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

144 files changed, 1016 insertions, 1041 deletions

diff --git a/sonar-batch/src/main/java/org/sonar/batch/ProjectConfigurator.java b/sonar-batch/src/main/java/org/sonar/batch/ProjectConfigurator.java
index b345f2e1b0a..21dd83e51ab 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/ProjectConfigurator.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/ProjectConfigurator.java
@@ -41,6 +41,10 @@ import java.util.Date;
 import static org.sonar.api.utils.DateUtils.formatDateTime;
 import static org.sonar.api.utils.DateUtils.longToDate;
 
+/**
+ * Used by views !!
+ *
+ */
 public class ProjectConfigurator implements BatchComponent {
 
   private static final Logger LOG = LoggerFactory.getLogger(ProjectConfigurator.class);
diff --git a/sonar-batch/src/main/java/org/sonar/batch/bootstrap/GlobalContainer.java b/sonar-batch/src/main/java/org/sonar/batch/bootstrap/GlobalContainer.java
index f55308c348c..80525697653 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/bootstrap/GlobalContainer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/bootstrap/GlobalContainer.java
@@ -19,6 +19,14 @@
  */
 package org.sonar.batch.bootstrap;
 
+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.sonar.batch.repository.user.UserRepository;
 import org.sonar.api.Plugin;
 import org.sonar.api.config.EmailSettings;
 import org.sonar.api.platform.ComponentContainer;
@@ -28,12 +36,6 @@ import org.sonar.api.utils.HttpDownloader;
 import org.sonar.api.utils.System2;
 import org.sonar.api.utils.UriReader;
 import org.sonar.api.utils.internal.TempFolderCleaner;
-import org.sonar.batch.components.PastSnapshotFinder;
-import org.sonar.batch.components.PastSnapshotFinderByDate;
-import org.sonar.batch.components.PastSnapshotFinderByDays;
-import org.sonar.batch.components.PastSnapshotFinderByPreviousAnalysis;
-import org.sonar.batch.components.PastSnapshotFinderByPreviousVersion;
-import org.sonar.batch.components.PastSnapshotFinderByVersion;
 import org.sonar.batch.platform.DefaultServer;
 import org.sonar.batch.repository.DefaultGlobalRepositoriesLoader;
 import org.sonar.batch.repository.DefaultPreviousIssuesLoader;
@@ -42,7 +44,6 @@ import org.sonar.batch.repository.GlobalRepositoriesLoader;
 import org.sonar.batch.repository.GlobalRepositoriesProvider;
 import org.sonar.batch.repository.PreviousIssuesLoader;
 import org.sonar.batch.repository.ProjectRepositoriesLoader;
-import org.sonar.batch.user.UserRepository;
 import org.sonar.core.cluster.NullQueue;
 import org.sonar.core.config.Logback;
 import org.sonar.core.i18n.DefaultI18n;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/bootstrap/TaskContainer.java b/sonar-batch/src/main/java/org/sonar/batch/bootstrap/TaskContainer.java
index d301f1aa476..b3fd7e46392 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/bootstrap/TaskContainer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/bootstrap/TaskContainer.java
@@ -19,6 +19,8 @@
  */
 package org.sonar.batch.bootstrap;
 
+import org.sonar.batch.components.PastMeasuresLoader;
+
 import org.apache.commons.lang.StringUtils;
 import org.sonar.api.CoreProperties;
 import org.sonar.api.platform.ComponentContainer;
@@ -28,19 +30,21 @@ import org.sonar.api.task.TaskComponent;
 import org.sonar.api.task.TaskDefinition;
 import org.sonar.api.utils.MessageException;
 import org.sonar.batch.bootstrapper.EnvironmentInformation;
-import org.sonar.batch.components.PastMeasuresLoader;
+import org.sonar.batch.deprecated.tasks.ListTask;
+import org.sonar.batch.deprecated.tasks.Tasks;
 import org.sonar.batch.scan.DeprecatedProjectReactorBuilder;
 import org.sonar.batch.scan.ProjectReactorBuilder;
 import org.sonar.batch.scan.ScanTask;
 import org.sonar.batch.scan.measure.DefaultMetricFinder;
 import org.sonar.batch.scan.measure.DeprecatedMetricFinder;
-import org.sonar.batch.tasks.ListTask;
-import org.sonar.batch.tasks.Tasks;
 import org.sonar.core.permission.PermissionFacade;
 import org.sonar.core.resource.DefaultResourcePermissions;
 
 import java.util.Map;
 
+/**
+ * Used by views !!
+ */
 public class TaskContainer extends ComponentContainer {
 
   private final Map<String, String> taskProperties;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/components/PastMeasuresLoader.java b/sonar-batch/src/main/java/org/sonar/batch/components/PastMeasuresLoader.java
index 6cfd61dcabe..d969e172338 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/components/PastMeasuresLoader.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/components/PastMeasuresLoader.java
@@ -38,6 +38,9 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 
+/**
+ * Can't be moved. Used by devcockpit.
+ */
 public class PastMeasuresLoader implements BatchComponent {
 
   private Map<Integer, Metric> metricByIds;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshot.java b/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshot.java
index 48955f9738f..a85eb172cf7 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshot.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshot.java
@@ -26,11 +26,15 @@ import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.utils.DateUtils;
 
 import javax.annotation.Nullable;
+
 import java.util.Calendar;
 import java.util.Date;
 
 import static org.sonar.api.utils.DateUtils.longToDate;
 
+/**
+ * Used by devcockpit
+ */
 public class PastSnapshot {
 
   private int index;
@@ -96,7 +100,7 @@ public class PastSnapshot {
     return this;
   }
 
-  Integer getProjectSnapshotId() {
+  public Integer getProjectSnapshotId() {
     return projectSnapshot != null ? projectSnapshot.getId() : null;
   }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinder.java b/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinder.java
index 56263637b14..745dcbf817b 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinder.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinder.java
@@ -27,6 +27,11 @@ import org.sonar.api.BatchExtension;
 import org.sonar.api.CoreProperties;
 import org.sonar.api.config.Settings;
 import org.sonar.api.database.model.Snapshot;
+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 javax.annotation.Nullable;
 
@@ -34,6 +39,9 @@ import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.Date;
 
+/**
+ * Can't be moved since it is used by devcockpit.
+ */
 public class PastSnapshotFinder implements BatchExtension {
 
   private static final Logger LOG = LoggerFactory.getLogger(PastSnapshotFinder.class);
diff --git a/sonar-batch/src/main/java/org/sonar/batch/components/TimeMachineConfiguration.java b/sonar-batch/src/main/java/org/sonar/batch/components/TimeMachineConfiguration.java
index 2d4c71bc9c1..ec346aa4dcc 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/components/TimeMachineConfiguration.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/components/TimeMachineConfiguration.java
@@ -27,8 +27,11 @@ import org.sonar.api.batch.RequiresDB;
 import org.sonar.api.database.DatabaseSession;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.resources.Qualifiers;
+import org.sonar.batch.deprecated.components.Period;
+import org.sonar.batch.deprecated.components.PeriodsDefinition;
 
 import javax.annotation.CheckForNull;
+
 import java.util.List;
 
 import static com.google.common.collect.Lists.newLinkedList;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/debt/NewDebtDecorator.java b/sonar-batch/src/main/java/org/sonar/batch/debt/NewDebtDecorator.java
index 43046d3763b..452fe02551c 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/debt/NewDebtDecorator.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/debt/NewDebtDecorator.java
@@ -20,6 +20,9 @@
 
 package org.sonar.batch.debt;
 
+import org.sonar.batch.components.TimeMachineConfiguration;
+
+import org.sonar.batch.deprecated.components.Period;
 import com.google.common.collect.ImmutableList;
 import org.sonar.api.batch.Decorator;
 import org.sonar.api.batch.DecoratorBarriers;
@@ -35,8 +38,6 @@ import org.sonar.api.measures.MeasureUtils;
 import org.sonar.api.measures.Metric;
 import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
-import org.sonar.batch.components.Period;
-import org.sonar.batch.components.TimeMachineConfiguration;
 
 import javax.annotation.Nullable;
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/DeprecatedSensorContext.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/DeprecatedSensorContext.java
index 49998b1d2f7..e02cadce624 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/DeprecatedSensorContext.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/DeprecatedSensorContext.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.apache.commons.lang.StringUtils;
 import org.slf4j.Logger;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/ResourceFilters.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/ResourceFilters.java
index 8680300a412..f60713506d7 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/ResourceFilters.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/ResourceFilters.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 com.google.common.base.Joiner;
 import org.slf4j.Logger;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/DefaultProjectClasspath.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/DefaultProjectClasspath.java
index d497906439f..f5a07c9889c 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/DefaultProjectClasspath.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/DefaultProjectClasspath.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.components;
 
 import com.google.common.collect.Lists;
 import org.apache.maven.project.MavenProject;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/DefaultResourceCreationLock.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/DefaultResourceCreationLock.java
index 1adb5074e64..52ca67c348e 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/DefaultResourceCreationLock.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/DefaultResourceCreationLock.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.components;
 
 import org.sonar.api.batch.ResourceCreationLock;
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/DefaultTimeMachine.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/DefaultTimeMachine.java
index 79d61dd2f74..460f3a647c4 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/DefaultTimeMachine.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/DefaultTimeMachine.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.components;
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinderByDate.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByDate.java
index fbae4382e43..5a5fff138a1 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinderByDate.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByDate.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.components;
+package org.sonar.batch.deprecated.components;
 
 import org.sonar.api.BatchExtension;
 import org.sonar.api.CoreProperties;
@@ -25,8 +25,10 @@ import org.sonar.api.database.DatabaseSession;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.resources.Qualifiers;
 import org.sonar.api.utils.DateUtils;
+import org.sonar.batch.components.PastSnapshot;
 
 import javax.annotation.CheckForNull;
+
 import java.text.SimpleDateFormat;
 import java.util.Date;
 import java.util.List;
@@ -41,7 +43,7 @@ public class PastSnapshotFinderByDate implements BatchExtension {
     this.session = session;
   }
 
-  PastSnapshot findByDate(Snapshot projectSnapshot, Date date) {
+  public PastSnapshot findByDate(Snapshot projectSnapshot, Date date) {
     Integer projectId = projectSnapshot != null ? projectSnapshot.getResourceId() : null;
     return findByDate(projectId, date);
   }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinderByDays.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByDays.java
index 0f802682c8a..5183236cc05 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinderByDays.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByDays.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.components;
+package org.sonar.batch.deprecated.components;
 
 import org.apache.commons.lang.time.DateUtils;
 import org.sonar.api.BatchExtension;
@@ -25,8 +25,10 @@ import org.sonar.api.CoreProperties;
 import org.sonar.api.database.DatabaseSession;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.resources.Qualifiers;
+import org.sonar.batch.components.PastSnapshot;
 
 import javax.annotation.CheckForNull;
+
 import java.util.Date;
 import java.util.List;
 
@@ -40,7 +42,7 @@ public class PastSnapshotFinderByDays implements BatchExtension {
     this.session = session;
   }
 
-  PastSnapshot findFromDays(Snapshot projectSnapshot, int days) {
+  public PastSnapshot findFromDays(Snapshot projectSnapshot, int days) {
     Date targetDate = DateUtils.addDays(longToDate(projectSnapshot.getCreatedAtMs()), -days);
     String hql = "from " + Snapshot.class.getSimpleName() + " where resourceId=:resourceId AND status=:status AND createdAt<:date AND qualifier<>:lib order by createdAt asc";
     List<Snapshot> snapshots = session.createQuery(hql)
diff --git a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinderByPreviousAnalysis.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousAnalysis.java
index 506295775ef..e770975d461 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinderByPreviousAnalysis.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousAnalysis.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.components;
+package org.sonar.batch.deprecated.components;
 
 import org.sonar.api.BatchExtension;
 import org.sonar.api.CoreProperties;
@@ -25,6 +25,7 @@ import org.sonar.api.database.DatabaseSession;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.resources.Qualifiers;
 import org.sonar.api.utils.DateUtils;
+import org.sonar.batch.components.PastSnapshot;
 
 import java.text.SimpleDateFormat;
 import java.util.Date;
@@ -40,17 +41,17 @@ public class PastSnapshotFinderByPreviousAnalysis implements BatchExtension {
     this.session = session;
   }
 
-  PastSnapshot findByPreviousAnalysis(Snapshot projectSnapshot) {
+  public PastSnapshot findByPreviousAnalysis(Snapshot projectSnapshot) {
     String hql = "from " + Snapshot.class.getSimpleName()
-        + " where createdAt<:date AND resourceId=:resourceId AND status=:status and last=:last and qualifier<>:lib order by createdAt desc";
+      + " where createdAt<:date AND resourceId=:resourceId AND status=:status and last=:last and qualifier<>:lib order by createdAt desc";
     List<Snapshot> snapshots = session.createQuery(hql)
-        .setParameter("date", projectSnapshot.getCreatedAtMs())
-        .setParameter("resourceId", projectSnapshot.getResourceId())
-        .setParameter("status", Snapshot.STATUS_PROCESSED)
-        .setParameter("last", true)
-        .setParameter("lib", Qualifiers.LIBRARY)
-        .setMaxResults(1)
-        .getResultList();
+      .setParameter("date", projectSnapshot.getCreatedAtMs())
+      .setParameter("resourceId", projectSnapshot.getResourceId())
+      .setParameter("status", Snapshot.STATUS_PROCESSED)
+      .setParameter("last", true)
+      .setParameter("lib", Qualifiers.LIBRARY)
+      .setMaxResults(1)
+      .getResultList();
 
     if (snapshots.isEmpty()) {
       return new PastSnapshot(CoreProperties.TIMEMACHINE_MODE_PREVIOUS_ANALYSIS);
diff --git a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinderByPreviousVersion.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousVersion.java
index 6437688bf68..0125fa7d4d7 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinderByPreviousVersion.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByPreviousVersion.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.components.PastSnapshot;
 
 import org.sonar.api.BatchExtension;
 import org.sonar.api.CoreProperties;
@@ -37,7 +39,7 @@ public class PastSnapshotFinderByPreviousVersion implements BatchExtension {
     this.session = session;
   }
 
-  PastSnapshot findByPreviousVersion(Snapshot projectSnapshot) {
+  public PastSnapshot findByPreviousVersion(Snapshot projectSnapshot) {
     String currentVersion = projectSnapshot.getVersion();
     Integer resourceId = projectSnapshot.getResourceId();
 
@@ -45,10 +47,10 @@ public class PastSnapshotFinderByPreviousVersion implements BatchExtension {
       " where name<>:version AND category='Version' AND resourceId=:resourceId ORDER BY date DESC";
 
     List<Event> events = session.createQuery(hql)
-        .setParameter("version", currentVersion)
-        .setParameter("resourceId", resourceId)
-        .setMaxResults(1)
-        .getResultList();
+      .setParameter("version", currentVersion)
+      .setParameter("resourceId", resourceId)
+      .setMaxResults(1)
+      .getResultList();
 
     if (events.isEmpty()) {
       return new PastSnapshot(CoreProperties.TIMEMACHINE_MODE_PREVIOUS_VERSION);
diff --git a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinderByVersion.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByVersion.java
index 161bd87b2ee..c6f5423ffab 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/components/PastSnapshotFinderByVersion.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PastSnapshotFinderByVersion.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.components.PastSnapshot;
 
 import org.sonar.api.BatchExtension;
 import org.sonar.api.CoreProperties;
@@ -38,15 +40,15 @@ public class PastSnapshotFinderByVersion implements BatchExtension {
     this.session = session;
   }
 
-  PastSnapshot findByVersion(Snapshot projectSnapshot, String version) {
+  public PastSnapshot findByVersion(Snapshot projectSnapshot, String version) {
     String hql = "from " + Snapshot.class.getSimpleName() + " where version=:version AND resourceId=:resourceId AND status=:status AND qualifier<>:lib order by createdAt desc";
     List<Snapshot> snapshots = session.createQuery(hql)
-        .setParameter("version", version)
-        .setParameter("resourceId", projectSnapshot.getResourceId())
-        .setParameter("status", Snapshot.STATUS_PROCESSED)
-        .setParameter("lib", Qualifiers.LIBRARY)
-        .setMaxResults(1)
-        .getResultList();
+      .setParameter("version", version)
+      .setParameter("resourceId", projectSnapshot.getResourceId())
+      .setParameter("status", Snapshot.STATUS_PROCESSED)
+      .setParameter("lib", Qualifiers.LIBRARY)
+      .setMaxResults(1)
+      .getResultList();
 
     PastSnapshot result;
     if (snapshots.isEmpty()) {
diff --git a/sonar-batch/src/main/java/org/sonar/batch/components/Period.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/Period.java
index 4e2f15e88b9..45ca282dd42 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/components/Period.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/Period.java
@@ -18,7 +18,7 @@
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
 
-package org.sonar.batch.components;
+package org.sonar.batch.deprecated.components;
 
 import javax.annotation.CheckForNull;
 import javax.annotation.Nullable;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/components/PeriodsDefinition.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PeriodsDefinition.java
index 6f1eb16a5bc..b235129693f 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/components/PeriodsDefinition.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/PeriodsDefinition.java
@@ -18,7 +18,7 @@
  * 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.api.BatchComponent;
 import org.sonar.api.config.Settings;
@@ -26,6 +26,8 @@ import org.sonar.api.database.DatabaseSession;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.resources.Qualifiers;
 import org.sonar.batch.ProjectTree;
+import org.sonar.batch.components.PastSnapshot;
+import org.sonar.batch.components.PastSnapshotFinder;
 
 import javax.persistence.Query;
 import java.util.List;
@@ -46,7 +48,7 @@ public class PeriodsDefinition implements BatchComponent {
   private List<PastSnapshot> projectPastSnapshots;
 
   public PeriodsDefinition(DatabaseSession session, ProjectTree projectTree, Settings settings,
-                           PastSnapshotFinder pastSnapshotFinder) {
+    PastSnapshotFinder pastSnapshotFinder) {
     this.session = session;
     this.projectTree = projectTree;
     this.settings = settings;
@@ -89,7 +91,7 @@ public class PeriodsDefinition implements BatchComponent {
   /**
    * @return past snapshots of root project
    */
-  List<PastSnapshot> getRootProjectPastSnapshots() {
+  public List<PastSnapshot> getRootProjectPastSnapshots() {
     return projectPastSnapshots;
   }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/package-info.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/package-info.java
new file mode 100644
index 00000000000..65baa1e8409
--- /dev/null
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/components/package-info.java
@@ -0,0 +1,23 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * SonarQube is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ */
+@ParametersAreNonnullByDefault
+package org.sonar.batch.deprecated.components;
+
+import javax.annotation.ParametersAreNonnullByDefault;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/DecoratorsSelector.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/decorator/DecoratorsSelector.java
index 7ce661aaa79..c50574fb637 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/DecoratorsSelector.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/decorator/DecoratorsSelector.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.HashMultimap;
 import com.google.common.collect.SetMultimap;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/DefaultDecoratorContext.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/decorator/DefaultDecoratorContext.java
index 3d18e06c5a9..1740a1aebd9 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/DefaultDecoratorContext.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/decorator/DefaultDecoratorContext.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.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/FormulaDecorator.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/decorator/FormulaDecorator.java
index 75de88257d8..8b60efcaf19 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/FormulaDecorator.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/decorator/FormulaDecorator.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 org.sonar.api.batch.*;
 import org.sonar.api.measures.FormulaData;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/tasks/package-info.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/package-info.java
index 0f2b4e035bb..ca1dcada4ba 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/tasks/package-info.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/package-info.java
@@ -18,6 +18,6 @@
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
 @ParametersAreNonnullByDefault
-package org.sonar.batch.tasks;
+package org.sonar.batch.deprecated;
 
 import javax.annotation.ParametersAreNonnullByDefault;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/tasks/ListTask.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/tasks/ListTask.java
index 93a0419b32f..bcd02a00e3b 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/tasks/ListTask.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/tasks/ListTask.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.sonar.api.task.Task;
 import org.sonar.api.task.TaskDefinition;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/tasks/Tasks.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/tasks/Tasks.java
index f68fb691269..c97bdea7d6a 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/tasks/Tasks.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/tasks/Tasks.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 com.google.common.collect.ImmutableSortedMap;
 import com.google.common.collect.Maps;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/deprecated/tasks/package-info.java b/sonar-batch/src/main/java/org/sonar/batch/deprecated/tasks/package-info.java
new file mode 100644
index 00000000000..f346de52eb4
--- /dev/null
+++ b/sonar-batch/src/main/java/org/sonar/batch/deprecated/tasks/package-info.java
@@ -0,0 +1,23 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * SonarQube is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ */
+@ParametersAreNonnullByDefault
+package org.sonar.batch.deprecated.tasks;
+
+import javax.annotation.ParametersAreNonnullByDefault;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/DefaultIndex.java b/sonar-batch/src/main/java/org/sonar/batch/index/DefaultIndex.java
index eeb37de63ed..6cf8ae826f4 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/index/DefaultIndex.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/index/DefaultIndex.java
@@ -38,7 +38,6 @@ import org.sonar.api.measures.CoreMetrics;
 import org.sonar.api.measures.Measure;
 import org.sonar.api.measures.MeasuresFilter;
 import org.sonar.api.measures.MeasuresFilters;
-import org.sonar.api.resources.Directory;
 import org.sonar.api.resources.File;
 import org.sonar.api.resources.Project;
 import org.sonar.api.resources.ProjectLink;
@@ -107,7 +106,6 @@ public class DefaultIndex extends SonarIndex {
   // caches
   private Project currentProject;
   private Map<Resource, Bucket> buckets = Maps.newLinkedHashMap();
-  private Map<String, Bucket> bucketsByDeprecatedKey = Maps.newLinkedHashMap();
   private Set<Dependency> dependencies = Sets.newLinkedHashSet();
   private Map<Resource, Map<Resource, Dependency>> outgoingDependenciesByResource = Maps.newLinkedHashMap();
   private Map<Resource, Map<Resource, Dependency>> incomingDependenciesByResource = Maps.newLinkedHashMap();
@@ -166,9 +164,6 @@ public class DefaultIndex extends SonarIndex {
 
   private void addBucket(Resource resource, Bucket bucket) {
     buckets.put(resource, bucket);
-    if (StringUtils.isNotBlank(resource.getDeprecatedKey())) {
-      bucketsByDeprecatedKey.put(resource.getDeprecatedKey(), bucket);
-    }
   }
 
   private void addModule(Project parent, Project module) {
@@ -613,12 +608,6 @@ public class DefaultIndex extends SonarIndex {
     return getBucket(reference) != null;
   }
 
-  /**
-   * Should support 2 situations
-   * 1) key = new key and deprecatedKey = old key : this is the standard use case in a perfect world
-   * 2) key = null and deprecatedKey = oldKey : this is for plugins that are using deprecated constructors of
-   * {@link File} and {@link Directory}
-   */
   private Bucket getBucket(@Nullable Resource reference) {
     if (reference == null) {
       return null;
@@ -626,17 +615,6 @@ public class DefaultIndex extends SonarIndex {
     if (StringUtils.isNotBlank(reference.getKey())) {
       return buckets.get(reference);
     }
-    if (StringUtils.isNotBlank(reference.getDeprecatedKey())) {
-      // Fallback to use deprecated key
-      Bucket bucket = bucketsByDeprecatedKey.get(reference.getDeprecatedKey());
-      if (bucket != null) {
-        // Fix reference resource
-        reference.setKey(bucket.getResource().getKey());
-        reference.setPath(bucket.getResource().getPath());
-        LOG.debug("Resource {} was found using deprecated key. Please update your plugin.", reference);
-        return bucket;
-      }
-    }
     return null;
   }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/ResourceKeyMigration.java b/sonar-batch/src/main/java/org/sonar/batch/index/ResourceKeyMigration.java
index 0cb5a0b182d..69b7dd98d85 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/index/ResourceKeyMigration.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/index/ResourceKeyMigration.java
@@ -24,20 +24,21 @@ import org.apache.commons.lang.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.sonar.api.BatchComponent;
-import org.sonar.api.batch.fs.FileSystem;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
 import org.sonar.api.database.DatabaseSession;
 import org.sonar.api.database.model.ResourceModel;
 import org.sonar.api.resources.Directory;
-import org.sonar.api.resources.File;
 import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Qualifiers;
-import org.sonar.api.resources.Resource;
 import org.sonar.api.resources.Scopes;
+import org.sonar.api.scan.filesystem.PathResolver;
 import org.sonar.api.utils.PathUtils;
+import org.sonar.batch.scan.filesystem.DefaultModuleFileSystem;
 import org.sonar.batch.util.DeprecatedKeyUtils;
 
+import javax.annotation.CheckForNull;
+
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -48,17 +49,19 @@ public class ResourceKeyMigration implements BatchComponent {
   private static final String COMPONENT_CHANGED_TO = "Component {} changed to {}";
   private final Logger logger;
   private final DatabaseSession session;
+  private final PathResolver pathResolver;
 
   private boolean migrationNeeded = false;
 
-  public ResourceKeyMigration(DatabaseSession session) {
-    this(session, LoggerFactory.getLogger(ResourceKeyMigration.class));
+  public ResourceKeyMigration(DatabaseSession session, PathResolver pathResolver) {
+    this(session, pathResolver, LoggerFactory.getLogger(ResourceKeyMigration.class));
   }
 
   @VisibleForTesting
-  ResourceKeyMigration(DatabaseSession session, Logger logger) {
+  ResourceKeyMigration(DatabaseSession session, PathResolver pathResolver, Logger logger) {
     this.session = session;
     this.logger = logger;
+    this.pathResolver = pathResolver;
   }
 
   public void checkIfMigrationNeeded(Project rootProject) {
@@ -68,19 +71,19 @@ public class ResourceKeyMigration implements BatchComponent {
     }
   }
 
-  public void migrateIfNeeded(Project module, FileSystem fs) {
+  public void migrateIfNeeded(Project module, DefaultModuleFileSystem fs) {
     if (migrationNeeded) {
-      migrateIfNeeded(module, fs.inputFiles(fs.predicates().all()));
+      migrateIfNeeded(module, fs.inputFiles(fs.predicates().all()), fs);
     }
   }
 
-  void migrateIfNeeded(Project module, Iterable<InputFile> inputFiles) {
+  void migrateIfNeeded(Project module, Iterable<InputFile> inputFiles, DefaultModuleFileSystem fs) {
     logger.info("Update component keys");
     Map<String, InputFile> deprecatedFileKeyMapper = new HashMap<String, InputFile>();
     Map<String, InputFile> deprecatedTestKeyMapper = new HashMap<String, InputFile>();
     Map<String, String> deprecatedDirectoryKeyMapper = new HashMap<String, String>();
     for (InputFile inputFile : inputFiles) {
-      String deprecatedKey = ((DeprecatedDefaultInputFile) inputFile).deprecatedKey();
+      String deprecatedKey = computeDeprecatedKey(module.getKey(), (DeprecatedDefaultInputFile) inputFile, fs);
       if (deprecatedKey != null) {
         if (InputFile.Type.TEST == inputFile.type() && !deprecatedTestKeyMapper.containsKey(deprecatedKey)) {
           deprecatedTestKeyMapper.put(deprecatedKey, inputFile);
@@ -97,6 +100,23 @@ public class ResourceKeyMigration implements BatchComponent {
     session.commit();
   }
 
+  @CheckForNull
+  private String computeDeprecatedKey(String moduleKey, DeprecatedDefaultInputFile inputFile, DefaultModuleFileSystem fs) {
+    List<java.io.File> sourceDirs = InputFile.Type.MAIN == inputFile.type() ? fs.sourceDirs() : fs.testDirs();
+    for (java.io.File sourceDir : sourceDirs) {
+      String sourceRelativePath = pathResolver.relativePath(sourceDir, inputFile.file());
+      if (sourceRelativePath != null) {
+        if ("java".equals(inputFile.language())) {
+          return new StringBuilder()
+            .append(moduleKey).append(":").append(DeprecatedKeyUtils.getJavaFileDeprecatedKey(sourceRelativePath)).toString();
+        } else {
+          return new StringBuilder().append(moduleKey).append(":").append(sourceRelativePath).toString();
+        }
+      }
+    }
+    return null;
+  }
+
   private void migrateFiles(Project module, Map<String, InputFile> deprecatedFileKeyMapper, Map<String, InputFile> deprecatedTestKeyMapper,
     Map<String, String> deprecatedDirectoryKeyMapper,
     int moduleId) {
@@ -113,13 +133,11 @@ public class ResourceKeyMigration implements BatchComponent {
         String newEffectiveKey = ((DeprecatedDefaultInputFile) matchedFile).key();
         // Now compute migration of the parent dir
         String oldKey = StringUtils.substringAfterLast(oldEffectiveKey, ":");
-        Resource sonarFile;
         String parentOldKey;
         if ("java".equals(resourceModel.getLanguageKey())) {
           parentOldKey = String.format("%s:%s", module.getEffectiveKey(), DeprecatedKeyUtils.getJavaFileParentDeprecatedKey(oldKey));
         } else {
-          sonarFile = new File(oldKey);
-          parentOldKey = String.format("%s:%s", module.getEffectiveKey(), sonarFile.getParent().getDeprecatedKey());
+          parentOldKey = String.format("%s:%s", module.getEffectiveKey(), oldParentKey(oldKey));
         }
         String parentNewKey = String.format("%s:%s", module.getEffectiveKey(), getParentKey(matchedFile));
         if (!deprecatedDirectoryKeyMapper.containsKey(parentOldKey)) {
@@ -137,6 +155,18 @@ public class ResourceKeyMigration implements BatchComponent {
     }
   }
 
+  private String oldParentKey(String oldKey) {
+    String cleanKey = StringUtils.trim(oldKey.replace('\\', '/'));
+    if (cleanKey.indexOf(Directory.SEPARATOR) >= 0) {
+      String oldParentKey = Directory.parseKey(StringUtils.substringBeforeLast(oldKey, Directory.SEPARATOR));
+      oldParentKey = StringUtils.removeStart(oldParentKey, Directory.SEPARATOR);
+      oldParentKey = StringUtils.removeEnd(oldParentKey, Directory.SEPARATOR);
+      return oldParentKey;
+    } else {
+      return Directory.ROOT;
+    }
+  }
+
   private void updateKey(ResourceModel resourceModel, String newEffectiveKey, Map<String, ResourceModel> disabledResourceByKey) {
     // Look for disabled resource with conflicting key
     if (disabledResourceByKey.containsKey(newEffectiveKey)) {
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/SourceDataFactory.java b/sonar-batch/src/main/java/org/sonar/batch/index/SourceDataFactory.java
index e3e9f33bc79..9a089eaef97 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/index/SourceDataFactory.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/index/SourceDataFactory.java
@@ -35,6 +35,7 @@ import org.sonar.api.utils.KeyValueFormat;
 import org.sonar.batch.duplication.DuplicationCache;
 import org.sonar.batch.highlighting.SyntaxHighlightingData;
 import org.sonar.batch.highlighting.SyntaxHighlightingRule;
+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.SymbolData;
@@ -72,18 +73,18 @@ public class SourceDataFactory implements BatchComponent {
     this.codeColorizers = codeColorizers;
   }
 
-  public byte[] consolidateData(DefaultInputFile inputFile) throws IOException {
+  public byte[] consolidateData(DefaultInputFile inputFile, InputFileMetadata metadata) throws IOException {
     FileSourceDb.Data.Builder dataBuilder = createForSource(inputFile);
     applyLineMeasures(inputFile, dataBuilder);
     applyDuplications(inputFile.key(), dataBuilder);
-    applyHighlighting(inputFile, dataBuilder);
-    applySymbolReferences(inputFile, dataBuilder);
+    applyHighlighting(inputFile, metadata, dataBuilder);
+    applySymbolReferences(inputFile, metadata, dataBuilder);
     return FileSourceDto.encodeData(dataBuilder.build());
   }
 
   FileSourceDb.Data.Builder createForSource(DefaultInputFile inputFile) throws IOException {
     FileSourceDb.Data.Builder result = FileSourceDb.Data.newBuilder();
-    List<String> lines = FileUtils.readLines(inputFile.file(), inputFile.encoding());
+    List<String> lines = FileUtils.readLines(inputFile.file(), inputFile.charset());
     // Missing empty last line
     if (lines.size() == inputFile.lines() - 1) {
       lines.add("");
@@ -191,11 +192,11 @@ public class SourceDataFactory implements BatchComponent {
     void apply(String value, FileSourceDb.Line.Builder lineBuilder);
   }
 
-  void applyHighlighting(DefaultInputFile inputFile, FileSourceDb.Data.Builder to) {
+  void applyHighlighting(DefaultInputFile inputFile, InputFileMetadata metadata, FileSourceDb.Data.Builder to) {
     SyntaxHighlightingData highlighting = componentDataCache.getData(inputFile.key(), SnapshotDataTypes.SYNTAX_HIGHLIGHTING);
     String language = inputFile.language();
     if (highlighting == null && language != null) {
-      highlighting = codeColorizers.toSyntaxHighlighting(inputFile.file(), inputFile.encoding(), language);
+      highlighting = codeColorizers.toSyntaxHighlighting(inputFile.file(), inputFile.charset(), language);
     }
     if (highlighting == null) {
       return;
@@ -204,12 +205,12 @@ public class SourceDataFactory implements BatchComponent {
     RuleItemWriter ruleItemWriter = new RuleItemWriter();
     int currentLineIdx = 1;
     for (SyntaxHighlightingRule rule : highlighting.syntaxHighlightingRuleSet()) {
-      while (currentLineIdx < inputFile.lines() && rule.getStartPosition() >= inputFile.originalLineOffsets()[currentLineIdx]) {
+      while (currentLineIdx < inputFile.lines() && rule.getStartPosition() >= metadata.originalLineOffsets()[currentLineIdx]) {
         // This rule starts on another line so advance
         currentLineIdx++;
       }
       // Now we know current rule starts on current line
-      writeDataPerLine(inputFile.originalLineOffsets(), rule, rule.getStartPosition(), rule.getEndPosition(), highlightingPerLine, currentLineIdx, ruleItemWriter);
+      writeDataPerLine(metadata.originalLineOffsets(), rule, rule.getStartPosition(), rule.getEndPosition(), highlightingPerLine, currentLineIdx, ruleItemWriter);
     }
     for (int i = 0; i < highlightingPerLine.length; i++) {
       StringBuilder sb = highlightingPerLine[i];
@@ -219,7 +220,7 @@ public class SourceDataFactory implements BatchComponent {
     }
   }
 
-  void applySymbolReferences(DefaultInputFile file, FileSourceDb.Data.Builder to) {
+  void applySymbolReferences(DefaultInputFile file, InputFileMetadata metadata, FileSourceDb.Data.Builder to) {
     SymbolData symbolRefs = componentDataCache.getData(file.key(), SnapshotDataTypes.SYMBOL_HIGHLIGHTING);
     if (symbolRefs != null) {
       StringBuilder[] refsPerLine = new StringBuilder[file.lines()];
@@ -236,13 +237,13 @@ public class SourceDataFactory implements BatchComponent {
         int declarationStartOffset = symbol.getDeclarationStartOffset();
         int declarationEndOffset = symbol.getDeclarationEndOffset();
         int length = declarationEndOffset - declarationStartOffset;
-        addSymbol(symbolId, declarationStartOffset, declarationEndOffset, file.originalLineOffsets(), refsPerLine);
+        addSymbol(symbolId, declarationStartOffset, declarationEndOffset, metadata.originalLineOffsets(), refsPerLine);
         for (Integer referenceStartOffset : symbolRefs.referencesBySymbol().get(symbol)) {
           if (referenceStartOffset == declarationStartOffset) {
             // Ignore old API that used to store reference as first declaration
             continue;
           }
-          addSymbol(symbolId, referenceStartOffset, referenceStartOffset + length, file.originalLineOffsets(), refsPerLine);
+          addSymbol(symbolId, referenceStartOffset, referenceStartOffset + length, metadata.originalLineOffsets(), refsPerLine);
         }
         symbolId++;
       }
@@ -255,12 +256,12 @@ public class SourceDataFactory implements BatchComponent {
     }
   }
 
-  private void addSymbol(int symbolId, int startOffset, int endOffset, long[] originalLineOffsets, StringBuilder[] result) {
+  private void addSymbol(int symbolId, int startOffset, int endOffset, int[] originalLineOffsets, StringBuilder[] result) {
     int startLine = binarySearchLine(startOffset, originalLineOffsets);
     writeDataPerLine(originalLineOffsets, symbolId, startOffset, endOffset, result, startLine, new SymbolItemWriter());
   }
 
-  private int binarySearchLine(int declarationStartOffset, long[] originalLineOffsets) {
+  private int binarySearchLine(int declarationStartOffset, int[] originalLineOffsets) {
     int begin = 0;
     int end = originalLineOffsets.length - 1;
     while (begin < end) {
@@ -274,7 +275,7 @@ public class SourceDataFactory implements BatchComponent {
     return begin + 1;
   }
 
-  private <G> void writeDataPerLine(long[] originalLineOffsets, G item, int globalStartOffset, int globalEndOffset, StringBuilder[] dataPerLine, int startLine,
+  private <G> void writeDataPerLine(int[] originalLineOffsets, G item, int globalStartOffset, int globalEndOffset, StringBuilder[] dataPerLine, int startLine,
     RangeItemWriter<G> writer) {
     int currentLineIdx = startLine;
     // We know current item starts on current line
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/SourcePersister.java b/sonar-batch/src/main/java/org/sonar/batch/index/SourcePersister.java
index a7a18548418..14cd85e371a 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/index/SourcePersister.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/index/SourcePersister.java
@@ -19,14 +19,14 @@
  */
 package org.sonar.batch.index;
 
-import org.apache.commons.codec.binary.Hex;
 import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.ibatis.session.ResultContext;
 import org.apache.ibatis.session.ResultHandler;
-import org.sonar.api.batch.fs.InputPath;
+import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.utils.System2;
 import org.sonar.batch.ProjectTree;
+import org.sonar.batch.scan.filesystem.InputFileMetadata;
 import org.sonar.batch.scan.filesystem.InputPathCache;
 import org.sonar.core.persistence.DbSession;
 import org.sonar.core.persistence.MyBatis;
@@ -35,7 +35,9 @@ import org.sonar.core.source.db.FileSourceMapper;
 
 import javax.annotation.CheckForNull;
 
+import java.io.BufferedReader;
 import java.io.IOException;
+import java.nio.file.Files;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -73,10 +75,8 @@ public class SourcePersister implements ScanPersister {
       });
 
       FileSourceMapper mapper = session.getMapper(FileSourceMapper.class);
-      for (InputPath inputPath : inputPathCache.all()) {
-        if (inputPath instanceof DefaultInputFile) {
-          persist(session, mapper, (DefaultInputFile) inputPath, previousDtosByUuid);
-        }
+      for (InputFile inputFile : inputPathCache.allFiles()) {
+        persist(session, mapper, (DefaultInputFile) inputFile, previousDtosByUuid);
       }
     } catch (Exception e) {
       throw new IllegalStateException("Unable to save file sources", e);
@@ -87,7 +87,8 @@ public class SourcePersister implements ScanPersister {
   private void persist(DbSession session, FileSourceMapper mapper, DefaultInputFile inputFile, Map<String, FileSourceDto> previousDtosByUuid) {
     String fileUuid = resourceCache.get(inputFile.key()).resource().getUuid();
 
-    byte[] data = computeData(inputFile);
+    InputFileMetadata metadata = inputPathCache.getFileMetadata(inputFile.moduleKey(), inputFile.relativePath());
+    byte[] data = computeData(inputFile, metadata);
     String dataHash = DigestUtils.md5Hex(data);
     FileSourceDto previousDto = previousDtosByUuid.get(fileUuid);
     if (previousDto == null) {
@@ -96,20 +97,20 @@ public class SourcePersister implements ScanPersister {
         .setFileUuid(fileUuid)
         .setBinaryData(data)
         .setDataHash(dataHash)
-        .setSrcHash(inputFile.hash())
-        .setLineHashes(lineHashesAsMd5Hex(inputFile))
+        .setSrcHash(metadata.hash())
+        .setLineHashes(lineHashesAsMd5Hex(inputFile, metadata))
         .setCreatedAt(system2.now())
         .setUpdatedAt(system2.now());
       mapper.insert(dto);
       session.commit();
     } else {
       // Update only if data_hash has changed or if src_hash is missing (progressive migration)
-      if (!dataHash.equals(previousDto.getDataHash()) || !inputFile.hash().equals(previousDto.getSrcHash())) {
+      if (!dataHash.equals(previousDto.getDataHash()) || !metadata.hash().equals(previousDto.getSrcHash())) {
         previousDto
           .setBinaryData(data)
           .setDataHash(dataHash)
-          .setSrcHash(inputFile.hash())
-          .setLineHashes(lineHashesAsMd5Hex(inputFile))
+          .setSrcHash(metadata.hash())
+          .setLineHashes(lineHashesAsMd5Hex(inputFile, metadata))
           .setUpdatedAt(system2.now());
         mapper.update(previousDto);
         session.commit();
@@ -118,24 +119,41 @@ public class SourcePersister implements ScanPersister {
   }
 
   @CheckForNull
-  private String lineHashesAsMd5Hex(DefaultInputFile inputFile) {
-    if (inputFile.lines() == 0) {
+  private String lineHashesAsMd5Hex(DefaultInputFile f, InputFileMetadata metadata) {
+    if (f.lines() == 0) {
       return null;
     }
     // A md5 string is 32 char long + '\n' = 33
-    StringBuilder result = new StringBuilder(inputFile.lines() * (32 + 1));
-    for (byte[] lineHash : inputFile.lineHashes()) {
-      if (result.length() > 0) {
-        result.append("\n");
+    StringBuilder result = new StringBuilder(f.lines() * (32 + 1));
+
+    try {
+      BufferedReader reader = Files.newBufferedReader(f.path(), f.charset());
+      StringBuilder sb = new StringBuilder();
+      for (int i = 0; i < f.lines(); i++) {
+        String lineStr = reader.readLine();
+        lineStr = lineStr == null ? "" : lineStr;
+        for (int j = 0; j < lineStr.length(); j++) {
+          char c = lineStr.charAt(j);
+          if (!Character.isWhitespace(c)) {
+            sb.append(c);
+          }
+        }
+        if (i > 0) {
+          result.append("\n");
+        }
+        result.append(sb.length() > 0 ? DigestUtils.md5Hex(sb.toString()) : "");
+        sb.setLength(0);
       }
-      result.append(lineHash != null ? Hex.encodeHexString(lineHash) : "");
+    } catch (Exception e) {
+      throw new IllegalStateException("Unable to compute line hashes of file " + f, e);
     }
+
     return result.toString();
   }
 
-  private byte[] computeData(DefaultInputFile inputFile) {
+  private byte[] computeData(DefaultInputFile inputFile, InputFileMetadata metadata) {
     try {
-      return dataFactory.consolidateData(inputFile);
+      return dataFactory.consolidateData(inputFile, metadata);
     } catch (IOException e) {
       throw new IllegalStateException("Fail to read file " + inputFile, e);
     }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/FileHashes.java b/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/FileHashes.java
index 49b0405787b..fbc293e8004 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/FileHashes.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/FileHashes.java
@@ -19,11 +19,17 @@
  */
 package org.sonar.batch.issue.tracking;
 
+import com.google.common.base.Charsets;
 import com.google.common.collect.LinkedHashMultimap;
 import com.google.common.collect.Multimap;
 import org.apache.commons.codec.binary.Hex;
+import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.commons.lang.ObjectUtils;
+import org.sonar.api.batch.fs.internal.DefaultInputFile;
 
+import java.io.BufferedReader;
+import java.nio.file.Files;
+import java.security.MessageDigest;
 import java.util.Collection;
 
 /**
@@ -49,7 +55,29 @@ public final class FileHashes {
     return new FileHashes(hashes, linesByHash);
   }
 
-  public static FileHashes create(byte[][] hashes) {
+  public static FileHashes create(DefaultInputFile f) {
+    byte[][] hashes = new byte[f.lines()][];
+    try {
+      BufferedReader reader = Files.newBufferedReader(f.path(), f.charset());
+      MessageDigest lineMd5Digest = DigestUtils.getMd5Digest();
+      StringBuilder sb = new StringBuilder();
+      for (int i = 0; i < f.lines(); i++) {
+        String lineStr = reader.readLine();
+        if (lineStr != null) {
+          for (int j = 0; j < lineStr.length(); j++) {
+            char c = lineStr.charAt(j);
+            if (!Character.isWhitespace(c)) {
+              sb.append(c);
+            }
+          }
+        }
+        hashes[i] = sb.length() > 0 ? lineMd5Digest.digest(sb.toString().getBytes(Charsets.UTF_8)) : null;
+        sb.setLength(0);
+      }
+    } catch (Exception e) {
+      throw new IllegalStateException("Unable to compute line hashes of file " + f, e);
+    }
+
     int size = hashes.length;
     Multimap<String, Integer> linesByHash = LinkedHashMultimap.create();
     String[] hexHashes = new String[size];
diff --git a/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/IssueHandlers.java b/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/IssueHandlers.java
index f8a98c29b00..b501e18ad66 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/IssueHandlers.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/IssueHandlers.java
@@ -19,7 +19,7 @@
  */
 package org.sonar.batch.issue.tracking;
 
-import org.sonar.api.BatchExtension;
+import org.sonar.api.BatchComponent;
 import org.sonar.api.issue.Issue;
 import org.sonar.api.issue.IssueHandler;
 import org.sonar.api.issue.internal.DefaultIssue;
@@ -30,7 +30,7 @@ import org.sonar.core.user.DefaultUser;
 
 import javax.annotation.Nullable;
 
-public class IssueHandlers implements BatchExtension {
+public class IssueHandlers implements BatchComponent {
   private final IssueHandler[] handlers;
   private final DefaultContext context;
 
@@ -117,7 +117,7 @@ public class IssueHandlers implements BatchExtension {
     @Override
     public IssueHandler.Context assign(@Nullable String assignee) {
       User user = null;
-      if(assignee != null) {
+      if (assignee != null) {
         user = new DefaultUser().setLogin(assignee).setName(assignee);
       }
       updater.assign(issue, user, changeContext);
diff --git a/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/IssueTrackingDecorator.java b/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/IssueTrackingDecorator.java
index c3826cbd391..c1ae052034c 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/IssueTrackingDecorator.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/IssueTrackingDecorator.java
@@ -19,8 +19,6 @@
  */
 package org.sonar.batch.issue.tracking;
 
-import org.sonar.api.batch.RequiresDB;
-
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Strings;
 import com.google.common.collect.Lists;
@@ -32,6 +30,7 @@ import org.sonar.api.batch.DecoratorBarriers;
 import org.sonar.api.batch.DecoratorContext;
 import org.sonar.api.batch.DependedUpon;
 import org.sonar.api.batch.DependsUpon;
+import org.sonar.api.batch.RequiresDB;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.component.ResourcePerspectives;
@@ -133,7 +132,7 @@ public class IssueTrackingDecorator implements Decorator {
       File sonarFile = (File) resource;
       InputFile file = inputPathCache.getFile(project.getEffectiveKey(), sonarFile.getPath());
       if (file == null) {
-        throw new IllegalStateException("Resource " + resource + " was not found in InputPath cache");
+        throw new IllegalStateException("File " + resource + " was not found in InputPath cache");
       }
       sourceHashHolder = new SourceHashHolder((DefaultInputFile) file, lastLineHashes);
     }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/LocalIssueTracking.java b/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/LocalIssueTracking.java
index f0c22e52c68..c4d9a65769f 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/LocalIssueTracking.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/LocalIssueTracking.java
@@ -24,7 +24,6 @@ import com.google.common.collect.Lists;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.sonar.api.BatchComponent;
-import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.rule.ActiveRule;
 import org.sonar.api.batch.rule.ActiveRules;
@@ -108,7 +107,7 @@ public class LocalIssueTracking implements BatchComponent {
 
     SourceHashHolder sourceHashHolder = null;
     if (component.isFile()) {
-      InputFile file = (InputFile) inputPathCache.getInputPath(component);
+      DefaultInputFile file = (DefaultInputFile) inputPathCache.getInputPath(component);
       if (file == null) {
         throw new IllegalStateException("Resource " + component.resource() + " was not found in InputPath cache");
       }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/SourceHashHolder.java b/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/SourceHashHolder.java
index 38f0af7745a..8151f4184f4 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/SourceHashHolder.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/issue/tracking/SourceHashHolder.java
@@ -43,7 +43,7 @@ public class SourceHashHolder {
 
   private void initHashes() {
     if (hashedSource == null) {
-      hashedSource = FileHashes.create(inputFile.lineHashes());
+      hashedSource = FileHashes.create(inputFile);
       Status status = inputFile.status();
       if (status == Status.ADDED) {
         hashedReference = null;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/mediumtest/TaskResult.java b/sonar-batch/src/main/java/org/sonar/batch/mediumtest/TaskResult.java
index 7bc120b37d6..4d89b9e4b3e 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/mediumtest/TaskResult.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/mediumtest/TaskResult.java
@@ -24,7 +24,6 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 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.DefaultInputFile;
 import org.sonar.api.batch.sensor.dependency.Dependency;
 import org.sonar.api.batch.sensor.duplication.DuplicationGroup;
@@ -165,12 +164,11 @@ public class TaskResult implements org.sonar.batch.mediumtest.ScanTaskObserver {
 
   private void storeFs(ProjectScanContainer container) {
     InputPathCache inputFileCache = container.getComponentByType(InputPathCache.class);
-    for (InputPath inputPath : inputFileCache.all()) {
-      if (inputPath instanceof InputFile) {
-        inputFiles.put(inputPath.relativePath(), (InputFile) inputPath);
-      } else {
-        inputDirs.put(inputPath.relativePath(), (InputDir) inputPath);
-      }
+    for (InputFile inputPath : inputFileCache.allFiles()) {
+      inputFiles.put(inputPath.relativePath(), inputPath);
+    }
+    for (InputDir inputPath : inputFileCache.allDirs()) {
+      inputDirs.put(inputPath.relativePath(), inputPath);
     }
   }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/phases/DecoratorsExecutor.java b/sonar-batch/src/main/java/org/sonar/batch/phases/DecoratorsExecutor.java
index 6da48d12bb8..b555f76ded9 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/phases/DecoratorsExecutor.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/phases/DecoratorsExecutor.java
@@ -19,6 +19,9 @@
  */
 package org.sonar.batch.phases;
 
+import org.sonar.batch.deprecated.decorator.DefaultDecoratorContext;
+
+import org.sonar.batch.deprecated.decorator.DecoratorsSelector;
 import com.google.common.collect.Lists;
 import org.sonar.api.BatchComponent;
 import org.sonar.api.batch.Decorator;
@@ -29,8 +32,6 @@ import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.utils.MessageException;
 import org.sonar.api.utils.SonarException;
-import org.sonar.batch.DecoratorsSelector;
-import org.sonar.batch.DefaultDecoratorContext;
 import org.sonar.batch.bootstrap.BatchExtensionDictionnary;
 import org.sonar.batch.duplication.DuplicationCache;
 import org.sonar.batch.events.EventBus;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/phases/Phases.java b/sonar-batch/src/main/java/org/sonar/batch/phases/Phases.java
index 6c84c6dff15..2a2e08056ad 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/phases/Phases.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/phases/Phases.java
@@ -24,6 +24,9 @@ import com.google.common.collect.Sets;
 import java.util.Arrays;
 import java.util.Set;
 
+/**
+ * Used by views
+ */
 public class Phases {
 
   public static enum Phase {
diff --git a/sonar-batch/src/main/java/org/sonar/batch/phases/SensorMatcher.java b/sonar-batch/src/main/java/org/sonar/batch/phases/SensorMatcher.java
index c50d3727184..38502235cff 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/phases/SensorMatcher.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/phases/SensorMatcher.java
@@ -27,6 +27,7 @@ import org.sonar.batch.bootstrap.ExtensionMatcher;
 
 /**
  * Allow to filter sensors that will be executed.
+ * Used by views !!
  * @since 3.6
  *
  */
diff --git a/sonar-batch/src/main/java/org/sonar/batch/languages/DefaultLanguagesReferential.java b/sonar-batch/src/main/java/org/sonar/batch/repository/language/DefaultLanguagesRepository.java
index 4d43ea2d8ce..fe5f50ba9ea 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/languages/DefaultLanguagesReferential.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/repository/language/DefaultLanguagesRepository.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.languages;
+package org.sonar.batch.repository.language;
 
 import org.sonar.api.resources.Languages;
 
@@ -27,14 +27,14 @@ import java.util.ArrayList;
 import java.util.Collection;
 
 /**
- * Languages referential using {@link Languages}
+ * Languages repository using {@link Languages}
  * @since 4.4
  */
-public class DefaultLanguagesReferential implements LanguagesReferential {
+public class DefaultLanguagesRepository implements LanguagesRepository {
 
   private Languages languages;
 
-  public DefaultLanguagesReferential(Languages languages) {
+  public DefaultLanguagesRepository(Languages languages) {
     this.languages = languages;
   }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/languages/Language.java b/sonar-batch/src/main/java/org/sonar/batch/repository/language/Language.java
index daeb7d50626..67629ae50ad 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/languages/Language.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/repository/language/Language.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.languages;
+package org.sonar.batch.repository.language;
 
 import java.util.Arrays;
 import java.util.Collection;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/languages/LanguagesReferential.java b/sonar-batch/src/main/java/org/sonar/batch/repository/language/LanguagesRepository.java
index da1596c2c10..dd80fee1dcd 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/languages/LanguagesReferential.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/repository/language/LanguagesRepository.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.languages;
+package org.sonar.batch.repository.language;
 
 import org.sonar.api.BatchComponent;
 
@@ -26,10 +26,10 @@ import javax.annotation.CheckForNull;
 import java.util.Collection;
 
 /**
- * Languages referential
+ * Languages repository
  * @since 4.4
  */
-public interface LanguagesReferential extends BatchComponent {
+public interface LanguagesRepository extends BatchComponent {
 
   /**
    * Get language.
diff --git a/sonar-batch/src/main/java/org/sonar/batch/languages/package-info.java b/sonar-batch/src/main/java/org/sonar/batch/repository/language/package-info.java
index 7a5d7a96ff6..03e334e21a0 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/languages/package-info.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/repository/language/package-info.java
@@ -18,4 +18,4 @@
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
 @javax.annotation.ParametersAreNonnullByDefault
-package org.sonar.batch.languages;
+package org.sonar.batch.repository.language;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/user/User.java b/sonar-batch/src/main/java/org/sonar/batch/repository/user/User.java
index bd96d273f8c..5323e18b943 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/user/User.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/repository/user/User.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.apache.commons.lang.builder.EqualsBuilder;
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/user/UserRepository.java b/sonar-batch/src/main/java/org/sonar/batch/repository/user/UserRepository.java
index c129bb704df..e7185b98645 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/user/UserRepository.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/repository/user/UserRepository.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 com.google.common.base.Joiner;
 import org.sonar.batch.bootstrap.ServerClient;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/user/package-info.java b/sonar-batch/src/main/java/org/sonar/batch/repository/user/package-info.java
index 6415ba162e8..a86ee26f141 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/user/package-info.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/repository/user/package-info.java
@@ -18,6 +18,6 @@
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
 @ParametersAreNonnullByDefault
-package org.sonar.batch.user;
+package org.sonar.batch.repository.user;
 
 import javax.annotation.ParametersAreNonnullByDefault;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/rule/QProfileSensor.java b/sonar-batch/src/main/java/org/sonar/batch/rule/QProfileSensor.java
index 13ab4448d78..37455f5b58a 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/rule/QProfileSensor.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/rule/QProfileSensor.java
@@ -19,6 +19,7 @@
  */
 package org.sonar.batch.rule;
 
+import org.sonar.api.batch.AnalysisMode;
 import org.sonar.api.batch.Sensor;
 import org.sonar.api.batch.SensorContext;
 import org.sonar.api.batch.fs.FileSystem;
@@ -33,16 +34,20 @@ public class QProfileSensor implements Sensor {
 
   private final ModuleQProfiles moduleQProfiles;
   private final FileSystem fs;
+  private final AnalysisMode analysisMode;
 
-  public QProfileSensor(ModuleQProfiles moduleQProfiles, FileSystem fs) {
+  public QProfileSensor(ModuleQProfiles moduleQProfiles, FileSystem fs, AnalysisMode analysisMode) {
     this.moduleQProfiles = moduleQProfiles;
     this.fs = fs;
+    this.analysisMode = analysisMode;
   }
 
   @Override
   public boolean shouldExecuteOnProject(Project project) {
     // Should be only executed on leaf modules
-    return project.getModules().isEmpty();
+    return project.getModules().isEmpty()
+      // Useless in preview mode
+      && !analysisMode.isPreview();
   }
 
   @Override
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/LanguageVerifier.java b/sonar-batch/src/main/java/org/sonar/batch/scan/LanguageVerifier.java
index 801fadddd44..f813c050681 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/LanguageVerifier.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/LanguageVerifier.java
@@ -19,7 +19,8 @@
  */
 package org.sonar.batch.scan;
 
-import org.sonar.batch.languages.Language;
+import org.sonar.batch.repository.language.Language;
+import org.sonar.batch.repository.language.LanguagesRepository;
 
 import org.picocontainer.Startable;
 import org.slf4j.Logger;
@@ -28,7 +29,6 @@ import org.sonar.api.CoreProperties;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.config.Settings;
 import org.sonar.api.utils.MessageException;
-import org.sonar.batch.languages.LanguagesReferential;
 
 /**
  * Verifies that the property sonar.language is valid
@@ -38,10 +38,10 @@ public class LanguageVerifier implements Startable {
   private static final Logger LOG = LoggerFactory.getLogger(LanguageVerifier.class);
 
   private final Settings settings;
-  private final LanguagesReferential languages;
+  private final LanguagesRepository languages;
   private final DefaultFileSystem fs;
 
-  public LanguageVerifier(Settings settings, LanguagesReferential languages, DefaultFileSystem fs) {
+  public LanguageVerifier(Settings settings, LanguagesRepository languages, DefaultFileSystem fs) {
     this.settings = settings;
     this.languages = languages;
     this.fs = fs;
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java b/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java
index e350fd28992..0f457c735d9 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java
@@ -29,11 +29,7 @@ import org.sonar.api.checks.NoSonarFilter;
 import org.sonar.api.platform.ComponentContainer;
 import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.FileExclusions;
-import org.sonar.batch.DefaultProjectClasspath;
-import org.sonar.batch.DefaultTimeMachine;
-import org.sonar.batch.DeprecatedSensorContext;
 import org.sonar.batch.ProjectTree;
-import org.sonar.batch.ResourceFilters;
 import org.sonar.batch.bootstrap.BatchExtensionDictionnary;
 import org.sonar.batch.bootstrap.DefaultAnalysisMode;
 import org.sonar.batch.bootstrap.ExtensionInstaller;
@@ -45,6 +41,10 @@ import org.sonar.batch.debt.IssueChangelogDebtCalculator;
 import org.sonar.batch.debt.NewDebtDecorator;
 import org.sonar.batch.debt.SqaleRatingDecorator;
 import org.sonar.batch.debt.SqaleRatingSettings;
+import org.sonar.batch.deprecated.DeprecatedSensorContext;
+import org.sonar.batch.deprecated.ResourceFilters;
+import org.sonar.batch.deprecated.components.DefaultProjectClasspath;
+import org.sonar.batch.deprecated.components.DefaultTimeMachine;
 import org.sonar.batch.events.EventBus;
 import org.sonar.batch.index.DefaultIndex;
 import org.sonar.batch.issue.IssuableFactory;
@@ -87,6 +87,7 @@ import org.sonar.batch.scan.filesystem.DefaultModuleFileSystem;
 import org.sonar.batch.scan.filesystem.DeprecatedFileFilters;
 import org.sonar.batch.scan.filesystem.ExclusionFilters;
 import org.sonar.batch.scan.filesystem.FileIndexer;
+import org.sonar.batch.scan.filesystem.FileMetadata;
 import org.sonar.batch.scan.filesystem.FileSystemLogger;
 import org.sonar.batch.scan.filesystem.InputFileBuilderFactory;
 import org.sonar.batch.scan.filesystem.LanguageDetectionFactory;
@@ -158,6 +159,7 @@ public class ModuleScanContainer extends ComponentContainer {
       ExclusionFilters.class,
       DeprecatedFileFilters.class,
       InputFileBuilderFactory.class,
+      FileMetadata.class,
       StatusDetectionFactory.class,
       LanguageDetectionFactory.class,
       FileIndexer.class,
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectScanContainer.java b/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectScanContainer.java
index 30ef5615488..98c46431093 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectScanContainer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectScanContainer.java
@@ -19,6 +19,10 @@
  */
 package org.sonar.batch.scan;
 
+import org.sonar.batch.deprecated.components.DefaultResourceCreationLock;
+
+import org.sonar.batch.deprecated.components.PeriodsDefinition;
+import org.sonar.batch.repository.language.DefaultLanguagesRepository;
 import com.google.common.annotations.VisibleForTesting;
 import org.sonar.api.BatchComponent;
 import org.sonar.api.CoreProperties;
@@ -32,7 +36,6 @@ import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.PathResolver;
 import org.sonar.api.utils.SonarException;
 import org.sonar.batch.DefaultFileLinesContextFactory;
-import org.sonar.batch.DefaultResourceCreationLock;
 import org.sonar.batch.ProjectConfigurator;
 import org.sonar.batch.ProjectTree;
 import org.sonar.batch.bootstrap.DefaultAnalysisMode;
@@ -40,7 +43,6 @@ import org.sonar.batch.bootstrap.ExtensionInstaller;
 import org.sonar.batch.bootstrap.ExtensionMatcher;
 import org.sonar.batch.bootstrap.ExtensionUtils;
 import org.sonar.batch.bootstrap.MetricProvider;
-import org.sonar.batch.components.PeriodsDefinition;
 import org.sonar.batch.debt.DebtModelProvider;
 import org.sonar.batch.debt.IssueChangelogDebtCalculator;
 import org.sonar.batch.duplication.BlockCache;
@@ -63,7 +65,6 @@ import org.sonar.batch.issue.IssueCache;
 import org.sonar.batch.issue.tracking.InitialOpenIssuesStack;
 import org.sonar.batch.issue.tracking.LocalIssueTracking;
 import org.sonar.batch.issue.tracking.PreviousIssueRepository;
-import org.sonar.batch.languages.DefaultLanguagesReferential;
 import org.sonar.batch.mediumtest.ScanTaskObservers;
 import org.sonar.batch.phases.GraphPersister;
 import org.sonar.batch.profiling.PhasesSumUpTimeProfiler;
@@ -177,7 +178,7 @@ public class ProjectScanContainer extends ComponentContainer {
 
       // lang
       Languages.class,
-      DefaultLanguagesReferential.class,
+      DefaultLanguagesRepository.class,
       HighlightableBuilder.class,
       SymbolizableBuilder.class,
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/AdditionalFilePredicates.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/AdditionalFilePredicates.java
index 4d4967ec1f3..83fbd745426 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/AdditionalFilePredicates.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/AdditionalFilePredicates.java
@@ -19,7 +19,6 @@
  */
 package org.sonar.batch.scan.filesystem;
 
-import org.apache.commons.io.FilenameUtils;
 import org.sonar.api.batch.fs.AbstractFilePredicate;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
@@ -47,42 +46,4 @@ class AdditionalFilePredicates {
     }
   }
 
-  static class DeprecatedKeyPredicate extends AbstractFilePredicate {
-    private final String key;
-
-    DeprecatedKeyPredicate(String key) {
-      this.key = key;
-    }
-
-    @Override
-    public boolean apply(InputFile f) {
-      return key.equals(((DeprecatedDefaultInputFile) f).deprecatedKey());
-    }
-  }
-
-  static class SourceRelativePathPredicate extends AbstractFilePredicate {
-    private final String path;
-
-    SourceRelativePathPredicate(String s) {
-      this.path = FilenameUtils.normalize(s, true);
-    }
-
-    @Override
-    public boolean apply(InputFile f) {
-      return path.equals(((DeprecatedDefaultInputFile) f).pathRelativeToSourceDir());
-    }
-  }
-
-  static class SourceDirPredicate extends AbstractFilePredicate {
-    private final String path;
-
-    SourceDirPredicate(String s) {
-      this.path = FilenameUtils.normalize(s, true);
-    }
-
-    @Override
-    public boolean apply(InputFile f) {
-      return path.equals(((DeprecatedDefaultInputFile) f).sourceDirAbsolutePath());
-    }
-  }
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ComponentIndexer.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ComponentIndexer.java
index 69438106d8f..460a08831b3 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ComponentIndexer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ComponentIndexer.java
@@ -21,16 +21,13 @@ package org.sonar.batch.scan.filesystem;
 
 import org.sonar.api.BatchComponent;
 import org.sonar.api.batch.SonarIndex;
-import org.sonar.api.batch.fs.FileSystem;
 import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
 import org.sonar.api.resources.File;
 import org.sonar.api.resources.Languages;
 import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
 import org.sonar.batch.index.ResourceKeyMigration;
 import org.sonar.batch.index.ResourcePersister;
-import org.sonar.batch.util.DeprecatedKeyUtils;
 
 import javax.annotation.Nullable;
 
@@ -60,7 +57,9 @@ public class ComponentIndexer implements BatchComponent {
     this(module, languages, sonarIndex, null, null);
   }
 
-  public void execute(FileSystem fs) {
+  public void execute(DefaultModuleFileSystem fs) {
+    module.setBaseDir(fs.baseDir());
+
     if (resourcePersister != null) {
       // Force persistence of module structure in order to know if project should be migrated
       resourcePersister.persist();
@@ -73,16 +72,7 @@ public class ComponentIndexer implements BatchComponent {
     for (InputFile inputFile : fs.inputFiles(fs.predicates().all())) {
       String languageKey = inputFile.language();
       boolean unitTest = InputFile.Type.TEST == inputFile.type();
-      String pathFromSourceDir = ((DeprecatedDefaultInputFile) inputFile).pathRelativeToSourceDir();
-      if (pathFromSourceDir == null) {
-        pathFromSourceDir = inputFile.relativePath();
-      }
-      Resource sonarFile = File.create(inputFile.relativePath(), pathFromSourceDir, languages.get(languageKey), unitTest);
-      if ("java".equals(languageKey)) {
-        sonarFile.setDeprecatedKey(DeprecatedKeyUtils.getJavaFileDeprecatedKey(pathFromSourceDir));
-      } else {
-        sonarFile.setDeprecatedKey(pathFromSourceDir);
-      }
+      Resource sonarFile = File.create(inputFile.relativePath(), languages.get(languageKey), unitTest);
       sonarIndex.index(sonarFile);
     }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultInputFileValueCoder.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultInputFileValueCoder.java
deleted file mode 100644
index 31e0880a8fe..00000000000
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultInputFileValueCoder.java
+++ /dev/null
@@ -1,92 +0,0 @@
-/*
- * SonarQube, open source software quality management tool.
- * Copyright (C) 2008-2014 SonarSource
- * mailto:contact AT sonarsource DOT com
- *
- * SonarQube is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
- * version 3 of the License, or (at your option) any later version.
- *
- * SonarQube is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
- */
-package org.sonar.batch.scan.filesystem;
-
-import com.persistit.Value;
-import com.persistit.encoding.CoderContext;
-import com.persistit.encoding.ValueCoder;
-import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
-
-import javax.annotation.Nullable;
-
-import java.io.File;
-
-class DefaultInputFileValueCoder implements ValueCoder {
-
-  @Override
-  public void put(Value value, Object object, CoderContext context) {
-    DeprecatedDefaultInputFile f = (DeprecatedDefaultInputFile) object;
-    putUTFOrNull(value, f.moduleKey());
-    putUTFOrNull(value, f.relativePath());
-    value.putString(f.getFileBaseDir().toString());
-    putUTFOrNull(value, f.deprecatedKey());
-    value.putString(f.sourceDirAbsolutePath());
-    putUTFOrNull(value, f.pathRelativeToSourceDir());
-    putUTFOrNull(value, f.absolutePath());
-    value.putString(f.language());
-    value.putString(f.type().name());
-    value.putString(f.status().name());
-    putUTFOrNull(value, f.hash());
-    value.put(f.lines());
-    value.put(f.nonBlankLines());
-    putUTFOrNull(value, f.encoding());
-    value.put(f.isEmpty());
-    value.putLongArray(f.originalLineOffsets());
-    for (int i = 0; i < f.lines(); i++) {
-      value.putByteArray(f.lineHashes()[i]);
-    }
-  }
-
-  private void putUTFOrNull(Value value, @Nullable String utfOrNull) {
-    if (utfOrNull != null) {
-      value.putUTF(utfOrNull);
-    } else {
-      value.putNull();
-    }
-  }
-
-  @Override
-  public Object get(Value value, Class clazz, CoderContext context) {
-    String moduleKey = value.getString();
-    DeprecatedDefaultInputFile file = new DeprecatedDefaultInputFile(moduleKey, value.getString());
-    file.setBasedir(new File(value.getString()));
-    file.setDeprecatedKey(value.getString());
-    file.setSourceDirAbsolutePath(value.getString());
-    file.setPathRelativeToSourceDir(value.getString());
-    file.setAbsolutePath(value.getString());
-    file.setLanguage(value.getString());
-    file.setType(InputFile.Type.valueOf(value.getString()));
-    file.setStatus(InputFile.Status.valueOf(value.getString()));
-    file.setHash(value.getString());
-    file.setLines(value.getInt());
-    file.setNonBlankLines(value.getInt());
-    file.setEncoding(value.getString());
-    file.setEmpty(value.getBoolean());
-    file.setOriginalLineOffsets(value.getLongArray());
-    byte[][] lineHashes = new byte[file.lines()][];
-    for (int i = 0; i < file.lines(); i++) {
-      lineHashes[i] = value.getByteArray();
-    }
-    file.setLineHashes(lineHashes);
-    return file;
-  }
-
-}
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystem.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystem.java
index 43006d48ef6..5f16313e853 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystem.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystem.java
@@ -19,13 +19,13 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Function;
 import com.google.common.collect.Collections2;
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Lists;
 import org.apache.commons.lang.StringUtils;
 import org.sonar.api.CoreProperties;
-import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.fs.FilePredicate;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.config.Settings;
@@ -45,8 +45,6 @@ import java.util.List;
 import java.util.Map;
 
 /**
- * This class can't be immutable because of execution of maven plugins that can change the project structure (see MavenPluginHandler and sonar.phase)
- *
  * @since 3.5
  */
 public class DefaultModuleFileSystem extends DefaultFileSystem implements ModuleFileSystem {
@@ -62,27 +60,26 @@ public class DefaultModuleFileSystem extends DefaultFileSystem implements Module
   private ComponentIndexer componentIndexer;
   private boolean initialized;
 
-  /**
-   * Used by scan2 
-   */
-  public DefaultModuleFileSystem(ModuleInputFileCache moduleInputFileCache, ProjectDefinition def, Settings settings,
-    FileIndexer indexer, ModuleFileSystemInitializer initializer) {
-    this(moduleInputFileCache, def.getKey(), settings, indexer, initializer, null);
-  }
-
   public DefaultModuleFileSystem(ModuleInputFileCache moduleInputFileCache, Project project,
-    Settings settings, FileIndexer indexer,
-    ModuleFileSystemInitializer initializer,
-    ComponentIndexer componentIndexer) {
-    this(moduleInputFileCache, project.getKey(), settings, indexer, initializer, componentIndexer);
+    Settings settings, FileIndexer indexer, ModuleFileSystemInitializer initializer, ComponentIndexer componentIndexer) {
+    super(initializer.baseDir().toPath(), moduleInputFileCache);
+    this.componentIndexer = componentIndexer;
+    this.moduleKey = project.getKey();
+    this.settings = settings;
+    this.indexer = indexer;
+    setWorkDir(initializer.workingDir());
+    this.buildDir = initializer.buildDir();
+    this.sourceDirsOrFiles = initializer.sources();
+    this.testDirsOrFiles = initializer.tests();
+    this.binaryDirs = initializer.binaryDirs();
   }
 
-  private DefaultModuleFileSystem(ModuleInputFileCache moduleInputFileCache, String moduleKey, Settings settings,
-    FileIndexer indexer, ModuleFileSystemInitializer initializer,
-    @Nullable ComponentIndexer componentIndexer) {
-    super(initializer.baseDir(), moduleInputFileCache);
+  @VisibleForTesting
+  public DefaultModuleFileSystem(Project project,
+    Settings settings, FileIndexer indexer, ModuleFileSystemInitializer initializer, ComponentIndexer componentIndexer) {
+    super(initializer.baseDir().toPath());
     this.componentIndexer = componentIndexer;
-    this.moduleKey = moduleKey;
+    this.moduleKey = project.getKey();
     this.settings = settings;
     this.indexer = indexer;
     setWorkDir(initializer.workingDir());
@@ -260,30 +257,6 @@ public class DefaultModuleFileSystem extends DefaultFileSystem implements Module
         }
       }));
     }
-    if ("CMP_DEPRECATED_KEY".equals(key)) {
-      return predicates().or(Collections2.transform(value, new Function<String, FilePredicate>() {
-        @Override
-        public FilePredicate apply(@Nullable String s) {
-          return s == null ? predicates().all() : new AdditionalFilePredicates.DeprecatedKeyPredicate(s);
-        }
-      }));
-    }
-    if ("SRC_REL_PATH".equals(key)) {
-      return predicates().or(Collections2.transform(value, new Function<String, FilePredicate>() {
-        @Override
-        public FilePredicate apply(@Nullable String s) {
-          return s == null ? predicates().all() : new AdditionalFilePredicates.SourceRelativePathPredicate(s);
-        }
-      }));
-    }
-    if ("SRC_DIR_PATH".equals(key)) {
-      return predicates().or(Collections2.transform(value, new Function<String, FilePredicate>() {
-        @Override
-        public FilePredicate apply(@Nullable String s) {
-          return s == null ? predicates().all() : new AdditionalFilePredicates.SourceDirPredicate(s);
-        }
-      }));
-    }
     throw new IllegalArgumentException("Unsupported file attribute: " + key);
   }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DeprecatedFileFilters.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DeprecatedFileFilters.java
index d52e19b0b0b..9fa6ea98a23 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DeprecatedFileFilters.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DeprecatedFileFilters.java
@@ -21,13 +21,10 @@ package org.sonar.batch.scan.filesystem;
 
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.InputFileFilter;
-import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
 import org.sonar.api.scan.filesystem.FileSystemFilter;
 import org.sonar.api.scan.filesystem.FileType;
 import org.sonar.api.scan.filesystem.ModuleFileSystem;
 
-import java.io.File;
-
 public class DeprecatedFileFilters implements InputFileFilter {
   private final FileSystemFilter[] filters;
 
@@ -71,13 +68,8 @@ public class DeprecatedFileFilters implements InputFileFilter {
     }
 
     @Override
-    public File relativeDir() {
-      return new File(((DeprecatedDefaultInputFile)inputFile).sourceDirAbsolutePath());
-    }
-
-    @Override
     public String relativePath() {
-      return ((DeprecatedDefaultInputFile)inputFile).pathRelativeToSourceDir();
+      return inputFile.relativePath();
     }
 
     @Override
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndexer.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndexer.java
index e78ae260ca3..d4626209aa2 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndexer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndexer.java
@@ -23,20 +23,18 @@ import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.filefilter.FileFilterUtils;
 import org.apache.commons.io.filefilter.HiddenFileFilter;
 import org.apache.commons.io.filefilter.IOFileFilter;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.sonar.api.BatchComponent;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
-import org.sonar.api.batch.fs.InputDir;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.InputFileFilter;
 import org.sonar.api.batch.fs.internal.DefaultInputDir;
-import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
 import org.sonar.api.scan.filesystem.PathResolver;
 import org.sonar.api.utils.MessageException;
+import org.sonar.batch.util.ProgressReport;
 
 import java.io.File;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
@@ -47,14 +45,13 @@ import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
+import java.util.concurrent.TimeUnit;
 
 /**
  * Index input files into {@link InputPathCache}.
  */
 public class FileIndexer implements BatchComponent {
 
-  private static final Logger LOG = LoggerFactory.getLogger(FileIndexer.class);
-
   private static final IOFileFilter DIR_FILTER = FileFilterUtils.and(HiddenFileFilter.VISIBLE, FileFilterUtils.notFileFilter(FileFilterUtils.prefixFileFilter(".")));
   private static final IOFileFilter FILE_FILTER = HiddenFileFilter.VISIBLE;
 
@@ -62,18 +59,19 @@ public class FileIndexer implements BatchComponent {
   private final boolean isAggregator;
   private final ExclusionFilters exclusionFilters;
   private final InputFileBuilderFactory inputFileBuilderFactory;
+  private final InputPathCache inputPathCache;
 
-  public FileIndexer(List<InputFileFilter> filters, ExclusionFilters exclusionFilters, InputFileBuilderFactory inputFileBuilderFactory,
-    ProjectDefinition def) {
-    this(filters, exclusionFilters, inputFileBuilderFactory, !def.getSubProjects().isEmpty());
-  }
+  private ProgressReport progressReport;
+  private ExecutorService executorService;
+  private List<Future<Void>> tasks;
 
-  private FileIndexer(List<InputFileFilter> filters, ExclusionFilters exclusionFilters, InputFileBuilderFactory inputFileBuilderFactory,
-    boolean isAggregator) {
+  public FileIndexer(List<InputFileFilter> filters, ExclusionFilters exclusionFilters, InputFileBuilderFactory inputFileBuilderFactory,
+    ProjectDefinition def, InputPathCache inputPathCache) {
+    this.inputPathCache = inputPathCache;
     this.filters = filters;
     this.exclusionFilters = exclusionFilters;
     this.inputFileBuilderFactory = inputFileBuilderFactory;
-    this.isAggregator = isAggregator;
+    this.isAggregator = !def.getSubProjects().isEmpty();
   }
 
   void index(DefaultModuleFileSystem fileSystem) {
@@ -81,47 +79,34 @@ public class FileIndexer implements BatchComponent {
       // No indexing for an aggregator module
       return;
     }
-    LOG.info("Index files");
+    progressReport = new ProgressReport("Report about progress of file indexation", TimeUnit.SECONDS.toMillis(10));
+    progressReport.start("Index files");
     exclusionFilters.prepare();
 
     Progress progress = new Progress();
 
     InputFileBuilder inputFileBuilder = inputFileBuilderFactory.create(fileSystem);
+    executorService = Executors.newFixedThreadPool(Math.max(1, Runtime.getRuntime().availableProcessors() - 1));
+    tasks = new ArrayList<Future<Void>>();
     indexFiles(fileSystem, progress, inputFileBuilder, fileSystem.sources(), InputFile.Type.MAIN);
     indexFiles(fileSystem, progress, inputFileBuilder, fileSystem.tests(), InputFile.Type.TEST);
 
-    indexAllConcurrently(progress);
-
-    // Populate FS in a synchronous way because PersistIt Exchange is not concurrent
-    for (InputFile indexed : progress.indexed) {
-      fileSystem.add(indexed);
-    }
-    for (InputDir indexed : progress.indexedDir) {
-      fileSystem.add(indexed);
-    }
-
-    LOG.info(String.format("%d files indexed", progress.count()));
+    waitForTasksToComplete();
 
+    progressReport.stop(progress.count() + " files indexed");
   }
 
-  private void indexAllConcurrently(Progress progress) {
-    ExecutorService executor = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors() + 1);
-    try {
-      List<Future<Void>> all = executor.invokeAll(progress.indexingTasks);
-      for (Future<Void> future : all) {
-        future.get();
-      }
-    } catch (InterruptedException e) {
-      throw new IllegalStateException("FileIndexer was interrupted", e);
-    } catch (ExecutionException e) {
-      Throwable cause = e.getCause();
-      if (cause instanceof RuntimeException) {
-        throw (RuntimeException) cause;
-      } else {
-        throw new IllegalStateException("Error during file indexing", e);
+  private void waitForTasksToComplete() {
+    for (Future<Void> task : tasks) {
+      try {
+        task.get();
+      } catch (ExecutionException e) {
+        // Unwrap ExecutionException
+        throw e.getCause() instanceof RuntimeException ? (RuntimeException) e.getCause() : new IllegalStateException(e.getCause());
+      } catch (InterruptedException e) {
+        throw new IllegalStateException(e);
       }
     }
-    executor.shutdown();
   }
 
   private void indexFiles(DefaultModuleFileSystem fileSystem, Progress progress, InputFileBuilder inputFileBuilder, List<File> sources, InputFile.Type type) {
@@ -151,25 +136,25 @@ public class FileIndexer implements BatchComponent {
   private void indexFile(final InputFileBuilder inputFileBuilder, final DefaultModuleFileSystem fs,
     final Progress status, final DeprecatedDefaultInputFile inputFile, final InputFile.Type type) {
 
-    Callable<Void> task = new Callable<Void>() {
-
+    tasks.add(executorService.submit(new Callable<Void>() {
       @Override
-      public Void call() throws Exception {
-        DefaultInputFile completedFile = inputFileBuilder.complete(inputFile, type);
-        if (completedFile != null && accept(completedFile)) {
+      public Void call() {
+        InputFileMetadata metadata = inputFileBuilder.completeAndComputeMetadata(inputFile, type);
+        if (metadata != null && accept(inputFile)) {
+          fs.add(inputFile);
           status.markAsIndexed(inputFile);
+          inputPathCache.put(inputFile.moduleKey(), inputFile.relativePath(), metadata);
           File parentDir = inputFile.file().getParentFile();
           String relativePath = new PathResolver().relativePath(fs.baseDir(), parentDir);
           if (relativePath != null) {
             DefaultInputDir inputDir = new DefaultInputDir(fs.moduleKey(), relativePath);
-            inputDir.setFile(parentDir);
-            status.markAsIndexed(inputDir);
+            fs.add(inputDir);
           }
         }
         return null;
       }
-    };
-    status.planForIndexing(task);
+    }));
+
   }
 
   private boolean accept(InputFile inputFile) {
@@ -182,31 +167,16 @@ public class FileIndexer implements BatchComponent {
     return true;
   }
 
-  private static class Progress {
-    private final Set<InputFile> indexed;
-    private final Set<InputDir> indexedDir;
-    private final List<Callable<Void>> indexingTasks;
-
-    Progress() {
-      this.indexed = new HashSet<InputFile>();
-      this.indexedDir = new HashSet<InputDir>();
-      this.indexingTasks = new ArrayList<Callable<Void>>();
-    }
-
-    void planForIndexing(Callable<Void> indexingTask) {
-      this.indexingTasks.add(indexingTask);
-    }
+  private class Progress {
+    private final Set<Path> indexed = new HashSet<>();
 
     synchronized void markAsIndexed(InputFile inputFile) {
-      if (indexed.contains(inputFile)) {
+      if (indexed.contains(inputFile.path())) {
         throw MessageException.of("File " + inputFile + " can't be indexed twice. Please check that inclusion/exclusion patterns produce "
           + "disjoint sets for main and test files");
       }
-      indexed.add(inputFile);
-    }
-
-    synchronized void markAsIndexed(InputDir inputDir) {
-      indexedDir.add(inputDir);
+      indexed.add(inputFile.path());
+      progressReport.message(indexed.size() + " files indexed...  (last one was " + inputFile.relativePath() + ")");
     }
 
     int count() {
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileMetadata.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileMetadata.java
index b3b4d1469fd..0f91e4ae3cc 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileMetadata.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileMetadata.java
@@ -20,17 +20,22 @@
 package org.sonar.batch.scan.filesystem;
 
 import com.google.common.base.Charsets;
-import com.google.common.primitives.Longs;
+import com.google.common.primitives.Ints;
 import org.apache.commons.codec.binary.Hex;
 import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.commons.io.ByteOrderMark;
 import org.apache.commons.io.input.BOMInputStream;
+import org.sonar.api.BatchComponent;
+import org.sonar.api.batch.AnalysisMode;
 
 import javax.annotation.CheckForNull;
 
-import java.io.*;
-import java.nio.ByteBuffer;
-import java.nio.CharBuffer;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.Reader;
 import java.nio.charset.Charset;
 import java.security.MessageDigest;
 import java.util.ArrayList;
@@ -40,10 +45,15 @@ import java.util.List;
  * Computes hash of files. Ends of Lines are ignored, so files with
  * same content but different EOL encoding have the same hash.
  */
-class FileMetadata {
+public class FileMetadata implements BatchComponent {
 
   private static final char LINE_FEED = '\n';
   private static final char CARRIAGE_RETURN = '\r';
+  private final AnalysisMode analysisMode;
+
+  public FileMetadata(AnalysisMode analysisMode) {
+    this.analysisMode = analysisMode;
+  }
 
   private abstract class CharHandler {
 
@@ -110,14 +120,25 @@ class FileMetadata {
   private class FileHashComputer extends CharHandler {
     private MessageDigest globalMd5Digest = DigestUtils.getMd5Digest();
 
+    StringBuffer sb = new StringBuffer();
+
     @Override
     void handleIgnoreEoL(char c) {
-      updateDigestUTF8Char(c, globalMd5Digest);
+      sb.append(c);
     }
 
     @Override
     void newLine() {
-      updateDigestUTF8Char(LINE_FEED, globalMd5Digest);
+      sb.append(LINE_FEED);
+      globalMd5Digest.update(sb.toString().getBytes(Charsets.UTF_8));
+      sb.setLength(0);
+    }
+
+    @Override
+    void eof() {
+      if (sb.length() > 0) {
+        globalMd5Digest.update(sb.toString().getBytes(Charsets.UTF_8));
+      }
     }
 
     @CheckForNull
@@ -127,11 +148,11 @@ class FileMetadata {
   }
 
   private class LineOffsetCounter extends CharHandler {
-    private long currentOriginalOffset = 0;
-    private List<Long> originalLineOffsets = new ArrayList<Long>();
+    private int currentOriginalOffset = 0;
+    private List<Integer> originalLineOffsets = new ArrayList<Integer>();
 
     public LineOffsetCounter() {
-      originalLineOffsets.add(0L);
+      originalLineOffsets.add(0);
     }
 
     @Override
@@ -144,41 +165,12 @@ class FileMetadata {
       originalLineOffsets.add(currentOriginalOffset);
     }
 
-    public List<Long> getOriginalLineOffsets() {
+    public List<Integer> getOriginalLineOffsets() {
       return originalLineOffsets;
     }
 
   }
 
-  private class LineHashesComputer extends CharHandler {
-    private List<Object> lineHashes = new ArrayList<Object>();
-    private MessageDigest lineMd5Digest = DigestUtils.getMd5Digest();
-    private boolean blankLine = true;
-
-    @Override
-    void handleIgnoreEoL(char c) {
-      if (!Character.isWhitespace(c)) {
-        blankLine = false;
-        updateDigestUTF8Char(c, lineMd5Digest);
-      }
-    }
-
-    @Override
-    void newLine() {
-      lineHashes.add(blankLine ? null : lineMd5Digest.digest());
-      blankLine = true;
-    }
-
-    @Override
-    void eof() {
-      lineHashes.add(blankLine ? null : lineMd5Digest.digest());
-    }
-
-    public byte[][] lineHashes() {
-      return lineHashes.toArray(new byte[0][]);
-    }
-  }
-
   /**
    * Compute hash of a file ignoring line ends differences.
    * Maximum performance is needed.
@@ -188,8 +180,13 @@ class FileMetadata {
     LineCounter lineCounter = new LineCounter();
     FileHashComputer fileHashComputer = new FileHashComputer();
     LineOffsetCounter lineOffsetCounter = new LineOffsetCounter();
-    LineHashesComputer lineHashesComputer = new LineHashesComputer();
-    CharHandler[] handlers = new CharHandler[] {lineCounter, fileHashComputer, lineOffsetCounter, lineHashesComputer};
+    CharHandler[] handlers;
+    if (analysisMode.isPreview()) {
+      // No need to compute line offsets in preview mode since there is no syntax highlighting
+      handlers = new CharHandler[] {lineCounter, fileHashComputer};
+    } else {
+      handlers = new CharHandler[] {lineCounter, fileHashComputer, lineOffsetCounter};
+    }
     try (BOMInputStream bomIn = new BOMInputStream(new FileInputStream(file),
       ByteOrderMark.UTF_8, ByteOrderMark.UTF_16LE, ByteOrderMark.UTF_16BE, ByteOrderMark.UTF_32LE, ByteOrderMark.UTF_32BE);
       Reader reader = new BufferedReader(new InputStreamReader(bomIn, encoding))) {
@@ -228,41 +225,26 @@ class FileMetadata {
         handler.eof();
       }
       return new Metadata(lineCounter.lines(), lineCounter.nonBlankLines(), fileHashComputer.getHash(), lineOffsetCounter.getOriginalLineOffsets(),
-        lineHashesComputer.lineHashes(), lineCounter.isEmpty());
+        lineCounter.isEmpty());
 
     } catch (IOException e) {
       throw new IllegalStateException(String.format("Fail to read file '%s' with encoding '%s'", file.getAbsolutePath(), encoding), e);
     }
   }
 
-  private void updateDigestUTF8Char(char c, MessageDigest md5Digest) {
-    CharBuffer cb = CharBuffer.allocate(1);
-    cb.put(c);
-    cb.flip();
-    ByteBuffer bb = Charsets.UTF_8.encode(cb);
-    byte[] array = bb.array();
-    for (int i = 0; i < array.length; i++) {
-      if (array[i] != 0) {
-        md5Digest.update(array[i]);
-      }
-    }
-  }
-
   static class Metadata {
     final int lines;
     final int nonBlankLines;
     final String hash;
-    final long[] originalLineOffsets;
-    final byte[][] lineHashes;
+    final int[] originalLineOffsets;
     final boolean empty;
 
-    private Metadata(int lines, int nonBlankLines, String hash, List<Long> originalLineOffsets, byte[][] lineHashes, boolean empty) {
+    private Metadata(int lines, int nonBlankLines, String hash, List<Integer> originalLineOffsets, boolean empty) {
       this.lines = lines;
       this.nonBlankLines = nonBlankLines;
       this.hash = hash;
       this.empty = empty;
-      this.originalLineOffsets = Longs.toArray(originalLineOffsets);
-      this.lineHashes = lineHashes;
+      this.originalLineOffsets = Ints.toArray(originalLineOffsets);
     }
   }
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilder.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilder.java
index 748410fea36..56b8319ac44 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilder.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilder.java
@@ -19,7 +19,6 @@
  */
 package org.sonar.batch.scan.filesystem;
 
-import org.apache.commons.io.FilenameUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.sonar.api.CoreProperties;
@@ -29,12 +28,10 @@ import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
 import org.sonar.api.config.Settings;
 import org.sonar.api.scan.filesystem.PathResolver;
 import org.sonar.batch.bootstrap.DefaultAnalysisMode;
-import org.sonar.batch.util.DeprecatedKeyUtils;
 
 import javax.annotation.CheckForNull;
 
 import java.io.File;
-import java.util.List;
 
 class InputFileBuilder {
 
@@ -47,9 +44,10 @@ class InputFileBuilder {
   private final DefaultModuleFileSystem fs;
   private final DefaultAnalysisMode analysisMode;
   private final Settings settings;
+  private final FileMetadata fileMetadata;
 
   InputFileBuilder(String moduleKey, PathResolver pathResolver, LanguageDetection langDetection,
-    StatusDetection statusDetection, DefaultModuleFileSystem fs, DefaultAnalysisMode analysisMode, Settings settings) {
+    StatusDetection statusDetection, DefaultModuleFileSystem fs, DefaultAnalysisMode analysisMode, Settings settings, FileMetadata fileMetadata) {
     this.moduleKey = moduleKey;
     this.pathResolver = pathResolver;
     this.langDetection = langDetection;
@@ -57,6 +55,7 @@ class InputFileBuilder {
     this.fs = fs;
     this.analysisMode = analysisMode;
     this.settings = settings;
+    this.fileMetadata = fileMetadata;
   }
 
   String moduleKey() {
@@ -86,20 +85,17 @@ class InputFileBuilder {
       LOG.warn("File '{}' is ignored. It is not located in module basedir '{}'.", file.getAbsolutePath(), fs.baseDir());
       return null;
     }
-    DeprecatedDefaultInputFile inputFile = new DeprecatedDefaultInputFile(moduleKey, relativePath);
-    inputFile.setBasedir(fs.baseDir());
-    inputFile.setFile(file);
-    return inputFile;
+    return new DeprecatedDefaultInputFile(moduleKey, relativePath);
   }
 
   /**
-   * Optimization to not set all InputFile data if the file is excluded from analysis.
+   * Optimization to not compute InputFile metadata if the file is excluded from analysis.
    */
   @CheckForNull
-  DeprecatedDefaultInputFile complete(DeprecatedDefaultInputFile inputFile, InputFile.Type type) {
+  InputFileMetadata completeAndComputeMetadata(DeprecatedDefaultInputFile inputFile, InputFile.Type type) {
     inputFile.setType(type);
-    inputFile.setBasedir(fs.baseDir());
-    inputFile.setEncoding(fs.encoding().name());
+    inputFile.setModuleBaseDir(fs.baseDir().toPath());
+    inputFile.setCharset(fs.encoding());
 
     String lang = langDetection.language(inputFile);
     if (lang == null && !settings.getBoolean(CoreProperties.IMPORT_UNKNOWN_FILES_KEY)) {
@@ -107,36 +103,21 @@ class InputFileBuilder {
     }
     inputFile.setLanguage(lang);
 
-    FileMetadata.Metadata metadata = new FileMetadata().read(inputFile.file(), fs.encoding());
+    InputFileMetadata result = new InputFileMetadata();
+
+    FileMetadata.Metadata metadata = fileMetadata.read(inputFile.file(), fs.encoding());
     inputFile.setLines(metadata.lines);
-    inputFile.setNonBlankLines(metadata.nonBlankLines);
-    inputFile.setHash(metadata.hash);
-    inputFile.setOriginalLineOffsets(metadata.originalLineOffsets);
-    inputFile.setLineHashes(metadata.lineHashes);
-    inputFile.setEmpty(metadata.empty);
+
+    result.setNonBlankLines(metadata.nonBlankLines);
+    result.setHash(metadata.hash);
+    result.setOriginalLineOffsets(metadata.originalLineOffsets);
+    result.setEmpty(metadata.empty);
+
     inputFile.setStatus(statusDetection.status(inputFile.moduleKey(), inputFile.relativePath(), metadata.hash));
     if (analysisMode.isIncremental() && inputFile.status() == InputFile.Status.SAME) {
       return null;
     }
-    fillDeprecatedData(inputFile);
-    return inputFile;
+    return result;
   }
 
-  private void fillDeprecatedData(DeprecatedDefaultInputFile inputFile) {
-    List<File> sourceDirs = InputFile.Type.MAIN == inputFile.type() ? fs.sourceDirs() : fs.testDirs();
-    for (File sourceDir : sourceDirs) {
-      String sourceRelativePath = pathResolver.relativePath(sourceDir, inputFile.file());
-      if (sourceRelativePath != null) {
-        inputFile.setPathRelativeToSourceDir(sourceRelativePath);
-        inputFile.setSourceDirAbsolutePath(FilenameUtils.normalize(sourceDir.getAbsolutePath(), true));
-
-        if ("java".equals(inputFile.language())) {
-          inputFile.setDeprecatedKey(new StringBuilder()
-            .append(moduleKey).append(":").append(DeprecatedKeyUtils.getJavaFileDeprecatedKey(sourceRelativePath)).toString());
-        } else {
-          inputFile.setDeprecatedKey(new StringBuilder().append(moduleKey).append(":").append(sourceRelativePath).toString());
-        }
-      }
-    }
-  }
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactory.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactory.java
index c3dde447e01..c173975fc53 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactory.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileBuilderFactory.java
@@ -33,15 +33,12 @@ public class InputFileBuilderFactory implements BatchComponent {
   private final StatusDetectionFactory statusDetectionFactory;
   private final DefaultAnalysisMode analysisMode;
   private final Settings settings;
+  private final FileMetadata fileMetadata;
 
   public InputFileBuilderFactory(ProjectDefinition def, PathResolver pathResolver, LanguageDetectionFactory langDetectionFactory,
-    StatusDetectionFactory statusDetectionFactory, DefaultAnalysisMode analysisMode, Settings settings) {
-    this(def.getKeyWithBranch(), pathResolver, langDetectionFactory, statusDetectionFactory, analysisMode, settings);
-  }
-
-  private InputFileBuilderFactory(String effectiveKey, PathResolver pathResolver, LanguageDetectionFactory langDetectionFactory,
-    StatusDetectionFactory statusDetectionFactory, DefaultAnalysisMode analysisMode, Settings settings) {
-    this.moduleKey = effectiveKey;
+    StatusDetectionFactory statusDetectionFactory, DefaultAnalysisMode analysisMode, Settings settings, FileMetadata fileMetadata) {
+    this.fileMetadata = fileMetadata;
+    this.moduleKey = def.getKeyWithBranch();
     this.pathResolver = pathResolver;
     this.langDetectionFactory = langDetectionFactory;
     this.statusDetectionFactory = statusDetectionFactory;
@@ -50,6 +47,6 @@ public class InputFileBuilderFactory implements BatchComponent {
   }
 
   InputFileBuilder create(DefaultModuleFileSystem fs) {
-    return new InputFileBuilder(moduleKey, pathResolver, langDetectionFactory.create(), statusDetectionFactory.create(), fs, analysisMode, settings);
+    return new InputFileBuilder(moduleKey, pathResolver, langDetectionFactory.create(), statusDetectionFactory.create(), fs, analysisMode, settings, fileMetadata);
   }
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileMetadata.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileMetadata.java
new file mode 100644
index 00000000000..f37c672d101
--- /dev/null
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputFileMetadata.java
@@ -0,0 +1,73 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * SonarQube is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ */
+package org.sonar.batch.scan.filesystem;
+
+import java.io.Serializable;
+
+/**
+ * Additional input file metadata that are stored in a disk storage to save memory
+ */
+public class InputFileMetadata implements Serializable {
+
+  private String hash;
+  private int nonBlankLines;
+  private int[] originalLineOffsets;
+  private boolean empty;
+
+  /**
+   * Digest hash of the file.
+   */
+  public String hash() {
+    return hash;
+  }
+
+  public int nonBlankLines() {
+    return nonBlankLines;
+  }
+
+  public int[] originalLineOffsets() {
+    return originalLineOffsets;
+  }
+
+  public InputFileMetadata setHash(String hash) {
+    this.hash = hash;
+    return this;
+  }
+
+  public InputFileMetadata setNonBlankLines(int nonBlankLines) {
+    this.nonBlankLines = nonBlankLines;
+    return this;
+  }
+
+  public InputFileMetadata setOriginalLineOffsets(int[] originalLineOffsets) {
+    this.originalLineOffsets = originalLineOffsets;
+    return this;
+  }
+
+  public boolean isEmpty() {
+    return this.empty;
+  }
+
+  public InputFileMetadata setEmpty(boolean empty) {
+    this.empty = empty;
+    return this;
+  }
+
+}
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputPathCache.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputPathCache.java
index adc1a16150c..6270eda9cf2 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputPathCache.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputPathCache.java
@@ -19,82 +19,133 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import com.google.common.base.Function;
+import com.google.common.collect.Iterables;
 import org.sonar.api.BatchComponent;
 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.DeprecatedDefaultInputFile;
 import org.sonar.batch.index.BatchResource;
-import org.sonar.batch.index.Cache;
-import org.sonar.batch.index.Caches;
 
 import javax.annotation.CheckForNull;
 
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
 /**
- * Cache of all files. This cache is shared amongst all project modules. Inclusion and
+ * Cache of all files and dirs. This cache is shared amongst all project modules. Inclusion and
  * exclusion patterns are already applied.
  */
 public class InputPathCache implements BatchComponent {
 
-  private static final String DIR = "DIR";
-  private static final String FILE = "FILE";
-  // [module key | type | path] -> InputPath
-  // For example:
-  // [struts-core | FILE | src/main/java/Action.java] -> InputFile
-  // [struts-core | FILE | src/main/java/Filter.java] -> InputFile
-  // [struts-core | DIR | src/main/java] -> InputDir
-  private final Cache<InputPath> cache;
-
-  public InputPathCache(Caches caches) {
-    caches.registerValueCoder(DeprecatedDefaultInputFile.class, new DefaultInputFileValueCoder());
-    cache = caches.createCache("inputFiles");
+  private final Map<String, Map<String, InputFile>> inputFileCache = new HashMap<>();
+  private final Map<String, Map<String, InputDir>> inputDirCache = new HashMap<>();
+  private final Map<String, Map<String, InputFileMetadata>> inputFileMetadataCache = new HashMap<>();
+
+  public Iterable<InputFile> allFiles() {
+    return Iterables.concat(Iterables.transform(inputFileCache.values(), new Function<Map<String, InputFile>, Collection<InputFile>>() {
+      @Override
+      public Collection<InputFile> apply(Map<String, InputFile> input) {
+        return input.values();
+      }
+    }));
   }
 
-  public Iterable<InputPath> all() {
-    return cache.values();
+  public Iterable<InputDir> allDirs() {
+    return Iterables.concat(Iterables.transform(inputDirCache.values(), new Function<Map<String, InputDir>, Collection<InputDir>>() {
+      @Override
+      public Collection<InputDir> apply(Map<String, InputDir> input) {
+        return input.values();
+      }
+    }));
   }
 
   public Iterable<InputFile> filesByModule(String moduleKey) {
-    return (Iterable) cache.values(moduleKey, FILE);
+    if (inputFileCache.containsKey(moduleKey)) {
+      return inputFileCache.get(moduleKey).values();
+    }
+    return Collections.emptyList();
   }
 
   public Iterable<InputDir> dirsByModule(String moduleKey) {
-    return (Iterable) cache.values(moduleKey, DIR);
+    if (inputDirCache.containsKey(moduleKey)) {
+      return inputDirCache.get(moduleKey).values();
+    }
+    return Collections.emptyList();
   }
 
   public InputPathCache removeModule(String moduleKey) {
-    cache.clear(moduleKey);
+    inputFileCache.remove(moduleKey);
+    inputDirCache.remove(moduleKey);
+    inputFileMetadataCache.remove(moduleKey);
     return this;
   }
 
   public InputPathCache remove(String moduleKey, InputFile inputFile) {
-    cache.remove(moduleKey, FILE, inputFile.relativePath());
+    if (inputFileCache.containsKey(moduleKey)) {
+      inputFileCache.get(moduleKey).remove(inputFile.relativePath());
+    }
+    if (inputFileMetadataCache.containsKey(moduleKey)) {
+      inputFileMetadataCache.get(moduleKey).remove(inputFile.relativePath());
+    }
     return this;
   }
 
   public InputPathCache remove(String moduleKey, InputDir inputDir) {
-    cache.remove(moduleKey, DIR, inputDir.relativePath());
+    if (inputDirCache.containsKey(moduleKey)) {
+      inputDirCache.get(moduleKey).remove(inputDir.relativePath());
+    }
     return this;
   }
 
   public InputPathCache put(String moduleKey, InputFile inputFile) {
-    cache.put(moduleKey, FILE, inputFile.relativePath(), inputFile);
+    if (!inputFileCache.containsKey(moduleKey)) {
+      inputFileCache.put(moduleKey, new HashMap<String, InputFile>());
+    }
+    inputFileCache.get(moduleKey).put(inputFile.relativePath(), inputFile);
+    return this;
+  }
+
+  public synchronized InputPathCache put(String moduleKey, String relativePath, InputFileMetadata metadata) {
+    if (!inputFileMetadataCache.containsKey(moduleKey)) {
+      inputFileMetadataCache.put(moduleKey, new HashMap<String, InputFileMetadata>());
+    }
+    inputFileMetadataCache.get(moduleKey).put(relativePath, metadata);
     return this;
   }
 
   public InputPathCache put(String moduleKey, InputDir inputDir) {
-    cache.put(moduleKey, DIR, inputDir.relativePath(), inputDir);
+    if (!inputDirCache.containsKey(moduleKey)) {
+      inputDirCache.put(moduleKey, new HashMap<String, InputDir>());
+    }
+    inputDirCache.get(moduleKey).put(inputDir.relativePath(), inputDir);
     return this;
   }
 
   @CheckForNull
   public InputFile getFile(String moduleKey, String relativePath) {
-    return (InputFile) cache.get(moduleKey, FILE, relativePath);
+    if (inputFileCache.containsKey(moduleKey)) {
+      return inputFileCache.get(moduleKey).get(relativePath);
+    }
+    return null;
+  }
+
+  @CheckForNull
+  public InputFileMetadata getFileMetadata(String moduleKey, String relativePath) {
+    if (inputFileMetadataCache.containsKey(moduleKey)) {
+      return inputFileMetadataCache.get(moduleKey).get(relativePath);
+    }
+    return null;
   }
 
   @CheckForNull
   public InputDir getDir(String moduleKey, String relativePath) {
-    return (InputDir) cache.get(moduleKey, DIR, relativePath);
+    if (inputDirCache.containsKey(moduleKey)) {
+      return inputDirCache.get(moduleKey).get(relativePath);
+    }
+    return null;
   }
 
   @CheckForNull
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageDetection.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageDetection.java
index 1ee5379f579..131ac8a4ca4 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageDetection.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageDetection.java
@@ -19,7 +19,8 @@
  */
 package org.sonar.batch.scan.filesystem;
 
-import org.sonar.batch.languages.Language;
+import org.sonar.batch.repository.language.Language;
+import org.sonar.batch.repository.language.LanguagesRepository;
 
 import com.google.common.base.Joiner;
 import com.google.common.collect.Lists;
@@ -32,7 +33,6 @@ import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.PathPattern;
 import org.sonar.api.config.Settings;
 import org.sonar.api.utils.MessageException;
-import org.sonar.batch.languages.LanguagesReferential;
 
 import javax.annotation.CheckForNull;
 
@@ -54,7 +54,7 @@ class LanguageDetection {
   private final List<String> languagesToConsider = Lists.newArrayList();
   private final String forcedLanguage;
 
-  LanguageDetection(Settings settings, LanguagesReferential languages) {
+  LanguageDetection(Settings settings, LanguagesRepository languages) {
     for (Language language : languages.all()) {
       String[] filePatterns = settings.getStringArray(getFileLangPatternPropKey(language.key()));
       PathPattern[] pathPatterns = PathPattern.create(filePatterns);
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageDetectionFactory.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageDetectionFactory.java
index 6ff579fd769..c52118612c3 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageDetectionFactory.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/LanguageDetectionFactory.java
@@ -19,15 +19,16 @@
  */
 package org.sonar.batch.scan.filesystem;
 
+import org.sonar.batch.repository.language.LanguagesRepository;
+
 import org.sonar.api.BatchComponent;
 import org.sonar.api.config.Settings;
-import org.sonar.batch.languages.LanguagesReferential;
 
 public class LanguageDetectionFactory implements BatchComponent {
   private final Settings settings;
-  private final LanguagesReferential languages;
+  private final LanguagesRepository languages;
 
-  public LanguageDetectionFactory(Settings settings, LanguagesReferential languages) {
+  public LanguageDetectionFactory(Settings settings, LanguagesRepository languages) {
     this.settings = settings;
     this.languages = languages;
   }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleInputFileCache.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleInputFileCache.java
index b932295dc40..17420fc2dc8 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleInputFileCache.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleInputFileCache.java
@@ -28,35 +28,35 @@ import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 public class ModuleInputFileCache extends DefaultFileSystem.Cache implements BatchComponent {
 
   private final String moduleKey;
-  private final InputPathCache projectCache;
+  private final InputPathCache inputPathCache;
 
   public ModuleInputFileCache(ProjectDefinition projectDef, InputPathCache projectCache) {
     this.moduleKey = projectDef.getKeyWithBranch();
-    this.projectCache = projectCache;
+    this.inputPathCache = projectCache;
   }
 
   @Override
   public Iterable<InputFile> inputFiles() {
-    return projectCache.filesByModule(moduleKey);
+    return inputPathCache.filesByModule(moduleKey);
   }
 
   @Override
   public InputFile inputFile(String relativePath) {
-    return projectCache.getFile(moduleKey, relativePath);
+    return inputPathCache.getFile(moduleKey, relativePath);
   }
 
   @Override
   public InputDir inputDir(String relativePath) {
-    return projectCache.getDir(moduleKey, relativePath);
+    return inputPathCache.getDir(moduleKey, relativePath);
   }
 
   @Override
   protected void doAdd(InputFile inputFile) {
-    projectCache.put(moduleKey, inputFile);
+    inputPathCache.put(moduleKey, inputFile);
   }
 
   @Override
   protected void doAdd(InputDir inputDir) {
-    projectCache.put(moduleKey, inputDir);
+    inputPathCache.put(moduleKey, inputDir);
   }
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/report/JSONReport.java b/sonar-batch/src/main/java/org/sonar/batch/scan/report/JSONReport.java
index d4fd9b69231..19523999ab0 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/report/JSONReport.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/report/JSONReport.java
@@ -30,7 +30,6 @@ import org.sonar.api.PropertyType;
 import org.sonar.api.batch.fs.FileSystem;
 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.DefaultInputDir;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.rule.ActiveRules;
@@ -43,9 +42,9 @@ import org.sonar.api.rule.RuleKey;
 import org.sonar.api.utils.SonarException;
 import org.sonar.api.utils.text.JsonWriter;
 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.BufferedWriter;
 import java.io.File;
@@ -167,27 +166,24 @@ public class JSONReport implements Reporter {
     json.name("components").beginArray();
     // Dump modules
     writeJsonModuleComponents(json, rootModule);
-    for (InputPath inputPath : fileCache.all()) {
-      if (inputPath instanceof InputFile) {
-        InputFile inputFile = (InputFile) inputPath;
-        String key = ((DefaultInputFile) inputFile).key();
-        json
-          .beginObject()
-          .prop("key", key)
-          .prop("path", inputFile.relativePath())
-          .prop("moduleKey", StringUtils.substringBeforeLast(key, ":"))
-          .prop("status", inputFile.status().name())
-          .endObject();
-      } else {
-        InputDir inputDir = (InputDir) inputPath;
-        String key = ((DefaultInputDir) inputDir).key();
-        json
-          .beginObject()
-          .prop("key", key)
-          .prop("path", inputDir.relativePath())
-          .prop("moduleKey", StringUtils.substringBeforeLast(key, ":"))
-          .endObject();
-      }
+    for (InputFile inputFile : fileCache.allFiles()) {
+      String key = ((DefaultInputFile) inputFile).key();
+      json
+        .beginObject()
+        .prop("key", key)
+        .prop("path", inputFile.relativePath())
+        .prop("moduleKey", StringUtils.substringBeforeLast(key, ":"))
+        .prop("status", inputFile.status().name())
+        .endObject();
+    }
+    for (InputDir inputDir : fileCache.allDirs()) {
+      String key = ((DefaultInputDir) inputDir).key();
+      json
+        .beginObject()
+        .prop("key", key)
+        .prop("path", inputDir.relativePath())
+        .prop("moduleKey", StringUtils.substringBeforeLast(key, ":"))
+        .endObject();
 
     }
     json.endArray();
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scm/ScmSensor.java b/sonar-batch/src/main/java/org/sonar/batch/scm/ScmSensor.java
index 2a33ed3b3fb..74fccaa446a 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scm/ScmSensor.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scm/ScmSensor.java
@@ -35,6 +35,8 @@ import org.sonar.api.measures.CoreMetrics;
 import org.sonar.api.utils.TimeProfiler;
 import org.sonar.batch.protocol.input.FileData;
 import org.sonar.batch.protocol.input.ProjectRepositories;
+import org.sonar.batch.scan.filesystem.InputFileMetadata;
+import org.sonar.batch.scan.filesystem.InputPathCache;
 
 import java.util.LinkedList;
 import java.util.List;
@@ -47,13 +49,15 @@ public final class ScmSensor implements Sensor {
   private final ScmConfiguration configuration;
   private final FileSystem fs;
   private final ProjectRepositories projectReferentials;
+  private final InputPathCache inputPathCache;
 
   public ScmSensor(ProjectDefinition projectDefinition, ScmConfiguration configuration,
-    ProjectRepositories projectReferentials, FileSystem fs) {
+    ProjectRepositories projectReferentials, FileSystem fs, InputPathCache inputPathCache) {
     this.projectDefinition = projectDefinition;
     this.configuration = configuration;
     this.projectReferentials = projectReferentials;
     this.fs = fs;
+    this.inputPathCache = inputPathCache;
   }
 
   @Override
@@ -104,7 +108,7 @@ public final class ScmSensor implements Sensor {
 
     if (f.status() == Status.SAME && fileData != null) {
       if (fileData.needBlame()) {
-        addIfNotEmpty(filesToBlame, f);
+        addIfNotEmpty(filesToBlame, (DefaultInputFile) f);
       } else {
         // Copy previous measures
         String scmAuthorsByLine = fileData.scmAuthorsByLine();
@@ -117,12 +121,13 @@ public final class ScmSensor implements Sensor {
         }
       }
     } else {
-      addIfNotEmpty(filesToBlame, f);
+      addIfNotEmpty(filesToBlame, (DefaultInputFile) f);
     }
   }
 
-  private void addIfNotEmpty(List<InputFile> filesToBlame, InputFile f) {
-    if (!((DefaultInputFile) f).isEmpty()) {
+  private void addIfNotEmpty(List<InputFile> filesToBlame, DefaultInputFile f) {
+    InputFileMetadata metadata = inputPathCache.getFileMetadata(f.moduleKey(), f.relativePath());
+    if (!metadata.isEmpty()) {
       filesToBlame.add(f);
     }
   }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/source/CodeColorizers.java b/sonar-batch/src/main/java/org/sonar/batch/source/CodeColorizers.java
index f0d4789f7bc..4b99191538a 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/source/CodeColorizers.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/source/CodeColorizers.java
@@ -37,6 +37,7 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.InputStreamReader;
 import java.io.Reader;
+import java.nio.charset.Charset;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -67,7 +68,7 @@ public class CodeColorizers implements BatchComponent {
   }
 
   @CheckForNull
-  public SyntaxHighlightingData toSyntaxHighlighting(File file, String encoding, String language) {
+  public SyntaxHighlightingData toSyntaxHighlighting(File file, Charset charset, String language) {
     CodeColorizerFormat format = byLang.get(language);
     List<Tokenizer> tokenizers;
     if (format == null) {
@@ -81,7 +82,7 @@ public class CodeColorizers implements BatchComponent {
     } else {
       tokenizers = format.getTokenizers();
     }
-    try (Reader reader = new BufferedReader(new InputStreamReader(new BOMInputStream(new FileInputStream(file)), encoding))) {
+    try (Reader reader = new BufferedReader(new InputStreamReader(new BOMInputStream(new FileInputStream(file)), charset))) {
       return new HighlightingRenderer().render(reader, tokenizers);
     } catch (Exception e) {
       throw new IllegalStateException("Unable to read source file for colorization", e);
diff --git a/sonar-batch/src/main/java/org/sonar/batch/source/LinesSensor.java b/sonar-batch/src/main/java/org/sonar/batch/source/LinesSensor.java
index 4829066972a..b2f159d0997 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/source/LinesSensor.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/source/LinesSensor.java
@@ -29,14 +29,16 @@ import org.sonar.api.batch.sensor.SensorContext;
 import org.sonar.api.batch.sensor.SensorDescriptor;
 import org.sonar.api.batch.sensor.measure.internal.DefaultMeasure;
 import org.sonar.api.measures.CoreMetrics;
+import org.sonar.batch.scan.filesystem.InputFileMetadata;
+import org.sonar.batch.scan.filesystem.InputPathCache;
 
 @Phase(name = Phase.Name.PRE)
 public final class LinesSensor implements Sensor {
 
-  private final FileSystem fs;
+  private final InputPathCache inputPathCache;
 
-  public LinesSensor(FileSystem fs) {
-    this.fs = fs;
+  public LinesSensor(InputPathCache inputPathCache) {
+    this.inputPathCache = inputPathCache;
   }
 
   @Override
@@ -46,6 +48,7 @@ public final class LinesSensor implements Sensor {
 
   @Override
   public void execute(final SensorContext context) {
+    FileSystem fs = context.fileSystem();
     for (InputFile f : fs.inputFiles(fs.predicates().hasType(Type.MAIN))) {
       ((DefaultMeasure<Integer>) context.<Integer>newMeasure()
         .onFile(f)
@@ -55,10 +58,11 @@ public final class LinesSensor implements Sensor {
         .save();
       if (f.language() == null) {
         // As an approximation for files with no language plugin we consider every non blank line as ncloc
+        InputFileMetadata metadata = inputPathCache.getFileMetadata(((DefaultInputFile) f).moduleKey(), f.relativePath());
         ((DefaultMeasure<Integer>) context.<Integer>newMeasure()
           .onFile(f)
           .forMetric(CoreMetrics.NCLOC)
-          .withValue(((DefaultInputFile) f).nonBlankLines()))
+          .withValue(metadata.nonBlankLines()))
           .save();
       }
     }
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]"