DigestUtils.md5;
+import java.io.File;
+
 import static org.apache.commons.codec.digest.DigestUtils.md5Hex;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.mock;
@@ -35,39 +40,48 @@ import static org.mockito.Mockito.when;
 
 public class SourceHashHolderTest {
 
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
   SourceHashHolder sourceHashHolder;
 
   LastLineHashes lastSnapshots;
   DefaultInputFile file;
 
+  private File ioFile;
+
   @Before
-  public void setUp() {
+  public void setUp() throws Exception {
     lastSnapshots = mock(LastLineHashes.class);
     file = mock(DefaultInputFile.class);
+    ioFile = temp.newFile();
+    when(file.file()).thenReturn(ioFile);
+    when(file.path()).thenReturn(ioFile.toPath());
+    when(file.lines()).thenReturn(1);
+    when(file.charset()).thenReturn(Charsets.UTF_8);
 
     sourceHashHolder = new SourceHashHolder(file, lastSnapshots);
   }
 
   @Test
-  public void should_lazy_load_line_hashes() {
+  public void should_lazy_load_line_hashes() throws Exception {
     final String source = "source";
-    when(file.lineHashes()).thenReturn(new byte[][] {md5(source), null});
+    FileUtils.write(ioFile, source + "\n", Charsets.UTF_8);
+    when(file.lines()).thenReturn(2);
 
     assertThat(sourceHashHolder.getHashedSource().getHash(1)).isEqualTo(md5Hex(source));
     assertThat(sourceHashHolder.getHashedSource().getHash(2)).isEqualTo("");
-    verify(file).lineHashes();
     verify(file).key();
     verify(file).status();
 
     assertThat(sourceHashHolder.getHashedSource().getHash(1)).isEqualTo(md5Hex(source));
-    Mockito.verifyNoMoreInteractions(file);
   }
 
   @Test
-  public void should_lazy_load_reference_hashes_when_status_changed() {
+  public void should_lazy_load_reference_hashes_when_status_changed() throws Exception {
     final String source = "source";
     String key = "foo:src/Foo.java";
-    when(file.lineHashes()).thenReturn(new byte[][] {md5(source)});
+    FileUtils.write(ioFile, source, Charsets.UTF_8);
     when(file.key()).thenReturn(key);
     when(file.status()).thenReturn(InputFile.Status.CHANGED);
     when(lastSnapshots.getLineHashes(key)).thenReturn(new String[] {md5Hex(source)});
@@ -80,23 +94,22 @@ public class SourceHashHolderTest {
   }
 
   @Test
-  public void should_not_load_reference_hashes_when_status_same() {
+  public void should_not_load_reference_hashes_when_status_same() throws Exception {
     final String source = "source";
     String key = "foo:src/Foo.java";
-    when(file.lineHashes()).thenReturn(new byte[][] {md5(source)});
+    FileUtils.write(ioFile, source, Charsets.UTF_8);
     when(file.key()).thenReturn(key);
     when(file.status()).thenReturn(InputFile.Status.SAME);
 
     assertThat(sourceHashHolder.getHashedReference().getHash(1)).isEqualTo(md5Hex(source));
-    assertThat(sourceHashHolder.getHashedReference().getHash(1)).isEqualTo(md5Hex(source));
     Mockito.verifyNoMoreInteractions(lastSnapshots);
   }
 
   @Test
-  public void no_reference_hashes_when_status_added() {
+  public void no_reference_hashes_when_status_added() throws Exception {
     final String source = "source";
     String key = "foo:src/Foo.java";
-    when(file.lineHashes()).thenReturn(new byte[][] {md5(source)});
+    FileUtils.write(ioFile, source, Charsets.UTF_8);
     when(file.key()).thenReturn(key);
     when(file.status()).thenReturn(InputFile.Status.ADDED);
 
diff --git a/sonar-batch/src/test/java/org/sonar/batch/phases/DecoratorsExecutorTest.java b/sonar-batch/src/test/java/org/sonar/batch/phases/DecoratorsExecutorTest.java
index 45774d11f95..7b644d27530 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/phases/DecoratorsExecutorTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/phases/DecoratorsExecutorTest.java
@@ -28,8 +28,8 @@ import org.sonar.api.resources.File;
 import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.utils.SonarException;
-import org.sonar.batch.DefaultDecoratorContext;
 import org.sonar.batch.bootstrap.BatchExtensionDictionnary;
+import org.sonar.batch.deprecated.decorator.DefaultDecoratorContext;
 import org.sonar.batch.duplication.DuplicationCache;
 import org.sonar.batch.events.EventBus;
 import org.sonar.batch.scan.measure.MeasureCache;
@@ -69,7 +69,7 @@ public class DecoratorsExecutorTest {
     DecoratorsExecutor executor = new DecoratorsExecutor(mock(BatchExtensionDictionnary.class), new Project("key"), mock(SonarIndex.class),
       mock(EventBus.class), mock(CoverageExclusions.class), mock(MeasureCache.class), mock(MetricFinder.class), mock(DuplicationCache.class));
     try {
-      executor.executeDecorator(decorator, mock(DefaultDecoratorContext.class), File.create("src/org/foo/Bar.java", "org/foo/Bar.java", null, false));
+      executor.executeDecorator(decorator, mock(DefaultDecoratorContext.class), File.create("src/org/foo/Bar.java", null, false));
       fail("Exception has not been thrown");
 
     } catch (SonarException e) {
diff --git a/sonar-batch/src/test/java/org/sonar/batch/qualitygate/GenerateQualityGateEventsTest.java b/sonar-batch/src/test/java/org/sonar/batch/qualitygate/GenerateQualityGateEventsTest.java
index 83cab61793e..e7e2c332838 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/qualitygate/GenerateQualityGateEventsTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/qualitygate/GenerateQualityGateEventsTest.java
@@ -19,8 +19,6 @@
  */
 package org.sonar.batch.qualitygate;
 
-import org.sonar.batch.qualitygate.GenerateQualityGateEvents;
-
 import org.junit.Before;
 import org.junit.Test;
 import org.sonar.api.batch.DecoratorContext;
@@ -35,14 +33,20 @@ import org.sonar.api.notifications.NotificationManager;
 import org.sonar.api.resources.File;
 import org.sonar.api.resources.Project;
 import org.sonar.api.test.ProjectTestBuilder;
-import org.sonar.batch.qualitygate.QualityGate;
 
 import java.util.Arrays;
 import java.util.Date;
 
 import static org.assertj.core.api.Assertions.assertThat;
-import static org.mockito.Matchers.*;
-import static org.mockito.Mockito.*;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Matchers.eq;
+import static org.mockito.Matchers.isNull;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.never;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
 
 public class GenerateQualityGateEventsTest {
   private GenerateQualityGateEvents decorator;
@@ -80,7 +84,7 @@ public class GenerateQualityGateEventsTest {
 
   @Test
   public void shouldNotDecorateIfNotRootProject() {
-    decorator.decorate(new File("Foo"), context);
+    decorator.decorate(File.create("Foo"), context);
     verify(context, never()).createEvent(anyString(), anyString(), anyString(), (Date) isNull());
   }
 
diff --git a/sonar-batch/src/test/java/org/sonar/batch/report/ComponentsPublisherTest.java b/sonar-batch/src/test/java/org/sonar/batch/report/ComponentsPublisherTest.java
index 87a72c6c057..30f56d3a46e 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/report/ComponentsPublisherTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/report/ComponentsPublisherTest.java
@@ -62,17 +62,17 @@ public class ComponentsPublisherTest {
     dir.setId(3).setUuid("DIR_UUID");
     resourceCache.add(dir, module1).setSnapshot(new Snapshot().setId(13));
 
-    org.sonar.api.resources.File file = org.sonar.api.resources.File.create("src/Foo.java", "Foo.java", Java.INSTANCE, false);
+    org.sonar.api.resources.File file = org.sonar.api.resources.File.create("src/Foo.java", Java.INSTANCE, false);
     file.setEffectiveKey("foo:src/Foo.java");
     file.setId(4).setUuid("FILE_UUID");
     resourceCache.add(file, dir).setSnapshot(new Snapshot().setId(14));
 
-    org.sonar.api.resources.File fileWithoutLang = org.sonar.api.resources.File.create("src/make", "make", null, false);
+    org.sonar.api.resources.File fileWithoutLang = org.sonar.api.resources.File.create("src/make", null, false);
     fileWithoutLang.setEffectiveKey("foo:src/make");
     fileWithoutLang.setId(5).setUuid("FILE_WITHOUT_LANG_UUID");
     resourceCache.add(fileWithoutLang, dir).setSnapshot(new Snapshot().setId(15));
 
-    org.sonar.api.resources.File testFile = org.sonar.api.resources.File.create("test/FooTest.java", "FooTest.java", Java.INSTANCE, true);
+    org.sonar.api.resources.File testFile = org.sonar.api.resources.File.create("test/FooTest.java", Java.INSTANCE, true);
     testFile.setEffectiveKey("foo:test/FooTest.java");
     testFile.setId(6).setUuid("TEST_FILE_UUID");
     resourceCache.add(testFile, dir).setSnapshot(new Snapshot().setId(16));
diff --git a/sonar-batch/src/test/java/org/sonar/batch/user/UserRepositoryTest.java b/sonar-batch/src/test/java/org/sonar/batch/repository/user/UserRepositoryTest.java
index 7191d185fa3..ad8c954e98f 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/user/UserRepositoryTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/repository/user/UserRepositoryTest.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.batch.user;
+package org.sonar.batch.repository.user;
 
 import org.junit.Test;
 import org.sonar.batch.bootstrap.ServerClient;
diff --git a/sonar-batch/src/test/java/org/sonar/batch/rule/QProfileSensorTest.java b/sonar-batch/src/test/java/org/sonar/batch/rule/QProfileSensorTest.java
index c9e6deabcaf..7c83baad914 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/rule/QProfileSensorTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/rule/QProfileSensorTest.java
@@ -23,6 +23,7 @@ import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
+import org.sonar.api.batch.AnalysisMode;
 import org.sonar.api.batch.SensorContext;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.measures.CoreMetrics;
@@ -57,20 +58,29 @@ public class QProfileSensorTest {
 
   @Before
   public void prepare() throws Exception {
-    fs = new DefaultFileSystem(temp.newFolder());
+    fs = new DefaultFileSystem(temp.newFolder().toPath());
   }
 
   @Test
   public void to_string() throws Exception {
-    QProfileSensor sensor = new QProfileSensor(moduleQProfiles, fs);
+    QProfileSensor sensor = new QProfileSensor(moduleQProfiles, fs, mock(AnalysisMode.class));
     assertThat(sensor.toString()).isEqualTo("QProfileSensor");
   }
 
   @Test
+  public void no_execution_in_preview() throws Exception {
+    AnalysisMode analysisMode = mock(AnalysisMode.class);
+    when(analysisMode.isPreview()).thenReturn(true);
+    QProfileSensor sensor = new QProfileSensor(moduleQProfiles, fs, analysisMode);
+    assertThat(sensor.shouldExecuteOnProject(project)).isFalse();
+
+  }
+
+  @Test
   public void no_qprofiles() throws Exception {
     when(moduleQProfiles.findAll()).thenReturn(Collections.<QProfile>emptyList());
 
-    QProfileSensor sensor = new QProfileSensor(moduleQProfiles, fs);
+    QProfileSensor sensor = new QProfileSensor(moduleQProfiles, fs, mock(AnalysisMode.class));
     assertThat(sensor.shouldExecuteOnProject(project)).isTrue();
     sensor.analyse(project, sensorContext);
 
@@ -85,7 +95,7 @@ public class QProfileSensorTest {
     when(moduleQProfiles.findByLanguage("abap")).thenReturn(null);
     fs.addLanguages("java", "php", "abap");
 
-    QProfileSensor sensor = new QProfileSensor(moduleQProfiles, fs);
+    QProfileSensor sensor = new QProfileSensor(moduleQProfiles, fs, mock(AnalysisMode.class));
     assertThat(sensor.shouldExecuteOnProject(project)).isTrue();
     sensor.analyse(project, sensorContext);
   }
@@ -97,7 +107,7 @@ public class QProfileSensorTest {
     when(moduleQProfiles.findByLanguage("abap")).thenReturn(null);
     fs.addLanguages("java");
 
-    QProfileSensor sensor = new QProfileSensor(moduleQProfiles, fs);
+    QProfileSensor sensor = new QProfileSensor(moduleQProfiles, fs, mock(AnalysisMode.class));
     assertThat(sensor.shouldExecuteOnProject(project)).isTrue();
     sensor.analyse(project, sensorContext);
 
@@ -113,7 +123,7 @@ public class QProfileSensorTest {
     when(moduleQProfiles.findByLanguage("abap")).thenReturn(null);
     fs.addLanguages("java", "php");
 
-    QProfileSensor sensor = new QProfileSensor(moduleQProfiles, fs);
+    QProfileSensor sensor = new QProfileSensor(moduleQProfiles, fs, mock(AnalysisMode.class));
     assertThat(sensor.shouldExecuteOnProject(project)).isTrue();
     sensor.analyse(project, sensorContext);
 
diff --git a/sonar-batch/src/test/java/org/sonar/batch/rule/QProfileVerifierTest.java b/sonar-batch/src/test/java/org/sonar/batch/rule/QProfileVerifierTest.java
index 9c5db0f6d6a..61463ae5742 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/rule/QProfileVerifierTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/rule/QProfileVerifierTest.java
@@ -47,7 +47,7 @@ public class QProfileVerifierTest {
 
   @Before
   public void before() throws Exception {
-    fs = new DefaultFileSystem(temp.newFolder());
+    fs = new DefaultFileSystem(temp.newFolder().toPath());
     profiles = mock(ModuleQProfiles.class);
     QProfile javaProfile = new QProfile().setKey("p1").setName("My Java profile").setLanguage("java");
     when(profiles.findByLanguage("java")).thenReturn(javaProfile);
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/LanguageVerifierTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/LanguageVerifierTest.java
index a60fd596e53..420d0641c36 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/LanguageVerifierTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/LanguageVerifierTest.java
@@ -29,8 +29,8 @@ import org.sonar.api.config.Settings;
 import org.sonar.api.resources.Java;
 import org.sonar.api.resources.Languages;
 import org.sonar.api.utils.MessageException;
-import org.sonar.batch.languages.DefaultLanguagesReferential;
-import org.sonar.batch.languages.LanguagesReferential;
+import org.sonar.batch.repository.language.DefaultLanguagesRepository;
+import org.sonar.batch.repository.language.LanguagesRepository;
 
 import static org.assertj.core.api.Assertions.assertThat;
 
@@ -43,12 +43,12 @@ public class LanguageVerifierTest {
   public ExpectedException thrown = ExpectedException.none();
 
   private Settings settings = new Settings();
-  private LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(Java.INSTANCE));
+  private LanguagesRepository languages = new DefaultLanguagesRepository(new Languages(Java.INSTANCE));
   private DefaultFileSystem fs;
 
   @Before
   public void prepare() throws Exception {
-    fs = new DefaultFileSystem(temp.newFolder());
+    fs = new DefaultFileSystem(temp.newFolder().toPath());
   }
 
   @Test
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/AdditionalFilePredicatesTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/AdditionalFilePredicatesTest.java
index ff6e76e0857..ad3dfffc491 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/AdditionalFilePredicatesTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/AdditionalFilePredicatesTest.java
@@ -26,8 +26,6 @@ import org.sonar.api.batch.fs.FilePredicate;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
 
-import java.io.File;
-
 import static org.assertj.core.api.Assertions.assertThat;
 
 public class AdditionalFilePredicatesTest {
@@ -45,38 +43,4 @@ public class AdditionalFilePredicatesTest {
     inputFile = new DeprecatedDefaultInputFile("struts", "Filter.java");
     assertThat(predicate.apply(inputFile)).isFalse();
   }
-
-  @Test
-  public void deprecated_key() throws Exception {
-    FilePredicate predicate = new AdditionalFilePredicates.DeprecatedKeyPredicate("struts:Action.java");
-
-    DeprecatedDefaultInputFile inputFile = new DeprecatedDefaultInputFile("struts", "Action.java").setDeprecatedKey("struts:Action.java");
-    assertThat(predicate.apply(inputFile)).isTrue();
-
-    inputFile = new DeprecatedDefaultInputFile("struts", "Filter.java").setDeprecatedKey("struts:Filter.java");
-    assertThat(predicate.apply(inputFile)).isFalse();
-  }
-
-  @Test
-  public void absolute_path_of_source_dir() throws Exception {
-    File dir = temp.newFolder();
-    FilePredicate predicate = new AdditionalFilePredicates.SourceDirPredicate(dir.getAbsolutePath());
-
-    DeprecatedDefaultInputFile inputFile = new DeprecatedDefaultInputFile("struts", "Action.java").setSourceDirAbsolutePath(dir.getAbsolutePath());
-    assertThat(predicate.apply(inputFile)).isTrue();
-
-    inputFile = new DeprecatedDefaultInputFile("struts", "Filter.java").setSourceDirAbsolutePath(temp.newFolder().getAbsolutePath());
-    assertThat(predicate.apply(inputFile)).isFalse();
-  }
-
-  @Test
-  public void path_relative_to_source_dir() throws Exception {
-    FilePredicate predicate = new AdditionalFilePredicates.SourceRelativePathPredicate("foo/Bar.php");
-
-    DeprecatedDefaultInputFile inputFile = new DeprecatedDefaultInputFile("foo", "src/php/foo/Bar.php").setPathRelativeToSourceDir("foo/Bar.php");
-    assertThat(predicate.apply(inputFile)).isTrue();
-
-    inputFile = new DeprecatedDefaultInputFile("foo", "foo/Bar.php").setPathRelativeToSourceDir("Bar.php");
-    assertThat(predicate.apply(inputFile)).isFalse();
-  }
 }
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 702aa2fb068..5960fab5c2d 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
@@ -42,6 +42,7 @@ import java.io.IOException;
 import static org.mockito.Matchers.argThat;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
 
 public class ComponentIndexerTest {
 
@@ -52,13 +53,17 @@ public class ComponentIndexerTest {
   private SonarIndex sonarIndex;
   private AbstractLanguage cobolLanguage;
   private Project project;
+  private ModuleFileSystemInitializer initializer;
 
   @Before
   public void prepare() throws IOException {
     baseDir = temp.newFolder();
-    fs = new DefaultFileSystem(baseDir);
+    fs = new DefaultFileSystem(baseDir.toPath());
     sonarIndex = mock(SonarIndex.class);
     project = new Project("myProject");
+    initializer = mock(ModuleFileSystemInitializer.class);
+    when(initializer.baseDir()).thenReturn(baseDir);
+    when(initializer.workingDir()).thenReturn(temp.newFolder());
     cobolLanguage = new AbstractLanguage("cobol") {
       @Override
       public String[] getFileSuffixes() {
@@ -69,15 +74,17 @@ public class ComponentIndexerTest {
 
   @Test
   public void should_index_java_files() throws IOException {
+    Languages languages = new Languages(Java.INSTANCE);
+    ComponentIndexer indexer = createIndexer(languages);
+    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(project, null, mock(FileIndexer.class), initializer, indexer);
     fs.add(newInputFile("src/main/java/foo/bar/Foo.java", "", "foo/bar/Foo.java", "java", false));
     fs.add(newInputFile("src/main/java2/foo/bar/Foo.java", "", "foo/bar/Foo.java", "java", false));
     fs.add(newInputFile("src/test/java/foo/bar/FooTest.java", "", "foo/bar/FooTest.java", "java", true));
-    Languages languages = new Languages(Java.INSTANCE);
-    ComponentIndexer indexer = createIndexer(languages);
-    indexer.execute(fs);
 
-    verify(sonarIndex).index(org.sonar.api.resources.File.create("src/main/java/foo/bar/Foo.java", "foo/bar/Foo.java", Java.INSTANCE, false));
-    verify(sonarIndex).index(org.sonar.api.resources.File.create("src/main/java2/foo/bar/Foo.java", "foo/bar/Foo.java", Java.INSTANCE, false));
+    fs.index();
+
+    verify(sonarIndex).index(org.sonar.api.resources.File.create("src/main/java/foo/bar/Foo.java", Java.INSTANCE, false));
+    verify(sonarIndex).index(org.sonar.api.resources.File.create("src/main/java2/foo/bar/Foo.java", Java.INSTANCE, false));
     verify(sonarIndex).index(argThat(new ArgumentMatcher<org.sonar.api.resources.File>() {
       @Override
       public boolean matches(Object arg0) {
@@ -95,25 +102,24 @@ public class ComponentIndexerTest {
 
   @Test
   public void should_index_cobol_files() throws IOException {
+    Languages languages = new Languages(cobolLanguage);
+    ComponentIndexer indexer = createIndexer(languages);
+    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(project, null, mock(FileIndexer.class), initializer, indexer);
     fs.add(newInputFile("src/foo/bar/Foo.cbl", "", "foo/bar/Foo.cbl", "cobol", false));
     fs.add(newInputFile("src2/foo/bar/Foo.cbl", "", "foo/bar/Foo.cbl", "cobol", false));
     fs.add(newInputFile("src/test/foo/bar/FooTest.cbl", "", "foo/bar/FooTest.cbl", "cobol", true));
 
-    Languages languages = new Languages(cobolLanguage);
-    ComponentIndexer indexer = createIndexer(languages);
-    indexer.execute(fs);
+    fs.index();
 
-    verify(sonarIndex).index(org.sonar.api.resources.File.create("/src/foo/bar/Foo.cbl", "foo/bar/Foo.cbl", cobolLanguage, false));
-    verify(sonarIndex).index(org.sonar.api.resources.File.create("/src2/foo/bar/Foo.cbl", "foo/bar/Foo.cbl", cobolLanguage, false));
-    verify(sonarIndex).index(org.sonar.api.resources.File.create("/src/test/foo/bar/FooTest.cbl", "foo/bar/FooTest.cbl", cobolLanguage, true));
+    verify(sonarIndex).index(org.sonar.api.resources.File.create("/src/foo/bar/Foo.cbl", cobolLanguage, false));
+    verify(sonarIndex).index(org.sonar.api.resources.File.create("/src2/foo/bar/Foo.cbl", cobolLanguage, false));
+    verify(sonarIndex).index(org.sonar.api.resources.File.create("/src/test/foo/bar/FooTest.cbl", cobolLanguage, true));
   }
 
   private DefaultInputFile newInputFile(String path, String content, String sourceRelativePath, String languageKey, boolean unitTest) throws IOException {
     File file = new File(baseDir, path);
     FileUtils.write(file, content);
     return new DeprecatedDefaultInputFile("foo", path)
-      .setPathRelativeToSourceDir(sourceRelativePath)
-      .setFile(file)
       .setLanguage(languageKey)
       .setType(unitTest ? InputFile.Type.TEST : InputFile.Type.MAIN);
   }
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 12be0438530..7f954c405a2 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
@@ -135,9 +135,9 @@ public class DefaultModuleFileSystemTest {
     DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache,
       new Project("foo"), settings, fileIndexer, initializer, componentIndexer);
 
-    File mainFile = temp.newFile();
-    InputFile mainInput = new DeprecatedDefaultInputFile("foo", "Main.java").setFile(mainFile).setType(InputFile.Type.MAIN);
-    InputFile testInput = new DeprecatedDefaultInputFile("foo", "Test.java").setFile(temp.newFile()).setType(InputFile.Type.TEST);
+    File baseDir = temp.newFile();
+    InputFile mainInput = new DeprecatedDefaultInputFile("foo", "Main.java").setModuleBaseDir(baseDir.toPath()).setType(InputFile.Type.MAIN);
+    InputFile testInput = new DeprecatedDefaultInputFile("foo", "Test.java").setModuleBaseDir(baseDir.toPath()).setType(InputFile.Type.TEST);
     when(moduleInputFileCache.inputFiles()).thenReturn(Lists.newArrayList(mainInput, testInput));
 
     fs.index();
@@ -145,7 +145,7 @@ public class DefaultModuleFileSystemTest {
     assertThat(inputFiles).containsOnly(mainInput);
 
     Iterable<File> files = fs.files(fs.predicates().hasType(InputFile.Type.MAIN));
-    assertThat(files).containsOnly(mainFile);
+    assertThat(files).containsOnly(new File(baseDir, "Main.java"));
   }
 
   @Test
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 4066080360b..3235301f031 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
@@ -49,7 +49,7 @@ public class DeprecatedFileFiltersTest {
   public void no_filters() throws Exception {
     DeprecatedFileFilters filters = new DeprecatedFileFilters();
 
-    InputFile inputFile = new DeprecatedDefaultInputFile("foo", "src/main/java/Foo.java").setFile(temp.newFile());
+    InputFile inputFile = new DeprecatedDefaultInputFile("foo", "src/main/java/Foo.java");
     assertThat(filters.accept(inputFile)).isTrue();
   }
 
@@ -58,11 +58,9 @@ public class DeprecatedFileFiltersTest {
     DeprecatedFileFilters filters = new DeprecatedFileFilters(new FileSystemFilter[] {filter});
 
     File basedir = temp.newFolder();
-    File file = temp.newFile();
+    File file = new File(basedir, "src/main/java/Foo.java");
     InputFile inputFile = new DeprecatedDefaultInputFile("foo", "src/main/java/Foo.java")
-      .setSourceDirAbsolutePath(new File(basedir, "src/main/java").getAbsolutePath())
-      .setPathRelativeToSourceDir("Foo.java")
-      .setFile(file)
+      .setModuleBaseDir(basedir.toPath())
       .setType(InputFile.Type.MAIN);
     when(filter.accept(eq(file), any(DeprecatedFileFilters.DeprecatedContext.class))).thenReturn(false);
 
@@ -73,8 +71,7 @@ public class DeprecatedFileFiltersTest {
 
     DeprecatedFileFilters.DeprecatedContext context = argument.getValue();
     assertThat(context.canonicalPath()).isEqualTo(FilenameUtils.separatorsToUnix(file.getAbsolutePath()));
-    assertThat(context.relativeDir()).isEqualTo(new File(basedir, "src/main/java"));
-    assertThat(context.relativePath()).isEqualTo("Foo.java");
+    assertThat(context.relativePath()).isEqualTo("src/main/java/Foo.java");
     assertThat(context.type()).isEqualTo(FileType.MAIN);
   }
 }
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 02478075c9c..c5bd36cddf5 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
@@ -28,6 +28,7 @@ import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.config.Settings;
 import org.sonar.api.scan.filesystem.FileExclusions;
 
+import java.io.File;
 import java.io.IOException;
 
 import static org.assertj.core.api.Assertions.assertThat;
@@ -43,7 +44,7 @@ public class ExclusionFiltersTest {
     filter.prepare();
 
     java.io.File file = temp.newFile();
-    DefaultInputFile inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/FooDao.java").setFile(file);
+    DefaultInputFile inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/FooDao.java").setModuleBaseDir(temp.newFolder().toPath());
     assertThat(filter.accept(inputFile, InputFile.Type.MAIN)).isTrue();
     assertThat(filter.accept(inputFile, InputFile.Type.TEST)).isTrue();
   }
@@ -56,10 +57,10 @@ public class ExclusionFiltersTest {
     filter.prepare();
 
     java.io.File file = temp.newFile();
-    DefaultInputFile inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/FooDao.java").setFile(file);
+    DefaultInputFile inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/FooDao.java").setModuleBaseDir(temp.newFolder().toPath());
     assertThat(filter.accept(inputFile, InputFile.Type.MAIN)).isTrue();
 
-    inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/Foo.java").setFile(file);
+    inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/Foo.java").setModuleBaseDir(temp.newFolder().toPath());
     assertThat(filter.accept(inputFile, InputFile.Type.MAIN)).isFalse();
   }
 
@@ -73,10 +74,10 @@ public class ExclusionFiltersTest {
 
     java.io.File file = temp.newFile();
 
-    DefaultInputFile inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/Foo.java").setFile(file);
+    DefaultInputFile inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/Foo.java").setModuleBaseDir(temp.newFolder().toPath());
     assertThat(filter.accept(inputFile, InputFile.Type.MAIN)).isFalse();
 
-    inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/FooDto.java").setFile(file);
+    inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/FooDto.java").setModuleBaseDir(temp.newFolder().toPath());
     assertThat(filter.accept(inputFile, InputFile.Type.MAIN)).isTrue();
   }
 
@@ -91,21 +92,21 @@ public class ExclusionFiltersTest {
     filter.prepare();
 
     java.io.File file = temp.newFile();
-    DefaultInputFile inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/FooDao.java").setFile(file);
+    DefaultInputFile inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/FooDao.java").setModuleBaseDir(temp.newFolder().toPath());
     assertThat(filter.accept(inputFile, InputFile.Type.MAIN)).isFalse();
 
-    inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/Foo.java").setFile(file);
+    inputFile = new DefaultInputFile("foo", "src/main/java/com/mycompany/Foo.java").setModuleBaseDir(temp.newFolder().toPath());
     assertThat(filter.accept(inputFile, InputFile.Type.MAIN)).isTrue();
 
     // source exclusions do not apply to tests
-    inputFile = new DefaultInputFile("foo", "src/test/java/com/mycompany/FooDao.java").setFile(file);
+    inputFile = new DefaultInputFile("foo", "src/test/java/com/mycompany/FooDao.java").setModuleBaseDir(temp.newFolder().toPath());
     assertThat(filter.accept(inputFile, InputFile.Type.TEST)).isTrue();
   }
 
   @Test
   public void match_exclusion_by_absolute_path() throws IOException {
-    java.io.File includedFile = temp.newFile("Foo.java");
-    java.io.File excludedFile = temp.newFile("Bar.java");
+    File baseDir = temp.newFile();
+    File excludedFile = new File(baseDir, "src/main/java/org/bar/Bar.java");
 
     Settings settings = new Settings();
     settings.setProperty(CoreProperties.PROJECT_INCLUSIONS_PROPERTY, "src/main/java/**/*");
@@ -114,10 +115,10 @@ public class ExclusionFiltersTest {
 
     filter.prepare();
 
-    DefaultInputFile inputFile = new DefaultInputFile("foo", "src/main/java/org/bar/Foo.java").setFile(includedFile);
+    DefaultInputFile inputFile = new DefaultInputFile("foo", "src/main/java/org/bar/Foo.java").setModuleBaseDir(baseDir.toPath());
     assertThat(filter.accept(inputFile, InputFile.Type.MAIN)).isTrue();
 
-    inputFile = new DefaultInputFile("foo", "src/main/java/org/bar/Bar.java").setFile(excludedFile);
+    inputFile = new DefaultInputFile("foo", "src/main/java/org/bar/Bar.java").setModuleBaseDir(baseDir.toPath());
     assertThat(filter.accept(inputFile, InputFile.Type.MAIN)).isFalse();
   }
 
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/FileMetadataTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/FileMetadataTest.java
index cbfcb03242b..b34c5d50271 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/FileMetadataTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/FileMetadataTest.java
@@ -25,12 +25,13 @@ import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
 import org.junit.rules.TemporaryFolder;
+import org.sonar.api.batch.AnalysisMode;
 
 import java.io.File;
 
-import static org.apache.commons.codec.digest.DigestUtils.md5;
 import static org.apache.commons.codec.digest.DigestUtils.md5Hex;
 import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.Mockito.mock;
 
 public class FileMetadataTest {
 
@@ -40,17 +41,18 @@ public class FileMetadataTest {
   @Rule
   public TemporaryFolder temp = new TemporaryFolder();
 
+  private AnalysisMode mode = mock(AnalysisMode.class);
+
   @Test
   public void empty_file() throws Exception {
     File tempFile = temp.newFile();
     FileUtils.touch(tempFile);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_8);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_8);
     assertThat(metadata.lines).isEqualTo(1);
     assertThat(metadata.nonBlankLines).isEqualTo(0);
     assertThat(metadata.hash).isNotEmpty();
     assertThat(metadata.originalLineOffsets).containsOnly(0);
-    assertThat(metadata.lineHashes[0]).isNull();
     assertThat(metadata.empty).isTrue();
   }
 
@@ -59,14 +61,11 @@ public class FileMetadataTest {
     File tempFile = temp.newFile();
     FileUtils.write(tempFile, "foo\r\nbar\r\nbaz", Charsets.UTF_8, true);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_8);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_8);
     assertThat(metadata.lines).isEqualTo(3);
     assertThat(metadata.nonBlankLines).isEqualTo(3);
     assertThat(metadata.hash).isEqualTo(md5Hex("foo\nbar\nbaz"));
     assertThat(metadata.originalLineOffsets).containsOnly(0, 5, 10);
-    assertThat(metadata.lineHashes[0]).containsOnly(md5("foo"));
-    assertThat(metadata.lineHashes[1]).containsOnly(md5("bar"));
-    assertThat(metadata.lineHashes[2]).containsOnly(md5("baz"));
     assertThat(metadata.empty).isFalse();
   }
 
@@ -75,15 +74,11 @@ public class FileMetadataTest {
     File tempFile = temp.newFile();
     FileUtils.write(tempFile, "föo\r\nbàr\r\n\u1D11Ebaßz\r\n", Charsets.UTF_8, true);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_8);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_8);
     assertThat(metadata.lines).isEqualTo(4);
     assertThat(metadata.nonBlankLines).isEqualTo(3);
     assertThat(metadata.hash).isEqualTo(md5Hex("föo\nbàr\n\u1D11Ebaßz\n"));
     assertThat(metadata.originalLineOffsets).containsOnly(0, 5, 10, 18);
-    assertThat(metadata.lineHashes[0]).containsExactly(md5("föo"));
-    assertThat(metadata.lineHashes[1]).containsExactly(md5("bàr"));
-    assertThat(metadata.lineHashes[2]).containsExactly(md5("\u1D11Ebaßz"));
-    assertThat(metadata.lineHashes[3]).isNull();
   }
 
   @Test
@@ -91,15 +86,11 @@ public class FileMetadataTest {
     File tempFile = temp.newFile();
     FileUtils.write(tempFile, "föo\r\nbàr\r\n\u1D11Ebaßz\r\n", Charsets.UTF_16, true);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_16);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_16);
     assertThat(metadata.lines).isEqualTo(4);
     assertThat(metadata.nonBlankLines).isEqualTo(3);
     assertThat(metadata.hash).isEqualTo(md5Hex("föo\nbàr\n\u1D11Ebaßz\n"));
     assertThat(metadata.originalLineOffsets).containsOnly(0, 5, 10, 18);
-    assertThat(metadata.lineHashes[0]).containsExactly(md5("föo"));
-    assertThat(metadata.lineHashes[1]).containsExactly(md5("bàr"));
-    assertThat(metadata.lineHashes[2]).containsExactly(md5("\u1D11Ebaßz"));
-    assertThat(metadata.lineHashes[3]).isNull();
   }
 
   @Test
@@ -107,14 +98,11 @@ public class FileMetadataTest {
     File tempFile = temp.newFile();
     FileUtils.write(tempFile, "foo\nbar\nbaz", Charsets.UTF_8, true);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_8);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_8);
     assertThat(metadata.lines).isEqualTo(3);
     assertThat(metadata.nonBlankLines).isEqualTo(3);
     assertThat(metadata.hash).isEqualTo(md5Hex("foo\nbar\nbaz"));
     assertThat(metadata.originalLineOffsets).containsOnly(0, 4, 8);
-    assertThat(metadata.lineHashes[0]).containsOnly(md5("foo"));
-    assertThat(metadata.lineHashes[1]).containsOnly(md5("bar"));
-    assertThat(metadata.lineHashes[2]).containsOnly(md5("baz"));
   }
 
   @Test
@@ -122,15 +110,11 @@ public class FileMetadataTest {
     File tempFile = temp.newFile();
     FileUtils.write(tempFile, "foo\nbar\nbaz\n", Charsets.UTF_8, true);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_8);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_8);
     assertThat(metadata.lines).isEqualTo(4);
     assertThat(metadata.nonBlankLines).isEqualTo(3);
     assertThat(metadata.hash).isEqualTo(md5Hex("foo\nbar\nbaz\n"));
     assertThat(metadata.originalLineOffsets).containsOnly(0, 4, 8, 12);
-    assertThat(metadata.lineHashes[0]).containsOnly(md5("foo"));
-    assertThat(metadata.lineHashes[1]).containsOnly(md5("bar"));
-    assertThat(metadata.lineHashes[2]).containsOnly(md5("baz"));
-    assertThat(metadata.lineHashes[3]).isNull();
   }
 
   @Test
@@ -138,15 +122,11 @@ public class FileMetadataTest {
     File tempFile = temp.newFile();
     FileUtils.write(tempFile, "foo\nbar\r\nbaz\n", Charsets.UTF_8, true);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_8);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_8);
     assertThat(metadata.lines).isEqualTo(4);
     assertThat(metadata.nonBlankLines).isEqualTo(3);
     assertThat(metadata.hash).isEqualTo(md5Hex("foo\nbar\nbaz\n"));
     assertThat(metadata.originalLineOffsets).containsOnly(0, 4, 9, 13);
-    assertThat(metadata.lineHashes[0]).containsOnly(md5("foo"));
-    assertThat(metadata.lineHashes[1]).containsOnly(md5("bar"));
-    assertThat(metadata.lineHashes[2]).containsOnly(md5("baz"));
-    assertThat(metadata.lineHashes[3]).isNull();
   }
 
   @Test
@@ -154,15 +134,11 @@ public class FileMetadataTest {
     File tempFile = temp.newFile();
     FileUtils.write(tempFile, "foo\n\n\nbar", Charsets.UTF_8, true);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_8);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_8);
     assertThat(metadata.lines).isEqualTo(4);
     assertThat(metadata.nonBlankLines).isEqualTo(2);
     assertThat(metadata.hash).isEqualTo(md5Hex("foo\n\n\nbar"));
     assertThat(metadata.originalLineOffsets).containsOnly(0, 4, 5, 6);
-    assertThat(metadata.lineHashes[0]).containsOnly(md5("foo"));
-    assertThat(metadata.lineHashes[1]).isNull();
-    assertThat(metadata.lineHashes[2]).isNull();
-    assertThat(metadata.lineHashes[3]).containsOnly(md5("bar"));
   }
 
   @Test
@@ -170,14 +146,11 @@ public class FileMetadataTest {
     File tempFile = temp.newFile();
     FileUtils.write(tempFile, "foo\nbar\r\nbaz", Charsets.UTF_8, true);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_8);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_8);
     assertThat(metadata.lines).isEqualTo(3);
     assertThat(metadata.nonBlankLines).isEqualTo(3);
     assertThat(metadata.hash).isEqualTo(md5Hex("foo\nbar\nbaz"));
     assertThat(metadata.originalLineOffsets).containsOnly(0, 4, 9);
-    assertThat(metadata.lineHashes[0]).containsOnly(md5("foo"));
-    assertThat(metadata.lineHashes[1]).containsOnly(md5("bar"));
-    assertThat(metadata.lineHashes[2]).containsOnly(md5("baz"));
   }
 
   @Test
@@ -185,15 +158,11 @@ public class FileMetadataTest {
     File tempFile = temp.newFile();
     FileUtils.write(tempFile, "\nfoo\nbar\r\nbaz", Charsets.UTF_8, true);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_8);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_8);
     assertThat(metadata.lines).isEqualTo(4);
     assertThat(metadata.nonBlankLines).isEqualTo(3);
     assertThat(metadata.hash).isEqualTo(md5Hex("\nfoo\nbar\nbaz"));
     assertThat(metadata.originalLineOffsets).containsOnly(0, 1, 5, 10);
-    assertThat(metadata.lineHashes[0]).isNull();
-    assertThat(metadata.lineHashes[1]).containsOnly(md5("foo"));
-    assertThat(metadata.lineHashes[2]).containsOnly(md5("bar"));
-    assertThat(metadata.lineHashes[3]).containsOnly(md5("baz"));
   }
 
   @Test
@@ -201,14 +170,11 @@ public class FileMetadataTest {
     File tempFile = temp.newFile();
     FileUtils.write(tempFile, "\uFEFFfoo\nbar\r\nbaz", Charsets.UTF_8, true);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_8);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_8);
     assertThat(metadata.lines).isEqualTo(3);
     assertThat(metadata.nonBlankLines).isEqualTo(3);
     assertThat(metadata.hash).isEqualTo(md5Hex("foo\nbar\nbaz"));
     assertThat(metadata.originalLineOffsets).containsOnly(0, 4, 9);
-    assertThat(metadata.lineHashes[0]).containsOnly(md5("foo"));
-    assertThat(metadata.lineHashes[1]).containsOnly(md5("bar"));
-    assertThat(metadata.lineHashes[2]).containsOnly(md5("baz"));
   }
 
   @Test
@@ -216,13 +182,10 @@ public class FileMetadataTest {
     File tempFile = temp.newFile();
     FileUtils.write(tempFile, " foo\nb ar\r\nbaz \t", Charsets.UTF_8, true);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(tempFile, Charsets.UTF_8);
+    FileMetadata.Metadata metadata = new FileMetadata(mode).read(tempFile, Charsets.UTF_8);
     assertThat(metadata.lines).isEqualTo(3);
     assertThat(metadata.nonBlankLines).isEqualTo(3);
     assertThat(metadata.hash).isEqualTo(md5Hex(" foo\nb ar\nbaz \t"));
-    assertThat(metadata.lineHashes[0]).containsOnly(md5("foo"));
-    assertThat(metadata.lineHashes[1]).containsOnly(md5("bar"));
-    assertThat(metadata.lineHashes[2]).containsOnly(md5("baz"));
   }
 
   @Test
@@ -233,7 +196,7 @@ public class FileMetadataTest {
     thrown.expect(IllegalStateException.class);
     thrown.expectMessage("Fail to read file '" + file.getAbsolutePath() + "' with encoding 'UTF-8'");
 
-    new FileMetadata().read(file, Charsets.UTF_8);
+    new FileMetadata(mode).read(file, Charsets.UTF_8);
   }
 
   @Test
@@ -248,9 +211,9 @@ public class FileMetadataTest {
     File file2 = temp.newFile();
     FileUtils.write(file2, "foo\nbar", Charsets.UTF_8, true);
 
-    String hash1 = new FileMetadata().read(file1, Charsets.UTF_8).hash;
-    String hash1a = new FileMetadata().read(file1a, Charsets.UTF_8).hash;
-    String hash2 = new FileMetadata().read(file2, Charsets.UTF_8).hash;
+    String hash1 = new FileMetadata(mode).read(file1, Charsets.UTF_8).hash;
+    String hash1a = new FileMetadata(mode).read(file1a, Charsets.UTF_8).hash;
+    String hash2 = new FileMetadata(mode).read(file2, Charsets.UTF_8).hash;
     assertThat(hash1).isEqualTo(hash1a);
     assertThat(hash1).isNotEqualTo(hash2);
   }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactoryTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactoryTest.java
index e702dbbfa81..2b5b1f4bcca 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactoryTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactoryTest.java
@@ -39,7 +39,7 @@ public class InputFileBuilderFactoryTest {
     DefaultAnalysisMode analysisMode = mock(DefaultAnalysisMode.class);
 
     InputFileBuilderFactory factory = new InputFileBuilderFactory(ProjectDefinition.create().setKey("struts"), pathResolver, langDetectionFactory,
-      statusDetectionFactory, analysisMode, new Settings());
+      statusDetectionFactory, analysisMode, new Settings(), new FileMetadata(analysisMode));
     InputFileBuilder builder = factory.create(fs);
 
     assertThat(builder.langDetection()).isNotNull();
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderTest.java
index 36682184b37..df058f13c8f 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputFileBuilderTest.java
@@ -32,7 +32,6 @@ import org.sonar.api.utils.PathUtils;
 import org.sonar.batch.bootstrap.DefaultAnalysisMode;
 
 import java.io.File;
-import java.util.Arrays;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Matchers.any;
@@ -67,9 +66,9 @@ public class InputFileBuilderTest {
       .thenReturn(InputFile.Status.ADDED);
 
     InputFileBuilder builder = new InputFileBuilder("struts", new PathResolver(),
-      langDetection, statusDetection, fs, analysisMode, new Settings());
+      langDetection, statusDetection, fs, analysisMode, new Settings(), new FileMetadata(analysisMode));
     DeprecatedDefaultInputFile inputFile = builder.create(srcFile);
-    inputFile = builder.complete(inputFile, InputFile.Type.MAIN);
+    builder.completeAndComputeMetadata(inputFile, InputFile.Type.MAIN);
 
     assertThat(inputFile.type()).isEqualTo(InputFile.Type.MAIN);
     assertThat(inputFile.file()).isEqualTo(srcFile.getAbsoluteFile());
@@ -78,9 +77,6 @@ public class InputFileBuilderTest {
     assertThat(inputFile.key()).isEqualTo("struts:src/main/java/foo/Bar.java");
     assertThat(inputFile.relativePath()).isEqualTo("src/main/java/foo/Bar.java");
     assertThat(inputFile.lines()).isEqualTo(1);
-    assertThat(inputFile.sourceDirAbsolutePath()).isNull();
-    assertThat(inputFile.pathRelativeToSourceDir()).isNull();
-    assertThat(inputFile.deprecatedKey()).isNull();
   }
 
   @Test
@@ -93,7 +89,7 @@ public class InputFileBuilderTest {
     when(fs.baseDir()).thenReturn(basedir);
 
     InputFileBuilder builder = new InputFileBuilder("struts", new PathResolver(),
-      langDetection, statusDetection, fs, analysisMode, new Settings());
+      langDetection, statusDetection, fs, analysisMode, new Settings(), new FileMetadata(analysisMode));
     DeprecatedDefaultInputFile inputFile = builder.create(srcFile);
 
     assertThat(inputFile).isNull();
@@ -113,69 +109,11 @@ public class InputFileBuilderTest {
     when(langDetection.language(any(InputFile.class))).thenReturn(null);
 
     InputFileBuilder builder = new InputFileBuilder("struts", new PathResolver(),
-      langDetection, statusDetection, fs, analysisMode, new Settings());
+      langDetection, statusDetection, fs, analysisMode, new Settings(), new FileMetadata(analysisMode));
     DeprecatedDefaultInputFile inputFile = builder.create(srcFile);
-    inputFile = builder.complete(inputFile, InputFile.Type.MAIN);
+    InputFileMetadata metadata = builder.completeAndComputeMetadata(inputFile, InputFile.Type.MAIN);
 
-    assertThat(inputFile).isNull();
-  }
-
-  @Test
-  public void fill_deprecated_data_of_java_file() throws Exception {
-    // file system
-    File basedir = temp.newFolder();
-    File srcFile = new File(basedir, "src/main/java/foo/Bar.java");
-    FileUtils.touch(srcFile);
-    FileUtils.write(srcFile, "single line");
-    when(fs.baseDir()).thenReturn(basedir);
-    when(fs.encoding()).thenReturn(Charsets.UTF_8);
-    File sourceDir = new File(basedir, "src/main/java");
-    when(fs.sourceDirs()).thenReturn(Arrays.asList(sourceDir));
-
-    // lang
-    when(langDetection.language(any(InputFile.class))).thenReturn("java");
-
-    // status
-    when(statusDetection.status("foo", "src/main/java/foo/Bar.java", "6c1d64c0b3555892fe7273e954f6fb5a"))
-      .thenReturn(InputFile.Status.ADDED);
-
-    InputFileBuilder builder = new InputFileBuilder("struts", new PathResolver(),
-      langDetection, statusDetection, fs, analysisMode, new Settings());
-    DeprecatedDefaultInputFile inputFile = builder.create(srcFile);
-    inputFile = builder.complete(inputFile, InputFile.Type.MAIN);
-
-    assertThat(inputFile.pathRelativeToSourceDir()).isEqualTo("foo/Bar.java");
-    assertThat(inputFile.sourceDirAbsolutePath()).isEqualTo(PathUtils.sanitize(sourceDir.getAbsolutePath()));
-    assertThat(inputFile.deprecatedKey()).isEqualTo("struts:foo.Bar");
+    assertThat(metadata).isNull();
   }
 
-  @Test
-  public void fill_deprecated_data_of_non_java_file() throws Exception {
-    // file system
-    File basedir = temp.newFolder();
-    File srcFile = new File(basedir, "src/foo/Bar.php");
-    FileUtils.touch(srcFile);
-    FileUtils.write(srcFile, "single line");
-    when(fs.baseDir()).thenReturn(basedir);
-    when(fs.encoding()).thenReturn(Charsets.UTF_8);
-    File sourceDir = new File(basedir, "src");
-    when(fs.sourceDirs()).thenReturn(Arrays.asList(sourceDir));
-
-    // lang
-    when(langDetection.language(any(InputFile.class))).thenReturn("php");
-
-    // status
-    when(statusDetection.status("foo", "src/Bar.php", "6c1d64c0b3555892fe7273e954f6fb5a"))
-      .thenReturn(InputFile.Status.ADDED);
-
-    InputFileBuilder builder = new InputFileBuilder("struts", new PathResolver(),
-      langDetection, statusDetection, fs, analysisMode, new Settings());
-    DeprecatedDefaultInputFile inputFile = builder.create(srcFile);
-    inputFile = builder.complete(inputFile, InputFile.Type.MAIN);
-
-    assertThat(inputFile.pathRelativeToSourceDir()).isEqualTo("foo/Bar.php");
-    assertThat(inputFile.sourceDirAbsolutePath()).isEqualTo(PathUtils.sanitize(sourceDir.getAbsolutePath()));
-    assertThat(inputFile.deprecatedKey()).isEqualTo("struts:foo/Bar.php");
-
-  }
 }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputPathCacheTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputPathCacheTest.java
index 1a38d6e998c..7c943e06f66 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputPathCacheTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputPathCacheTest.java
@@ -19,7 +19,7 @@
  */
 package org.sonar.batch.scan.filesystem;
 
-import org.apache.commons.codec.digest.DigestUtils;
+import com.google.common.base.Charsets;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Rule;
@@ -30,8 +30,6 @@ import org.sonar.api.batch.fs.InputFile.Type;
 import org.sonar.api.batch.fs.InputPath;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
-import org.sonar.batch.index.Caches;
-import org.sonar.batch.index.CachesTest;
 
 import static org.assertj.core.api.Assertions.assertThat;
 
@@ -40,59 +38,61 @@ public class InputPathCacheTest {
   @Rule
   public TemporaryFolder temp = new TemporaryFolder();
 
-  Caches caches;
-
   @Before
   public void start() throws Exception {
-    caches = CachesTest.createCacheOnTemp(temp);
-    caches.start();
   }
 
   @After
   public void stop() {
-    caches.stop();
   }
 
   @Test
   public void should_add_input_file() throws Exception {
-    InputPathCache cache = new InputPathCache(caches);
-    DefaultInputFile fooFile = new DefaultInputFile("foo", "src/main/java/Foo.java").setFile(temp.newFile("Foo.java"));
+    InputPathCache cache = new InputPathCache();
+    DefaultInputFile fooFile = new DefaultInputFile("foo", "src/main/java/Foo.java").setModuleBaseDir(temp.newFolder().toPath());
     cache.put("struts", fooFile);
     cache.put("struts-core", new DeprecatedDefaultInputFile("foo", "src/main/java/Bar.java")
-      .setBasedir(temp.newFolder())
-      .setDeprecatedKey("foo")
-      .setSourceDirAbsolutePath("foo")
-      .setPathRelativeToSourceDir("foo")
       .setLanguage("bla")
       .setType(Type.MAIN)
       .setStatus(Status.ADDED)
-      .setHash("xyz")
       .setLines(2)
-      .setEncoding("UTF-8")
-      .setOriginalLineOffsets(new long[] {0, 4})
-      .setLineHashes(new byte[][] {DigestUtils.md5("foo"), DigestUtils.md5("bar")})
-      .setFile(temp.newFile("Bar.java")));
+      .setCharset(Charsets.UTF_8)
+      .setModuleBaseDir(temp.newFolder().toPath()));
 
     DefaultInputFile loadedFile = (DefaultInputFile) cache.getFile("struts-core", "src/main/java/Bar.java");
     assertThat(loadedFile.relativePath()).isEqualTo("src/main/java/Bar.java");
-    assertThat(loadedFile.encoding()).isEqualTo("UTF-8");
-    assertThat(loadedFile.originalLineOffsets()).containsOnly(0, 4);
-    assertThat(loadedFile.lineHashes()[0]).containsOnly(DigestUtils.md5("foo"));
-    assertThat(loadedFile.lineHashes()[1]).containsOnly(DigestUtils.md5("bar"));
+    assertThat(loadedFile.charset()).isEqualTo(Charsets.UTF_8);
 
     assertThat(cache.filesByModule("struts")).hasSize(1);
     assertThat(cache.filesByModule("struts-core")).hasSize(1);
-    assertThat(cache.all()).hasSize(2);
-    for (InputPath inputPath : cache.all()) {
+    assertThat(cache.allFiles()).hasSize(2);
+    for (InputPath inputPath : cache.allFiles()) {
       assertThat(inputPath.relativePath()).startsWith("src/main/java/");
     }
 
     cache.remove("struts", fooFile);
-    assertThat(cache.all()).hasSize(1);
+    assertThat(cache.allFiles()).hasSize(1);
 
     cache.removeModule("struts");
     assertThat(cache.filesByModule("struts")).hasSize(0);
     assertThat(cache.filesByModule("struts-core")).hasSize(1);
-    assertThat(cache.all()).hasSize(1);
+    assertThat(cache.allFiles()).hasSize(1);
+  }
+
+  @Test
+  public void should_add_input_file_metadata() throws Exception {
+    InputPathCache cache = new InputPathCache();
+    cache.put("struts-core", "src/main/java/Bar.java", new InputFileMetadata()
+      .setHash("xyz")
+      .setNonBlankLines(2)
+      .setEmpty(true)
+      .setOriginalLineOffsets(new int[] {0, 4}));
+
+    InputFileMetadata loadedFileMetadata = cache.getFileMetadata("struts-core", "src/main/java/Bar.java");
+    assertThat(loadedFileMetadata.originalLineOffsets()).containsOnly(0, 4);
+    assertThat(loadedFileMetadata.hash()).isEqualTo("xyz");
+    assertThat(loadedFileMetadata.nonBlankLines()).isEqualTo(2);
+    assertThat(loadedFileMetadata.isEmpty()).isTrue();
+
   }
 }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageDetectionFactoryTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageDetectionFactoryTest.java
index af30dcfc706..93b4d05145a 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageDetectionFactoryTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageDetectionFactoryTest.java
@@ -19,19 +19,19 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.batch.repository.language.DefaultLanguagesRepository;
+import org.sonar.batch.repository.language.LanguagesRepository;
+
 import org.junit.Test;
 import org.sonar.api.config.Settings;
 import org.sonar.api.resources.Java;
 import org.sonar.api.resources.Languages;
-import org.sonar.batch.languages.DefaultLanguagesReferential;
-import org.sonar.batch.languages.LanguagesReferential;
-
 import static org.assertj.core.api.Assertions.assertThat;
 
 public class LanguageDetectionFactoryTest {
   @Test
   public void testCreate() throws Exception {
-    LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(Java.INSTANCE));
+    LanguagesRepository languages = new DefaultLanguagesRepository(new Languages(Java.INSTANCE));
     LanguageDetectionFactory factory = new LanguageDetectionFactory(new Settings(), languages);
     LanguageDetection languageDetection = factory.create();
     assertThat(languageDetection).isNotNull();
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageDetectionTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageDetectionTest.java
index e9155fd9c8a..95d3631eaa5 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageDetectionTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/LanguageDetectionTest.java
@@ -30,8 +30,8 @@ import org.sonar.api.config.Settings;
 import org.sonar.api.resources.Language;
 import org.sonar.api.resources.Languages;
 import org.sonar.api.utils.MessageException;
-import org.sonar.batch.languages.DefaultLanguagesReferential;
-import org.sonar.batch.languages.LanguagesReferential;
+import org.sonar.batch.repository.language.DefaultLanguagesRepository;
+import org.sonar.batch.repository.language.LanguagesRepository;
 
 import java.io.File;
 import java.io.IOException;
@@ -58,7 +58,7 @@ public class LanguageDetectionTest {
 
   @Test
   public void search_by_file_extension() throws Exception {
-    LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(new MockLanguage("java", "java", "jav"), new MockLanguage("cobol", "cbl", "cob")));
+    LanguagesRepository languages = new DefaultLanguagesRepository(new Languages(new MockLanguage("java", "java", "jav"), new MockLanguage("cobol", "cbl", "cob")));
     LanguageDetection detection = new LanguageDetection(new Settings(), languages);
 
     assertThat(detection.language(newInputFile("Foo.java"))).isEqualTo("java");
@@ -76,13 +76,13 @@ public class LanguageDetectionTest {
 
   @Test
   public void should_not_fail_if_no_language() throws Exception {
-    LanguageDetection detection = spy(new LanguageDetection(new Settings(), new DefaultLanguagesReferential(new Languages())));
+    LanguageDetection detection = spy(new LanguageDetection(new Settings(), new DefaultLanguagesRepository(new Languages())));
     assertThat(detection.language(newInputFile("Foo.java"))).isNull();
   }
 
   @Test
   public void plugin_can_declare_a_file_extension_twice_for_case_sensitivity() throws Exception {
-    LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(new MockLanguage("abap", "abap", "ABAP")));
+    LanguagesRepository languages = new DefaultLanguagesRepository(new Languages(new MockLanguage("abap", "abap", "ABAP")));
 
     LanguageDetection detection = new LanguageDetection(new Settings(), languages);
     assertThat(detection.language(newInputFile("abc.abap"))).isEqualTo("abap");
@@ -92,7 +92,7 @@ public class LanguageDetectionTest {
   public void language_with_no_extension() throws Exception {
     // abap does not declare any file extensions.
     // When analyzing an ABAP project, then all source files must be parsed.
-    LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(new MockLanguage("java", "java"), new MockLanguage("abap")));
+    LanguagesRepository languages = new DefaultLanguagesRepository(new Languages(new MockLanguage("java", "java"), new MockLanguage("abap")));
 
     // No side-effect on non-ABAP projects
     LanguageDetection detection = new LanguageDetection(new Settings(), languages);
@@ -110,7 +110,7 @@ public class LanguageDetectionTest {
 
   @Test
   public void force_language_using_deprecated_property() throws Exception {
-    LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(new MockLanguage("java", "java"), new MockLanguage("php", "php")));
+    LanguagesRepository languages = new DefaultLanguagesRepository(new Languages(new MockLanguage("java", "java"), new MockLanguage("php", "php")));
 
     Settings settings = new Settings();
     settings.setProperty(CoreProperties.PROJECT_LANGUAGE_PROPERTY, "java");
@@ -126,7 +126,7 @@ public class LanguageDetectionTest {
     thrown.expect(MessageException.class);
     thrown.expectMessage("No language is installed with key 'unknown'. Please update property 'sonar.language'");
 
-    LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(new MockLanguage("java", "java"), new MockLanguage("php", "php")));
+    LanguagesRepository languages = new DefaultLanguagesRepository(new Languages(new MockLanguage("java", "java"), new MockLanguage("php", "php")));
     Settings settings = new Settings();
     settings.setProperty(CoreProperties.PROJECT_LANGUAGE_PROPERTY, "unknown");
     new LanguageDetection(settings, languages);
@@ -134,7 +134,7 @@ public class LanguageDetectionTest {
 
   @Test
   public void fail_if_conflicting_language_suffix() throws Exception {
-    LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(new MockLanguage("xml", "xhtml"), new MockLanguage("web", "xhtml")));
+    LanguagesRepository languages = new DefaultLanguagesRepository(new Languages(new MockLanguage("xml", "xhtml"), new MockLanguage("web", "xhtml")));
     LanguageDetection detection = new LanguageDetection(new Settings(), languages);
     try {
       detection.language(newInputFile("abc.xhtml"));
@@ -149,7 +149,7 @@ public class LanguageDetectionTest {
 
   @Test
   public void solve_conflict_using_filepattern() throws Exception {
-    LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(new MockLanguage("xml", "xhtml"), new MockLanguage("web", "xhtml")));
+    LanguagesRepository languages = new DefaultLanguagesRepository(new Languages(new MockLanguage("xml", "xhtml"), new MockLanguage("web", "xhtml")));
 
     Settings settings = new Settings();
     settings.setProperty("sonar.lang.patterns.xml", "xml/**");
@@ -161,7 +161,7 @@ public class LanguageDetectionTest {
 
   @Test
   public void fail_if_conflicting_filepattern() throws Exception {
-    LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(new MockLanguage("abap", "abap"), new MockLanguage("cobol", "cobol")));
+    LanguagesRepository languages = new DefaultLanguagesRepository(new Languages(new MockLanguage("abap", "abap"), new MockLanguage("cobol", "cobol")));
     Settings settings = new Settings();
     settings.setProperty("sonar.lang.patterns.abap", "*.abap,*.txt");
     settings.setProperty("sonar.lang.patterns.cobol", "*.cobol,*.txt");
@@ -183,7 +183,7 @@ public class LanguageDetectionTest {
 
   private InputFile newInputFile(String path) throws IOException {
     File basedir = temp.newFolder();
-    return new DefaultInputFile("foo", path).setFile(new File(basedir, path));
+    return new DefaultInputFile("foo", path).setModuleBaseDir(basedir.toPath());
   }
 
   static class MockLanguage implements Language {
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/measure/MeasureCacheTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/measure/MeasureCacheTest.java
index ebb97af6492..7aa5c49856d 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/measure/MeasureCacheTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/measure/MeasureCacheTest.java
@@ -233,9 +233,9 @@ public class MeasureCacheTest {
   @Test
   public void should_get_measures() throws Exception {
     Project p = new Project("struts");
-    Resource dir = new Directory("foo/bar").setEffectiveKey("struts:foo/bar");
-    Resource file1 = new File("foo/bar/File1.txt").setEffectiveKey("struts:foo/bar/File1.txt");
-    Resource file2 = new File("foo/bar/File2.txt").setEffectiveKey("struts:foo/bar/File2.txt");
+    Resource dir = Directory.create("foo/bar").setEffectiveKey("struts:foo/bar");
+    Resource file1 = Directory.create("foo/bar/File1.txt").setEffectiveKey("struts:foo/bar/File1.txt");
+    Resource file2 = Directory.create("foo/bar/File2.txt").setEffectiveKey("struts:foo/bar/File2.txt");
 
     assertThat(cache.entries()).hasSize(0);
 
@@ -271,7 +271,7 @@ public class MeasureCacheTest {
 
   @Test
   public void test_measure_coder() throws Exception {
-    Resource file1 = new File("foo/bar/File1.txt").setEffectiveKey("struts:foo/bar/File1.txt");
+    Resource file1 = File.create("foo/bar/File1.txt").setEffectiveKey("struts:foo/bar/File1.txt");
 
     Measure measure = new Measure(CoreMetrics.NCLOC, 1.786, 5);
     cache.put(file1, measure);
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/report/JSONReportTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/report/JSONReportTest.java
index 786d5a7f040..1e61491a8c1 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/report/JSONReportTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/report/JSONReportTest.java
@@ -27,8 +27,8 @@ import org.junit.Before;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
 import org.skyscreamer.jsonassert.JSONAssert;
+import org.sonar.api.batch.fs.InputDir;
 import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.InputPath;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.batch.fs.internal.DefaultInputDir;
 import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
@@ -42,9 +42,9 @@ import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.rule.RuleKey;
 import org.sonar.batch.issue.IssueCache;
+import org.sonar.batch.repository.user.User;
+import org.sonar.batch.repository.user.UserRepository;
 import org.sonar.batch.scan.filesystem.InputPathCache;
-import org.sonar.batch.user.User;
-import org.sonar.batch.user.UserRepository;
 
 import java.io.File;
 import java.io.IOException;
@@ -77,7 +77,7 @@ public class JSONReportTest {
 
   @Before
   public void before() throws Exception {
-    fs = new DefaultFileSystem(temp.newFolder());
+    fs = new DefaultFileSystem(temp.newFolder().toPath());
     SIMPLE_DATE_FORMAT.setTimeZone(TimeZone.getTimeZone("GMT+02:00"));
     when(resource.getEffectiveKey()).thenReturn("Action.java");
     when(server.getVersion()).thenReturn("3.6");
@@ -86,7 +86,8 @@ public class JSONReportTest {
     DeprecatedDefaultInputFile inputFile = new DeprecatedDefaultInputFile("struts", "src/main/java/org/apache/struts/Action.java");
     inputFile.setStatus(InputFile.Status.CHANGED);
     InputPathCache fileCache = mock(InputPathCache.class);
-    when(fileCache.all()).thenReturn(Arrays.<InputPath>asList(inputDir, inputFile));
+    when(fileCache.allFiles()).thenReturn(Arrays.<InputFile>asList(inputFile));
+    when(fileCache.allDirs()).thenReturn(Arrays.<InputDir>asList(inputDir));
     Project rootModule = new Project("struts");
     Project moduleA = new Project("struts-core");
     moduleA.setParent(rootModule).setPath("core");
diff --git a/sonar-batch/src/test/java/org/sonar/batch/sensor/AnalyzerOptimizerTest.java b/sonar-batch/src/test/java/org/sonar/batch/sensor/AnalyzerOptimizerTest.java
index d0cf02f65a3..1850fe2b001 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/sensor/AnalyzerOptimizerTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/sensor/AnalyzerOptimizerTest.java
@@ -53,7 +53,7 @@ public class AnalyzerOptimizerTest {
 
   @Before
   public void prepare() throws Exception {
-    fs = new DefaultFileSystem(temp.newFolder());
+    fs = new DefaultFileSystem(temp.newFolder().toPath());
     settings = new Settings();
     analysisMode = mock(AnalysisMode.class);
     optimizer = new AnalyzerOptimizer(fs, new ActiveRulesBuilder().build(), settings, analysisMode);
diff --git a/sonar-batch/src/test/java/org/sonar/batch/sensor/DefaultSensorContextTest.java b/sonar-batch/src/test/java/org/sonar/batch/sensor/DefaultSensorContextTest.java
index e6d24b0643f..1812fde5cf4 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/sensor/DefaultSensorContextTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/sensor/DefaultSensorContextTest.java
@@ -58,7 +58,7 @@ public class DefaultSensorContextTest {
   @Before
   public void prepare() throws Exception {
     activeRules = new ActiveRulesBuilder().build();
-    fs = new DefaultFileSystem(temp.newFolder());
+    fs = new DefaultFileSystem(temp.newFolder().toPath());
     MetricFinder metricFinder = mock(MetricFinder.class);
     when(metricFinder.findByKey(CoreMetrics.NCLOC_KEY)).thenReturn(CoreMetrics.NCLOC);
     when(metricFinder.findByKey(CoreMetrics.FUNCTION_COMPLEXITY_DISTRIBUTION_KEY)).thenReturn(CoreMetrics.FUNCTION_COMPLEXITY_DISTRIBUTION);
diff --git a/sonar-batch/src/test/java/org/sonar/batch/sensor/DefaultSensorStorageTest.java b/sonar-batch/src/test/java/org/sonar/batch/sensor/DefaultSensorStorageTest.java
index 658f48e41fd..506bcd328e1 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/sensor/DefaultSensorStorageTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/sensor/DefaultSensorStorageTest.java
@@ -84,7 +84,7 @@ public class DefaultSensorStorageTest {
   @Before
   public void prepare() throws Exception {
     activeRules = new ActiveRulesBuilder().build();
-    fs = new DefaultFileSystem(temp.newFolder());
+    fs = new DefaultFileSystem(temp.newFolder().toPath());
     MetricFinder metricFinder = mock(MetricFinder.class);
     when(metricFinder.findByKey(CoreMetrics.NCLOC_KEY)).thenReturn(CoreMetrics.NCLOC);
     when(metricFinder.findByKey(CoreMetrics.FUNCTION_COMPLEXITY_DISTRIBUTION_KEY)).thenReturn(CoreMetrics.FUNCTION_COMPLEXITY_DISTRIBUTION);
@@ -279,7 +279,7 @@ public class DefaultSensorStorageTest {
     when(sonarIndex.getEdge(foo, bar)).thenReturn(new Dependency(foo, bar));
 
     thrown.expect(IllegalStateException.class);
-    thrown.expectMessage("Dependency between [moduleKey=foo, relative=src/Foo.java, abs=null] and [moduleKey=foo, relative=src/Bar.java, abs=null] was already saved.");
+    thrown.expectMessage("Dependency between [moduleKey=foo, relative=src/Foo.java, basedir=null] and [moduleKey=foo, relative=src/Bar.java, basedir=null] was already saved.");
 
     sensorStorage.store(new DefaultDependency()
       .from(new DefaultInputFile("foo", "src/Foo.java").setType(Type.MAIN))
diff --git a/sonar-batch/src/test/java/org/sonar/batch/sensor/coverage/CoverageExclusionsTest.java b/sonar-batch/src/test/java/org/sonar/batch/sensor/coverage/CoverageExclusionsTest.java
index ec592a7962e..0e2efc2782a 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/sensor/coverage/CoverageExclusionsTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/sensor/coverage/CoverageExclusionsTest.java
@@ -54,7 +54,7 @@ public class CoverageExclusionsTest {
 
   @Test
   public void shouldFilterFileBasedOnPattern() {
-    Resource resource = File.create("src/org/polop/File.php", "org/polop/File.php", null, false);
+    Resource resource = File.create("src/org/polop/File.php", null, false);
     Measure coverageMeasure = mock(Measure.class);
     when(coverageMeasure.getMetric()).thenReturn(CoreMetrics.LINES_TO_COVER);
 
@@ -65,7 +65,7 @@ public class CoverageExclusionsTest {
 
   @Test
   public void shouldNotFilterFileBasedOnPattern() {
-    Resource resource = File.create("src/org/polop/File.php", "org/polop/File.php", null, false);
+    Resource resource = File.create("src/org/polop/File.php", null, false);
     Measure coverageMeasure = mock(Measure.class);
     when(coverageMeasure.getMetric()).thenReturn(CoreMetrics.COVERAGE);
 
diff --git a/sonar-batch/src/test/java/org/sonar/batch/source/CodeColorizersTest.java b/sonar-batch/src/test/java/org/sonar/batch/source/CodeColorizersTest.java
index 58f1d3f86c8..a7486ad376b 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/source/CodeColorizersTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/source/CodeColorizersTest.java
@@ -19,6 +19,7 @@
  */
 package org.sonar.batch.source;
 
+import com.google.common.base.Charsets;
 import com.google.common.collect.ImmutableList;
 import org.apache.commons.io.FileUtils;
 import org.junit.Rule;
@@ -52,7 +53,7 @@ public class CodeColorizersTest {
 
     File jsFile = new File(this.getClass().getResource("CodeColorizersTest/Person.js").toURI());
 
-    SyntaxHighlightingData syntaxHighlighting = codeColorizers.toSyntaxHighlighting(jsFile, "UTF-8", "js");
+    SyntaxHighlightingData syntaxHighlighting = codeColorizers.toSyntaxHighlighting(jsFile, Charsets.UTF_8, "js");
 
     assertThat(syntaxHighlighting.writeString()).isEqualTo(HIGHLIGHTING_JS);
 
@@ -67,7 +68,7 @@ public class CodeColorizersTest {
     File jsFile = new File(this.getClass().getResource("CodeColorizersTest/Person.js").toURI());
     FileUtils.write(fileWithBom, FileUtils.readFileToString(jsFile), "UTF-8", true);
 
-    SyntaxHighlightingData syntaxHighlighting = codeColorizers.toSyntaxHighlighting(fileWithBom, "UTF-8", "js");
+    SyntaxHighlightingData syntaxHighlighting = codeColorizers.toSyntaxHighlighting(fileWithBom, Charsets.UTF_8, "js");
 
     assertThat(syntaxHighlighting.writeString()).isEqualTo(HIGHLIGHTING_JS);
   }
@@ -78,7 +79,7 @@ public class CodeColorizersTest {
 
     File javaFile = new File(this.getClass().getResource("CodeColorizersTest/Person.java").toURI());
 
-    SyntaxHighlightingData syntaxHighlighting = codeColorizers.toSyntaxHighlighting(javaFile, "UTF-8", "java");
+    SyntaxHighlightingData syntaxHighlighting = codeColorizers.toSyntaxHighlighting(javaFile, Charsets.UTF_8, "java");
 
     assertThat(syntaxHighlighting.writeString()).isEqualTo(HIGHLIGHTING_JAVA);
 
diff --git a/sonar-batch/src/test/java/org/sonar/batch/source/HighlightableBuilderTest.java b/sonar-batch/src/test/java/org/sonar/batch/source/HighlightableBuilderTest.java
index 4a26c3b4bbf..e2adf2dd0db 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/source/HighlightableBuilderTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/source/HighlightableBuilderTest.java
@@ -37,7 +37,7 @@ public class HighlightableBuilderTest {
 
   @Test
   public void should_load_default_perspective() throws Exception {
-    Resource file = new File("foo.c").setEffectiveKey("myproject:path/to/foo.c");
+    Resource file = File.create("foo.c").setEffectiveKey("myproject:path/to/foo.c");
     Component component = new ResourceComponent(file);
 
     HighlightableBuilder builder = new HighlightableBuilder(cache);
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByDateTest/shared.xml b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByDateTest/shared.xml
index d794c3a2422..d794c3a2422 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByDateTest/shared.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByDateTest/shared.xml
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByDaysTest/shared.xml b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByDaysTest/shared.xml
index 119f7399b4d..119f7399b4d 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByDaysTest/shared.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByDaysTest/shared.xml
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByDaysTest/shouldNotFindSelf.xml b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByDaysTest/shouldNotFindSelf.xml
index 166f7c18ea8..166f7c18ea8 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByDaysTest/shouldNotFindSelf.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByDaysTest/shouldNotFindSelf.xml
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByPreviousAnalysisTest/shouldFindPreviousAnalysis.xml b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousAnalysisTest/shouldFindPreviousAnalysis.xml
index eb5136dc808..eb5136dc808 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByPreviousAnalysisTest/shouldFindPreviousAnalysis.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousAnalysisTest/shouldFindPreviousAnalysis.xml
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByPreviousAnalysisTest/shouldNotFindPreviousAnalysis.xml b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousAnalysisTest/shouldNotFindPreviousAnalysis.xml
index 5809598e5d7..5809598e5d7 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByPreviousAnalysisTest/shouldNotFindPreviousAnalysis.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousAnalysisTest/shouldNotFindPreviousAnalysis.xml
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByPreviousVersionTest/no-previous-version.xml b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousVersionTest/no-previous-version.xml
index 2f01f86b989..2f01f86b989 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByPreviousVersionTest/no-previous-version.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousVersionTest/no-previous-version.xml
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByPreviousVersionTest/with-previous-version-deleted.xml b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousVersionTest/with-previous-version-deleted.xml
index d990e648414..d990e648414 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByPreviousVersionTest/with-previous-version-deleted.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousVersionTest/with-previous-version-deleted.xml
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByPreviousVersionTest/with-previous-version.xml b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousVersionTest/with-previous-version.xml
index 5ecbc2fa959..5ecbc2fa959 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByPreviousVersionTest/with-previous-version.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousVersionTest/with-previous-version.xml
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByVersionTest/shared.xml b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByVersionTest/shared.xml
index 289a362f781..289a362f781 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/components/PastSnapshotFinderByVersionTest/shared.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PastSnapshotFinderByVersionTest/shared.xml
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/components/PeriodsDefinitionTest/shared.xml b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PeriodsDefinitionTest/shared.xml
index c8796e2bb80..c8796e2bb80 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/components/PeriodsDefinitionTest/shared.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/deprecated/components/PeriodsDefinitionTest/shared.xml
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/index/ResourcePersisterTest/shouldSaveNewMultiModulesProject-result.xml b/sonar-batch/src/test/resources/org/sonar/batch/index/ResourcePersisterTest/shouldSaveNewMultiModulesProject-result.xml
index bed6ddbad3d..e168b6bc85d 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/index/ResourcePersisterTest/shouldSaveNewMultiModulesProject-result.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/index/ResourcePersisterTest/shouldSaveNewMultiModulesProject-result.xml
@@ -31,7 +31,7 @@
             enabled="true" language="[null]" copy_resource_id="[null]" person_id="[null]" path="src/main/java/org" deprecated_kee="[null]" />
 
   <projects id="1006" scope="FIL" qualifier="FIL" kee="b1:src/main/java/org/Foo.java" root_id="1004"
-            name="src/main/java/org/Foo.java" long_name="src/main/java/org/Foo.java" description="[null]"
+            name="Foo.java" long_name="src/main/java/org/Foo.java" description="[null]"
             enabled="true" language="[null]" copy_resource_id="[null]" person_id="[null]" path="src/main/java/org/Foo.java" deprecated_kee="[null]" />
 
   <snapshots purge_status="[null]" period1_mode="[null]" period1_param="[null]" period1_date="[null]" period2_mode="[null]" period2_param="[null]" period2_date="[null]" period3_mode="[null]" period3_param="[null]" period3_date="[null]" period4_mode="[null]" period4_param="[null]" period4_date="[null]" period5_mode="[null]" period5_param="[null]" period5_date="[null]" id="3001" project_id="1001" root_project_id="1001" parent_snapshot_id="[null]"  root_snapshot_id="[null]"
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/index/ResourcePersisterTest/shouldSaveNewMultiModulesProjectAndLibrary-result.xml b/sonar-batch/src/test/resources/org/sonar/batch/index/ResourcePersisterTest/shouldSaveNewMultiModulesProjectAndLibrary-result.xml
index 86b94e27622..f475284edcb 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/index/ResourcePersisterTest/shouldSaveNewMultiModulesProjectAndLibrary-result.xml
+++ b/sonar-batch/src/test/resources/org/sonar/batch/index/ResourcePersisterTest/shouldSaveNewMultiModulesProjectAndLibrary-result.xml
@@ -31,7 +31,7 @@
             enabled="true" language="[null]" copy_resource_id="[null]" person_id="[null]" path="src/main/java/org" deprecated_kee="[null]" />
 
   <projects id="1006" scope="FIL" qualifier="FIL" kee="b1:src/main/java/org/Foo.java" root_id="1004"
-            name="src/main/java/org/Foo.java" long_name="src/main/java/org/Foo.java" description="[null]"
+            name="Foo.java" long_name="src/main/java/org/Foo.java" description="[null]"
             enabled="true" language="[null]" copy_resource_id="[null]" person_id="[null]" path="src/main/java/org/Foo.java" deprecated_kee="[null]" />
 
   <snapshots purge_status="[null]" period1_mode="[null]" period1_param="[null]" period1_date="[null]" period2_mode="[null]" period2_param="[null]" period2_date="[null]" period3_mode="[null]" period3_param="[null]" period3_date="[null]" period4_mode="[null]" period4_param="[null]" period4_date="[null]" period5_mode="[null]" period5_param="[null]" period5_date="[null]" id="3001" project_id="1001" root_project_id="1001" parent_snapshot_id="[null]"  root_snapshot_id="[null]"