Refactor resources API

30 files changed, 316 insertions, 701 deletions

diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/ProjectConfiguratorTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/ProjectConfiguratorTest.java
deleted file mode 100644
index 95b1673bf82..00000000000
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/ProjectConfiguratorTest.java
+++ /dev/null
@@ -1,85 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2016 SonarSource SA
- * mailto:contact AT sonarsource DOT com
- *
- * This program 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.
- *
- * This program 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.scanner;
-
-import java.text.SimpleDateFormat;
-import java.util.TimeZone;
-import org.junit.Before;
-import org.junit.Test;
-import org.sonar.api.CoreProperties;
-import org.sonar.api.config.Settings;
-import org.sonar.api.config.MapSettings;
-import org.sonar.api.resources.Project;
-import org.sonar.api.utils.System2;
-
-import static org.assertj.core.api.Assertions.assertThat;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
-
-public class ProjectConfiguratorTest {
-
-  System2 system2;
-
-  @Before
-  public void setUp() {
-    system2 = mock(System2.class);
-  }
-
-  @Test
-  public void analysis_is_today_by_default() {
-    Long now = System.currentTimeMillis();
-    when(system2.now()).thenReturn(now);
-
-    Project project = new Project("key");
-    new ProjectConfigurator(new MapSettings(), system2).configure(project);
-    assertThat(now - project.getAnalysisDate().getTime()).isLessThan(1000);
-  }
-
-  @Test
-  public void analysis_date_could_be_explicitly_set() {
-    Settings settings = new MapSettings();
-    settings.setProperty(CoreProperties.PROJECT_DATE_PROPERTY, "2005-01-30");
-    Project project = new Project("key");
-    new ProjectConfigurator(settings, system2).configure(project);
-
-    assertThat(new SimpleDateFormat("ddMMyyyy").format(project.getAnalysisDate())).isEqualTo("30012005");
-  }
-
-  @Test
-  public void analysis_timestamp_could_be_explicitly_set() {
-    Settings settings = new MapSettings();
-    settings.setProperty(CoreProperties.PROJECT_DATE_PROPERTY, "2005-01-30T08:45:10+0000");
-    Project project = new Project("key");
-    new ProjectConfigurator(settings, system2).configure(project);
-
-    SimpleDateFormat dateFormat = new SimpleDateFormat("ddMMyyyy-mmss");
-    dateFormat.setTimeZone(TimeZone.getTimeZone("GMT"));
-    assertThat(dateFormat.format(project.getAnalysisDate())).isEqualTo("30012005-4510");
-  }
-
-  @Test(expected = RuntimeException.class)
-  public void fail_if_analyis_date_is_not_valid() {
-    Settings configuration = new MapSettings();
-    configuration.setProperty(CoreProperties.PROJECT_DATE_PROPERTY, "2005/30/01");
-    Project project = new Project("key");
-    new ProjectConfigurator(configuration, system2).configure(project);
-  }
-
-}
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/bootstrap/ScannerExtensionDictionnaryTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/bootstrap/ScannerExtensionDictionnaryTest.java
index 28b9321deaa..ff5e3fc0c3e 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/bootstrap/ScannerExtensionDictionnaryTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/bootstrap/ScannerExtensionDictionnaryTest.java
@@ -34,6 +34,7 @@ import org.sonar.api.batch.Phase;
 import org.sonar.api.batch.PostJob;
 import org.sonar.api.batch.Sensor;
 import org.sonar.api.batch.SensorContext;
+import org.sonar.api.batch.fs.internal.DefaultInputModule;
 import org.sonar.api.batch.postjob.PostJobContext;
 import org.sonar.api.resources.Project;
 import org.sonar.core.platform.ComponentContainer;
@@ -54,7 +55,8 @@ public class ScannerExtensionDictionnaryTest {
     for (Object extension : extensions) {
       iocContainer.addSingleton(extension);
     }
-    return new ScannerExtensionDictionnary(iocContainer, mock(DefaultSensorContext.class), mock(SensorOptimizer.class), mock(PostJobContext.class),
+    return new ScannerExtensionDictionnary(iocContainer, mock(DefaultSensorContext.class), mock(SensorOptimizer.class),
+      mock(PostJobContext.class),
       mock(PostJobOptimizer.class));
   }
 
@@ -102,7 +104,8 @@ public class ScannerExtensionDictionnaryTest {
     ComponentContainer child = parent.createChild();
     child.addSingleton(c);
 
-    ScannerExtensionDictionnary dictionnary = new ScannerExtensionDictionnary(child, mock(DefaultSensorContext.class), mock(SensorOptimizer.class), mock(PostJobContext.class),
+    ScannerExtensionDictionnary dictionnary = new ScannerExtensionDictionnary(child, mock(DefaultSensorContext.class),
+      mock(SensorOptimizer.class), mock(PostJobContext.class),
       mock(PostJobOptimizer.class));
     assertThat(dictionnary.select(Sensor.class, null, true, null)).containsOnly(a, b, c);
   }
@@ -235,7 +238,7 @@ public class ScannerExtensionDictionnaryTest {
     BatchExtension ko = new CheckProjectKO();
 
     ScannerExtensionDictionnary selector = newSelector(ok, ko);
-    List<BatchExtension> extensions = Lists.newArrayList(selector.select(BatchExtension.class, new Project("key"), true, null));
+    List<BatchExtension> extensions = Lists.newArrayList(selector.select(BatchExtension.class, new DefaultInputModule("foo"), true, null));
 
     assertThat(extensions).hasSize(1);
     assertThat(extensions.get(0)).isInstanceOf(CheckProjectOK.class);
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/cpd/CpdExecutorTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/cpd/CpdExecutorTest.java
index 15545a45716..33a74f0662e 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/cpd/CpdExecutorTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/cpd/CpdExecutorTest.java
@@ -31,11 +31,11 @@ import org.junit.Test;
 import org.junit.rules.ExpectedException;
 import org.junit.rules.TemporaryFolder;
 import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.DefaultInputModule;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.api.config.MapSettings;
 import org.sonar.api.config.Settings;
-import org.sonar.api.resources.Project;
 import org.sonar.api.utils.log.LogTester;
 import org.sonar.api.utils.log.LoggerLevel;
 import org.sonar.core.util.CloseableIterator;
@@ -44,13 +44,12 @@ import org.sonar.duplications.block.ByteArray;
 import org.sonar.duplications.index.CloneGroup;
 import org.sonar.duplications.index.ClonePart;
 import org.sonar.scanner.cpd.index.SonarCpdBlockIndex;
-import org.sonar.scanner.index.BatchComponent;
-import org.sonar.scanner.index.BatchComponentCache;
 import org.sonar.scanner.protocol.output.ScannerReport.Duplicate;
 import org.sonar.scanner.protocol.output.ScannerReport.Duplication;
 import org.sonar.scanner.protocol.output.ScannerReportReader;
 import org.sonar.scanner.protocol.output.ScannerReportWriter;
 import org.sonar.scanner.report.ReportPublisher;
+import org.sonar.scanner.scan.filesystem.InputComponentStore;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.mock;
@@ -61,7 +60,6 @@ public class CpdExecutorTest {
   private Settings settings;
   private SonarCpdBlockIndex index;
   private ReportPublisher publisher;
-  private BatchComponentCache componentCache;
 
   @Rule
   public LogTester logTester = new LogTester();
@@ -73,10 +71,11 @@ public class CpdExecutorTest {
   public ExpectedException thrown = ExpectedException.none();
 
   private ScannerReportReader reader;
-  private BatchComponent batchComponent1;
-  private BatchComponent batchComponent2;
-  private BatchComponent batchComponent3;
+  private DefaultInputFile batchComponent1;
+  private DefaultInputFile batchComponent2;
+  private DefaultInputFile batchComponent3;
   private File baseDir;
+  private InputComponentStore componentStore;
 
   @Before
   public void setUp() throws IOException {
@@ -86,26 +85,25 @@ public class CpdExecutorTest {
     settings = new MapSettings();
     publisher = mock(ReportPublisher.class);
     when(publisher.getWriter()).thenReturn(new ScannerReportWriter(outputDir));
-    componentCache = new BatchComponentCache();
-    index = new SonarCpdBlockIndex(publisher, componentCache, settings);
-    executor = new CpdExecutor(settings, index, publisher, componentCache);
+    index = new SonarCpdBlockIndex(publisher, settings);
+    componentStore = new InputComponentStore();
+    executor = new CpdExecutor(settings, index, publisher, componentStore);
     reader = new ScannerReportReader(outputDir);
 
-    Project p = new Project("foo");
-    componentCache.add(p, null).setInputComponent(new DefaultInputModule("foo"));
+    componentStore.put(new DefaultInputModule("foo"));
 
     batchComponent1 = createComponent("src/Foo.php", 5);
     batchComponent2 = createComponent("src/Foo2.php", 5);
     batchComponent3 = createComponent("src/Foo3.php", 5);
   }
 
-  private BatchComponent createComponent(String relativePath, int lines) {
-    org.sonar.api.resources.Resource sampleFile = org.sonar.api.resources.File.create("relativePath").setEffectiveKey("foo:" + relativePath);
-    return componentCache.add(sampleFile, null)
-      .setInputComponent(new TestInputFileBuilder("foo", relativePath)
-        .setModuleBaseDir(baseDir.toPath())
-        .setLines(lines)
-        .build());
+  private DefaultInputFile createComponent(String relativePath, int lines) {
+    DefaultInputFile file = new TestInputFileBuilder("foo", relativePath)
+      .setModuleBaseDir(baseDir.toPath())
+      .setLines(lines)
+      .build();
+    componentStore.put(file);
+    return file;
   }
 
   @Test
@@ -163,7 +161,7 @@ public class CpdExecutorTest {
     assertThat(dups[0].getDuplicateList()).hasSize(CpdExecutor.MAX_CLONE_PART_PER_GROUP);
 
     assertThat(logTester.logs(LoggerLevel.WARN))
-      .contains("Too many duplication references on file " + batchComponent1.inputComponent() + " for block at line 0. Keep only the first "
+      .contains("Too many duplication references on file " + batchComponent1 + " for block at line 0. Keep only the first "
         + CpdExecutor.MAX_CLONE_PART_PER_GROUP + " references.");
   }
 
@@ -181,7 +179,7 @@ public class CpdExecutorTest {
     assertThat(reader.readComponentDuplications(batchComponent1.batchId())).hasSize(CpdExecutor.MAX_CLONE_GROUP_PER_FILE);
 
     assertThat(logTester.logs(LoggerLevel.WARN))
-      .contains("Too many duplication groups on file " + batchComponent1.inputComponent() + ". Keep only the first " + CpdExecutor.MAX_CLONE_GROUP_PER_FILE + " groups.");
+      .contains("Too many duplication groups on file " + batchComponent1 + ". Keep only the first " + CpdExecutor.MAX_CLONE_GROUP_PER_FILE + " groups.");
   }
 
   @Test
@@ -218,7 +216,7 @@ public class CpdExecutorTest {
   @Test
   public void timeout() {
     for (int i = 1; i <= 2; i++) {
-      BatchComponent component = createComponent("src/Foo" + i + ".php", 100);
+      DefaultInputFile component = createComponent("src/Foo" + i + ".php", 100);
       List<Block> blocks = new ArrayList<>();
       for (int j = 1; j <= 10000; j++) {
         blocks.add(Block.builder()
@@ -229,7 +227,7 @@ public class CpdExecutorTest {
           .setBlockHash(new ByteArray("abcd1234".getBytes()))
           .build());
       }
-      index.insert((InputFile) component.inputComponent(), blocks);
+      index.insert((InputFile) component, blocks);
     }
     executor.execute(1);
 
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/cpd/deprecated/JavaCpdBlockIndexerTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/cpd/deprecated/JavaCpdBlockIndexerTest.java
index 77908318914..a40589be0f7 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/cpd/deprecated/JavaCpdBlockIndexerTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/cpd/deprecated/JavaCpdBlockIndexerTest.java
@@ -40,7 +40,6 @@ import org.sonar.api.config.Settings;
 import org.sonar.api.config.MapSettings;
 import org.sonar.duplications.block.Block;
 import org.sonar.scanner.cpd.index.SonarCpdBlockIndex;
-import org.sonar.scanner.index.BatchComponentCache;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Matchers.eq;
@@ -72,8 +71,6 @@ public class JavaCpdBlockIndexerTest {
     DefaultFileSystem fs = new DefaultFileSystem(baseDir);
     file = new TestInputFileBuilder("foo", "src/ManyStatements.java").setLanguage(JAVA).build();
     fs.add(file);
-    BatchComponentCache batchComponentCache = new BatchComponentCache();
-    batchComponentCache.add(org.sonar.api.resources.File.create("src/Foo.java").setEffectiveKey("foo:src/ManyStatements.java"), null).setInputComponent(file);
     File ioFile = file.file();
     FileUtils.copyURLToFile(this.getClass().getResource("ManyStatements.java"), ioFile);
 
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/index/BatchComponentCacheTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/index/BatchComponentCacheTest.java
deleted file mode 100644
index b7c5a956593..00000000000
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/index/BatchComponentCacheTest.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2016 SonarSource SA
- * mailto:contact AT sonarsource DOT com
- *
- * This program 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.
- *
- * This program 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.scanner.index;
-
-import org.junit.Test;
-import org.sonar.api.resources.File;
-import org.sonar.api.resources.Resource;
-import org.sonar.scanner.index.BatchComponentCache;
-
-import static org.assertj.core.api.Assertions.assertThat;
-import static org.junit.Assert.fail;
-
-public class BatchComponentCacheTest {
-  @Test
-  public void should_cache_resource() {
-    BatchComponentCache cache = new BatchComponentCache();
-    String componentKey = "struts:src/org/struts/Action.java";
-    Resource resource = File.create("org/struts/Action.java").setEffectiveKey(componentKey);
-    cache.add(resource, null);
-
-    assertThat(cache.get(componentKey).resource()).isSameAs(resource);
-    assertThat(cache.get("other")).isNull();
-  }
-
-  @Test
-  public void should_fail_if_missing_component_key() {
-    BatchComponentCache cache = new BatchComponentCache();
-    Resource resource = File.create("org/struts/Action.java").setEffectiveKey(null);
-    try {
-      cache.add(resource, null);
-      fail();
-    } catch (IllegalStateException e) {
-      // success
-      assertThat(e).hasMessage("Missing resource effective key");
-    }
-  }
-}
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/index/BucketTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/index/BucketTest.java
deleted file mode 100644
index 9c5a0fc0359..00000000000
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/index/BucketTest.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2016 SonarSource SA
- * mailto:contact AT sonarsource DOT com
- *
- * This program 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.
- *
- * This program 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.scanner.index;
-
-import org.junit.Test;
-import org.sonar.api.measures.Metric;
-import org.sonar.api.resources.Directory;
-import org.sonar.api.resources.File;
-import org.sonar.scanner.index.Bucket;
-
-import static org.assertj.core.api.Assertions.assertThat;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-
-public class BucketTest {
-
-  Directory directory = Directory.create("org/foo");
-  File javaFile = File.create("org/foo/Bar.java");
-  Metric ncloc = new Metric("ncloc");
-
-  @Test
-  public void shouldManageRelationships() {
-    Bucket packageBucket = new Bucket(directory);
-    Bucket fileBucket = new Bucket(javaFile);
-    fileBucket.setParent(packageBucket);
-
-    assertThat(fileBucket.getParent()).isEqualTo(packageBucket);
-    assertThat(packageBucket.getChildren()).containsExactly(fileBucket);
-  }
-
-  @Test
-  public void shouldBeEquals() {
-    assertEquals(new Bucket(directory), new Bucket(directory));
-    assertEquals(new Bucket(directory).hashCode(), new Bucket(directory).hashCode());
-  }
-
-  @Test
-  public void shouldNotBeEquals() {
-    assertFalse(new Bucket(directory).equals(new Bucket(javaFile)));
-    assertThat(new Bucket(directory).hashCode()).isNotEqualTo(new Bucket(javaFile).hashCode());
-  }
-}
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/index/DefaultIndexTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/index/DefaultIndexTest.java
index 4c0565b2e09..d8cc87b574a 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/index/DefaultIndexTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/index/DefaultIndexTest.java
@@ -35,7 +35,6 @@ import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.rules.Rule;
 import org.sonar.api.rules.RuleFinder;
-import org.sonar.scanner.DefaultProjectTree;
 import org.sonar.scanner.FakeJava;
 import org.sonar.scanner.scan.measure.MeasureCache;
 import org.sonar.scanner.sensor.DefaultSensorStorage;
@@ -58,6 +57,9 @@ public class DefaultIndexTest {
   Project moduleB1;
 
   private java.io.File baseDir;
+  // TODO
+/*
+ * 
 
   @Before
   public void createIndex() throws IOException {
@@ -112,19 +114,6 @@ public class DefaultIndexTest {
   }
 
   @Test
-  public void shouldGetSource() throws Exception {
-    Directory directory = Directory.create("src/org/foo");
-    File file = File.create("src/org/foo/Bar.java", FakeJava.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", null, false);
-    assertThat(index.getSource(fileRef)).isEqualTo("Foo bar");
-  }
-
-  @Test
   public void shouldNotIndexResourceIfParentNotIndexed() {
     Directory directory = Directory.create("src/org/other");
     File file = File.create("src/org/foo/Bar.java", null, false);
@@ -151,5 +140,5 @@ public class DefaultIndexTest {
     assertThat(index.getResource(moduleB).getPath()).isEqualTo("moduleB");
     assertThat(index.getResource(moduleB1).getPath()).isEqualTo("moduleB1");
   }
-
+ */
 }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/DefaultFilterableIssueTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/DefaultFilterableIssueTest.java
index 98f90f14b6c..37728872293 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/DefaultFilterableIssueTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/DefaultFilterableIssueTest.java
@@ -22,7 +22,8 @@ package org.sonar.scanner.issue;
 import java.util.Date;
 import org.junit.Before;
 import org.junit.Test;
-import org.sonar.api.resources.Project;
+import org.sonar.api.batch.fs.internal.DefaultInputModule;
+import org.sonar.scanner.ProjectAnalysisInfo;
 import org.sonar.scanner.issue.DefaultFilterableIssue;
 import org.sonar.scanner.protocol.Constants.Severity;
 import org.sonar.scanner.protocol.output.ScannerReport.Issue;
@@ -34,13 +35,15 @@ import static org.mockito.Mockito.when;
 
 public class DefaultFilterableIssueTest {
   private DefaultFilterableIssue issue;
-  private Project mockedProject;
+  private DefaultInputModule mockedProject;
+  private ProjectAnalysisInfo projectAnalysisInfo;
   private String componentKey;
   private Issue rawIssue;
 
   @Before
   public void setUp() {
-    mockedProject = mock(Project.class);
+    mockedProject = mock(DefaultInputModule.class);
+    projectAnalysisInfo = mock(ProjectAnalysisInfo.class);
     componentKey = "component";
   }
 
@@ -62,10 +65,10 @@ public class DefaultFilterableIssueTest {
   @Test
   public void testRoundTrip() {
     rawIssue = createIssue();
-    issue = new DefaultFilterableIssue(mockedProject, rawIssue, componentKey);
+    issue = new DefaultFilterableIssue(mockedProject, projectAnalysisInfo, rawIssue, componentKey);
 
-    when(mockedProject.getAnalysisDate()).thenReturn(new Date(10_000));
-    when(mockedProject.getEffectiveKey()).thenReturn("projectKey");
+    when(projectAnalysisInfo.analysisDate()).thenReturn(new Date(10_000));
+    when(mockedProject.key()).thenReturn("projectKey");
 
     assertThat(issue.componentKey()).isEqualTo(componentKey);
     assertThat(issue.creationDate()).isEqualTo(new Date(10_000));
@@ -78,7 +81,7 @@ public class DefaultFilterableIssueTest {
   @Test
   public void nullValues() {
     rawIssue = createIssueWithoutFields();
-    issue = new DefaultFilterableIssue(mockedProject, rawIssue, componentKey);
+    issue = new DefaultFilterableIssue(mockedProject, projectAnalysisInfo, rawIssue, componentKey);
 
     assertThat(issue.line()).isNull();
     assertThat(issue.effortToFix()).isNull();
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/DeprecatedIssueAdapterForFilterTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/DeprecatedIssueAdapterForFilterTest.java
index c3cc585c04a..af726074d4c 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/DeprecatedIssueAdapterForFilterTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/DeprecatedIssueAdapterForFilterTest.java
@@ -21,15 +21,18 @@ package org.sonar.scanner.issue;
 
 import java.util.Date;
 import org.junit.Test;
+import org.sonar.api.batch.fs.internal.DefaultInputModule;
 import org.sonar.api.issue.Issue;
-import org.sonar.api.resources.Project;
 import org.sonar.api.rule.RuleKey;
+import org.sonar.scanner.ProjectAnalysisInfo;
 import org.sonar.scanner.issue.DeprecatedIssueAdapterForFilter;
 import org.sonar.scanner.protocol.Constants.Severity;
 import org.sonar.scanner.protocol.output.ScannerReport.TextRange;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.assertj.core.api.Assertions.fail;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 public class DeprecatedIssueAdapterForFilterTest {
 
@@ -39,7 +42,11 @@ public class DeprecatedIssueAdapterForFilterTest {
 
   @Test
   public void improve_coverage() {
-    DeprecatedIssueAdapterForFilter issue = new DeprecatedIssueAdapterForFilter(new Project(PROJECT_KEY).setAnalysisDate(ANALYSIS_DATE),
+    DefaultInputModule module = new DefaultInputModule(PROJECT_KEY);
+    ProjectAnalysisInfo projectAnalysisInfo = mock(ProjectAnalysisInfo.class);
+    when(projectAnalysisInfo.analysisDate()).thenReturn(ANALYSIS_DATE);
+
+    DeprecatedIssueAdapterForFilter issue = new DeprecatedIssueAdapterForFilter(module, projectAnalysisInfo,
       org.sonar.scanner.protocol.output.ScannerReport.Issue.newBuilder()
         .setRuleRepository("repo")
         .setRuleKey("key")
@@ -47,7 +54,8 @@ public class DeprecatedIssueAdapterForFilterTest {
         .setMsg("msg")
         .build(),
       COMPONENT_KEY);
-    DeprecatedIssueAdapterForFilter issue2 = new DeprecatedIssueAdapterForFilter(new Project(PROJECT_KEY).setAnalysisDate(ANALYSIS_DATE),
+
+    DeprecatedIssueAdapterForFilter issue2 = new DeprecatedIssueAdapterForFilter(module, projectAnalysisInfo,
       org.sonar.scanner.protocol.output.ScannerReport.Issue.newBuilder()
         .setRuleRepository("repo")
         .setRuleKey("key")
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/IssuableFactoryTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/IssuableFactoryTest.java
index 1cbed75f3e5..5b734b00f73 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/IssuableFactoryTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/IssuableFactoryTest.java
@@ -23,7 +23,6 @@ import org.junit.Test;
 import org.sonar.api.batch.fs.internal.DefaultInputModule;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.api.issue.Issuable;
-import org.sonar.scanner.DefaultProjectTree;
 import org.sonar.scanner.sensor.DefaultSensorContext;
 
 import static org.assertj.core.api.Assertions.assertThat;
@@ -32,7 +31,6 @@ import static org.mockito.Mockito.mock;
 public class IssuableFactoryTest {
 
   ModuleIssues moduleIssues = mock(ModuleIssues.class);
-  DefaultProjectTree projectTree = mock(DefaultProjectTree.class);
 
   @Test
   public void file_should_be_issuable() {
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/ModuleIssuesTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/ModuleIssuesTest.java
index d2f75e47d62..ba62f2d1fe1 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/ModuleIssuesTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/ModuleIssuesTest.java
@@ -19,23 +19,20 @@
  */
 package org.sonar.scanner.issue;
 
-import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.mockito.ArgumentCaptor;
 import org.mockito.Mock;
 import org.mockito.runners.MockitoJUnitRunner;
-import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.api.batch.rule.internal.ActiveRulesBuilder;
 import org.sonar.api.batch.rule.internal.RulesBuilder;
 import org.sonar.api.batch.sensor.issue.internal.DefaultIssue;
 import org.sonar.api.batch.sensor.issue.internal.DefaultIssueLocation;
-import org.sonar.api.resources.File;
 import org.sonar.api.rule.RuleKey;
 import org.sonar.api.rule.Severity;
 import org.sonar.api.utils.MessageException;
-import org.sonar.scanner.index.BatchComponentCache;
 import org.sonar.scanner.issue.IssueFilters;
 import org.sonar.scanner.issue.ModuleIssues;
 import org.sonar.scanner.protocol.output.ScannerReport;
@@ -66,15 +63,9 @@ public class ModuleIssuesTest {
 
   ModuleIssues moduleIssues;
 
-  BatchComponentCache componentCache = new BatchComponentCache();
-  InputFile file = new TestInputFileBuilder("foo", "src/Foo.php").initMetadata("Foo\nBar\nBiz\n").build();
+  DefaultInputFile file = new TestInputFileBuilder("foo", "src/Foo.php").initMetadata("Foo\nBar\nBiz\n").build();
   ReportPublisher reportPublisher = mock(ReportPublisher.class, RETURNS_DEEP_STUBS);
 
-  @Before
-  public void prepare() {
-    componentCache.add(File.create("src/Foo.php").setEffectiveKey("foo:src/Foo.php"), null).setInputComponent(file);
-  }
-
   @Test
   public void fail_on_unknown_rule() {
     initModuleIssues();
@@ -153,7 +144,7 @@ public class ModuleIssuesTest {
 
     assertThat(added).isTrue();
     ArgumentCaptor<ScannerReport.Issue> argument = ArgumentCaptor.forClass(ScannerReport.Issue.class);
-    verify(reportPublisher.getWriter()).appendComponentIssue(eq(1), argument.capture());
+    verify(reportPublisher.getWriter()).appendComponentIssue(eq(file.batchId()), argument.capture());
     assertThat(argument.getValue().getSeverity()).isEqualTo(org.sonar.scanner.protocol.Constants.Severity.CRITICAL);
   }
 
@@ -170,7 +161,7 @@ public class ModuleIssuesTest {
     moduleIssues.initAndAddIssue(issue);
 
     ArgumentCaptor<ScannerReport.Issue> argument = ArgumentCaptor.forClass(ScannerReport.Issue.class);
-    verify(reportPublisher.getWriter()).appendComponentIssue(eq(1), argument.capture());
+    verify(reportPublisher.getWriter()).appendComponentIssue(eq(file.batchId()), argument.capture());
     assertThat(argument.getValue().getSeverity()).isEqualTo(org.sonar.scanner.protocol.Constants.Severity.INFO);
   }
 
@@ -189,7 +180,7 @@ public class ModuleIssuesTest {
 
     assertThat(added).isTrue();
     ArgumentCaptor<ScannerReport.Issue> argument = ArgumentCaptor.forClass(ScannerReport.Issue.class);
-    verify(reportPublisher.getWriter()).appendComponentIssue(eq(1), argument.capture());
+    verify(reportPublisher.getWriter()).appendComponentIssue(eq(file.batchId()), argument.capture());
     assertThat(argument.getValue().getMsg()).isEqualTo("Avoid Cycle");
   }
 
@@ -215,7 +206,7 @@ public class ModuleIssuesTest {
    * Every rules and active rules has to be added in builders before creating ModuleIssues
    */
   private void initModuleIssues() {
-    moduleIssues = new ModuleIssues(activeRulesBuilder.build(), ruleBuilder.build(), filters, reportPublisher, componentCache);
+    moduleIssues = new ModuleIssues(activeRulesBuilder.build(), ruleBuilder.build(), filters, reportPublisher);
   }
 
 }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/branch/BranchMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/branch/BranchMediumTest.java
index ba3e5e03284..d579e26a77e 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/branch/BranchMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/branch/BranchMediumTest.java
@@ -32,6 +32,7 @@ import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
 import org.junit.rules.TemporaryFolder;
+import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.scanner.mediumtest.ScannerMediumTester;
 import org.sonar.scanner.mediumtest.TaskResult;
 import org.sonar.xoo.XooPlugin;
@@ -93,7 +94,12 @@ public class BranchMediumTest {
       .start();
 
     assertThat(result.inputFiles()).hasSize(1);
-    assertThat(result.inputFile("src/sample.xoo").key()).isEqualTo("com.foo.project:branch:src/sample.xoo");
+    assertThat(result.inputFile("src/sample.xoo").key()).isEqualTo("com.foo.project:src/sample.xoo");
+
+    DefaultInputFile inputfile = (DefaultInputFile) result.inputFile("src/sample.xoo");
+    assertThat(result.getReportReader().readComponent(inputfile.batchId()).getPath()).isEqualTo("src/sample.xoo");
+
+    assertThat(result.getReportReader().readMetadata().getBranch()).isEqualTo("branch");
 
     result = tester.newTask()
       .properties(ImmutableMap.<String, String>builder()
@@ -123,7 +129,16 @@ public class BranchMediumTest {
       .start();
 
     assertThat(result.inputFiles()).hasSize(1);
-    assertThat(result.inputFile("src/sample.xoo").key()).isEqualTo("com.foo.project:moduleA:branch:src/sample.xoo");
+    assertThat(result.inputFile("src/sample.xoo").key()).isEqualTo("com.foo.project:moduleA:src/sample.xoo");
+
+    // no branch in the report
+    DefaultInputFile inputfile = (DefaultInputFile) result.inputFile("src/sample.xoo");
+    assertThat(result.getReportReader().readComponent(inputfile.batchId()).getPath()).isEqualTo("src/sample.xoo");
+
+    // no branch in InputModule's key or in report
+    assertThat(result.getReportComponent("com.foo.project:moduleA").getKey()).isEqualTo("com.foo.project:moduleA");
+
+    assertThat(result.getReportReader().readMetadata().getBranch()).isEqualTo("branch");
 
     result = tester.newTask()
       .properties(ImmutableMap.<String, String>builder()
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java
index a47c22d7456..6c83a42f045 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java
@@ -81,6 +81,7 @@ public class FileSystemMediumTest {
   public void scanProjectWithoutProjectName() throws IOException {
     builder = ImmutableMap.<String, String>builder()
       .put("sonar.task", "scan")
+      .put("sonar.verbose", "true")
       .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
       .put("sonar.projectKey", "com.foo.project")
       .put("sonar.projectVersion", "1.0-SNAPSHOT")
@@ -200,6 +201,7 @@ public class FileSystemMediumTest {
       .start();
 
     assertThat(result.inputFiles()).hasSize(4);
+    assertThat(result.inputDirs()).hasSize(3);
   }
 
   @Test
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/ProjectBuilderMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/ProjectBuilderMediumTest.java
index cb8bdc8a2bb..5a5a8a5feea 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/ProjectBuilderMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/ProjectBuilderMediumTest.java
@@ -142,6 +142,7 @@ public class ProjectBuilderMediumTest {
         .put("sonar.projectVersion", "1.0-SNAPSHOT")
         .put("sonar.projectDescription", "Description of Foo Project")
         .put("sonar.sources", ".")
+        .put("sonar.verbose", "true")
         .put("sonar.xoo.enableProjectBuilder", "true")
         .build())
       .start();
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issuesmode/IssueModeAndReportsMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issuesmode/IssueModeAndReportsMediumTest.java
index be6739793c6..31617bb1703 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issuesmode/IssueModeAndReportsMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issuesmode/IssueModeAndReportsMediumTest.java
@@ -253,6 +253,7 @@ public class IssueModeAndReportsMediumTest {
     TaskResult result = tester
       .newScanTask(new File(projectDir, "sonar-project.properties"))
       .setIssueListener(issueListener)
+      .property("sonar.verbose", "true")
       .start();
 
     assertThat(result.trackedIssues()).hasSize(19);
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/phases/PostJobsExecutorTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/phases/PostJobsExecutorTest.java
index 4c5f4210d54..c312468e47c 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/phases/PostJobsExecutorTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/phases/PostJobsExecutorTest.java
@@ -23,6 +23,7 @@ import org.junit.Before;
 import org.junit.Test;
 import org.sonar.api.batch.PostJob;
 import org.sonar.api.batch.SensorContext;
+import org.sonar.api.batch.fs.internal.DefaultInputModule;
 import org.sonar.api.resources.Project;
 import org.sonar.scanner.bootstrap.ScannerExtensionDictionnary;
 import org.sonar.scanner.events.EventBus;
@@ -32,11 +33,13 @@ import java.util.Arrays;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
+import static org.mockito.Mockito.eq;
+import static org.mockito.Mockito.any;
 
 public class PostJobsExecutorTest {
   PostJobsExecutor executor;
 
-  Project project = new Project("project");
+  DefaultInputModule module = new DefaultInputModule("project");
   ScannerExtensionDictionnary selector = mock(ScannerExtensionDictionnary.class);
   PostJob job1 = mock(PostJob.class);
   PostJob job2 = mock(PostJob.class);
@@ -44,17 +47,16 @@ public class PostJobsExecutorTest {
 
   @Before
   public void setUp() {
-    executor = new PostJobsExecutor(selector, project, mock(EventBus.class));
+    executor = new PostJobsExecutor(selector, module, mock(EventBus.class));
   }
 
   @Test
   public void should_execute_post_jobs() {
-    when(selector.select(PostJob.class, project, true, null)).thenReturn(Arrays.asList(job1, job2));
+    when(selector.select(PostJob.class, module, true, null)).thenReturn(Arrays.asList(job1, job2));
 
     executor.execute(context);
 
-    verify(job1).executeOn(project, context);
-    verify(job2).executeOn(project, context);
-
+    verify(job1).executeOn(any(Project.class), eq(context));
+    verify(job2).executeOn(any(Project.class), eq(context));
   }
 }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/postjob/DefaultPostJobContextTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/postjob/DefaultPostJobContextTest.java
index 8a977c8644f..89c9ec0d33e 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/postjob/DefaultPostJobContextTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/postjob/DefaultPostJobContextTest.java
@@ -23,15 +23,14 @@ import java.util.Arrays;
 import org.junit.Before;
 import org.junit.Test;
 import org.sonar.api.batch.AnalysisMode;
-import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.api.batch.postjob.issue.PostJobIssue;
 import org.sonar.api.batch.rule.Severity;
 import org.sonar.api.config.Settings;
 import org.sonar.api.config.MapSettings;
-import org.sonar.api.resources.File;
-import org.sonar.scanner.index.BatchComponentCache;
 import org.sonar.scanner.issue.IssueCache;
 import org.sonar.scanner.issue.tracking.TrackedIssue;
+import org.sonar.scanner.scan.filesystem.InputComponentStore;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.mock;
@@ -40,7 +39,7 @@ import static org.mockito.Mockito.when;
 public class DefaultPostJobContextTest {
 
   private IssueCache issueCache;
-  private BatchComponentCache resourceCache;
+  private InputComponentStore componentStore;
   private DefaultPostJobContext context;
   private Settings settings;
   private AnalysisMode analysisMode;
@@ -48,10 +47,10 @@ public class DefaultPostJobContextTest {
   @Before
   public void prepare() {
     issueCache = mock(IssueCache.class);
-    resourceCache = new BatchComponentCache();
+    componentStore = new InputComponentStore();
     settings = new MapSettings();
     analysisMode = mock(AnalysisMode.class);
-    context = new DefaultPostJobContext(settings, issueCache, resourceCache, analysisMode);
+    context = new DefaultPostJobContext(settings, issueCache, componentStore, analysisMode);
   }
 
   @Test
@@ -79,9 +78,8 @@ public class DefaultPostJobContextTest {
     assertThat(issue.severity()).isEqualTo(Severity.BLOCKER);
     assertThat(issue.inputComponent()).isNull();
 
-    InputFile inputPath = mock(InputFile.class);
-    resourceCache.add(File.create("src/Foo.php").setEffectiveKey("foo:src/Foo.php"), null).setInputComponent(inputPath);
-    assertThat(issue.inputComponent()).isEqualTo(inputPath);
+    componentStore.put(new TestInputFileBuilder("foo", "src/Foo.php").build());
+    assertThat(issue.inputComponent()).isNotNull();
 
   }
 }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/profiling/PhasesSumUpTimeProfilerTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/profiling/PhasesSumUpTimeProfilerTest.java
index 9f31c75f631..6d7249b1eba 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/profiling/PhasesSumUpTimeProfilerTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/profiling/PhasesSumUpTimeProfilerTest.java
@@ -19,11 +19,11 @@
  */
 package org.sonar.scanner.profiling;
 
-import com.google.common.collect.Maps;
-import java.util.Arrays;
-import java.util.Collections;
+import static org.assertj.core.api.Assertions.assertThat;
+
 import java.util.List;
 import java.util.Map;
+
 import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
@@ -34,6 +34,7 @@ import org.sonar.api.batch.Initializer;
 import org.sonar.api.batch.PostJob;
 import org.sonar.api.batch.Sensor;
 import org.sonar.api.batch.SensorContext;
+import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.events.DecoratorExecutionHandler;
 import org.sonar.api.batch.events.DecoratorsPhaseHandler;
 import org.sonar.api.batch.events.InitializerExecutionHandler;
@@ -50,13 +51,8 @@ import org.sonar.api.resources.Project;
 import org.sonar.api.utils.System2;
 import org.sonar.scanner.bootstrap.GlobalProperties;
 import org.sonar.scanner.events.BatchStepEvent;
-import org.sonar.scanner.profiling.AbstractTimeProfiling;
-import org.sonar.scanner.profiling.Phase;
-import org.sonar.scanner.profiling.PhasesSumUpTimeProfiler;
 
-import static org.assertj.core.api.Assertions.assertThat;
-import static org.mockito.Mockito.spy;
-import static org.mockito.Mockito.when;
+import com.google.common.collect.Maps;
 
 public class PhasesSumUpTimeProfilerTest {
 
@@ -78,7 +74,6 @@ public class PhasesSumUpTimeProfilerTest {
   public void testSimpleProject() throws InterruptedException {
 
     final Project project = mockProject("my:project", true);
-    when(project.getModules()).thenReturn(Collections.<Project>emptyList());
 
     fakeAnalysis(profiler, project);
 
@@ -93,7 +88,9 @@ public class PhasesSumUpTimeProfilerTest {
     final Project project = mockProject("project root", true);
     final Project moduleA = mockProject("moduleA", false);
     final Project moduleB = mockProject("moduleB", false);
-    when(project.getModules()).thenReturn(Arrays.asList(moduleA, moduleB));
+
+    project.definition().addSubProject(moduleA.definition());
+    project.definition().addSubProject(moduleA.definition());
 
     fakeAnalysis(profiler, moduleA);
     fakeAnalysis(profiler, moduleB);
@@ -140,10 +137,7 @@ public class PhasesSumUpTimeProfilerTest {
   }
 
   private Project mockProject(String name, boolean isRoot) {
-    final Project project = spy(new Project("myProject"));
-    when(project.isRoot()).thenReturn(isRoot);
-    when(project.getName()).thenReturn(name);
-    return project;
+    return new Project(ProjectDefinition.create().setName(name).setKey(name));
   }
 
   private void fakeAnalysis(PhasesSumUpTimeProfiler profiler, final Project module) {
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/ComponentsPublisherTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/ComponentsPublisherTest.java
index abd3a13b8dd..1fbb2ad50b4 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/ComponentsPublisherTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/ComponentsPublisherTest.java
@@ -21,79 +21,88 @@ package org.sonar.scanner.report;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.Collections;
 
+import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
 import org.sonar.api.CoreProperties;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
+import org.sonar.api.batch.fs.InputFile.Type;
 import org.sonar.api.batch.fs.internal.DefaultInputDir;
+import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.DefaultInputModule;
+import org.sonar.api.batch.fs.internal.InputModuleHierarchy;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
-import org.sonar.api.resources.Directory;
-import org.sonar.api.resources.Project;
 import org.sonar.api.utils.DateUtils;
-import org.sonar.scanner.FakeJava;
-import org.sonar.scanner.index.BatchComponentCache;
+import org.sonar.scanner.ProjectAnalysisInfo;
 import org.sonar.scanner.protocol.output.FileStructure;
 import org.sonar.scanner.protocol.output.ScannerReport.Component;
 import org.sonar.scanner.protocol.output.ScannerReport.ComponentLink.ComponentLinkType;
 import org.sonar.scanner.report.ComponentsPublisher;
-import org.sonar.scanner.scan.ImmutableProjectReactor;
+import org.sonar.scanner.scan.DefaultComponentTree;
 import org.sonar.scanner.protocol.output.ScannerReportReader;
 import org.sonar.scanner.protocol.output.ScannerReportWriter;
 
 import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 public class ComponentsPublisherTest {
-
   @Rule
   public TemporaryFolder temp = new TemporaryFolder();
 
-  BatchComponentCache resourceCache = new BatchComponentCache();
+  private DefaultComponentTree tree;
+  private InputModuleHierarchy moduleHierarchy;
+  private File outputDir;
+  private ScannerReportWriter writer;
+
+  @Before
+  public void setUp() throws IOException {
+    tree = new DefaultComponentTree();
+    outputDir = temp.newFolder();
+    writer = new ScannerReportWriter(outputDir);
+  }
 
   @Test
   public void add_components_to_report() throws Exception {
+    ProjectAnalysisInfo projectAnalysisInfo = mock(ProjectAnalysisInfo.class);
+    when(projectAnalysisInfo.analysisDate()).thenReturn(DateUtils.parseDate("2012-12-12"));
+
+    ProjectDefinition rootDef = ProjectDefinition.create()
+      .setKey("foo")
+      .setProperty(CoreProperties.PROJECT_VERSION_PROPERTY, "1.0")
+      .setName("Root project")
+      .setDescription("Root description");
+    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
+
+    ProjectDefinition module1Def = ProjectDefinition.create()
+      .setKey("module1")
+      .setName("Module1")
+      .setDescription("Module description");
+    rootDef.addSubProject(module1Def);
+
+    DefaultInputModule module1 = new DefaultInputModule(module1Def, 2);
+
+    moduleHierarchy = mock(InputModuleHierarchy.class);
+    when(moduleHierarchy.root()).thenReturn(root);
+    when(moduleHierarchy.children(root)).thenReturn(Collections.singleton(module1));
+    tree.index(module1, root);
+
+    DefaultInputDir dir = new DefaultInputDir("module1", "src", 3);
+    tree.index(dir, module1);
+
+    DefaultInputFile file = new TestInputFileBuilder("module1", "src/Foo.java", 4).setLines(2).build();
+    tree.index(file, dir);
+
+    DefaultInputFile fileWithoutLang = new TestInputFileBuilder("module1", "src/make", 5).setLines(10).build();
+    tree.index(fileWithoutLang, dir);
 
-    ProjectDefinition rootDef = ProjectDefinition.create().setKey("foo");
-    rootDef.properties().put(CoreProperties.PROJECT_VERSION_PROPERTY, "1.0");
-    Project root = new Project("foo").setName("Root project").setDescription("Root description")
-      .setAnalysisDate(DateUtils.parseDate(("2012-12-12")));
-    root.setId(1).setUuid("PROJECT_UUID");
-    resourceCache.add(root, null).setInputComponent(new DefaultInputModule("foo"));
-
-    Project module1 = new Project("module1").setName("Module1").setDescription("Module description");
-    module1.setParent(root);
-    module1.setId(2).setUuid("MODULE_UUID");
-    resourceCache.add(module1, root).setInputComponent(new DefaultInputModule("module1"));
-    rootDef.addSubProject(ProjectDefinition.create().setKey("module1"));
-
-    Directory dir = Directory.create("src");
-    dir.setEffectiveKey("module1:src");
-    dir.setId(3).setUuid("DIR_UUID");
-    resourceCache.add(dir, module1).setInputComponent(new DefaultInputDir("foo", "src"));
-
-    org.sonar.api.resources.File file = org.sonar.api.resources.File.create("src/Foo.java", FakeJava.INSTANCE, false);
-    file.setEffectiveKey("module1:src/Foo.java");
-    file.setId(4).setUuid("FILE_UUID");
-    resourceCache.add(file, dir).setInputComponent(new TestInputFileBuilder("module1", "src/Foo.java").setLines(2).build());
-
-    org.sonar.api.resources.File fileWithoutLang = org.sonar.api.resources.File.create("src/make", null, false);
-    fileWithoutLang.setEffectiveKey("module1:src/make");
-    fileWithoutLang.setId(5).setUuid("FILE_WITHOUT_LANG_UUID");
-    resourceCache.add(fileWithoutLang, dir).setInputComponent(new TestInputFileBuilder("module1", "src/make").setLines(10).build());
-
-    org.sonar.api.resources.File testFile = org.sonar.api.resources.File.create("test/FooTest.java", FakeJava.INSTANCE, true);
-    testFile.setEffectiveKey("module1:test/FooTest.java");
-    testFile.setId(6).setUuid("TEST_FILE_UUID");
-    resourceCache.add(testFile, dir).setInputComponent(new TestInputFileBuilder("module1", "test/FooTest.java").setLines(4).build());
-
-    ImmutableProjectReactor reactor = new ImmutableProjectReactor(rootDef);
-
-    ComponentsPublisher publisher = new ComponentsPublisher(reactor, resourceCache);
-
-    File outputDir = temp.newFolder();
-    ScannerReportWriter writer = new ScannerReportWriter(outputDir);
+    DefaultInputFile testFile = new TestInputFileBuilder("module1", "test/FooTest.java", 6).setType(Type.TEST).setLines(4).build();
+    tree.index(testFile, dir);
+
+    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree);
     publisher.publish(writer);
 
     assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 1)).isTrue();
@@ -121,44 +130,38 @@ public class ComponentsPublisherTest {
 
   @Test
   public void add_components_without_version_and_name() throws IOException {
-    ProjectDefinition rootDef = ProjectDefinition.create().setKey("foo");
-    Project root = new Project("foo").setDescription("Root description")
-      .setAnalysisDate(DateUtils.parseDate(("2012-12-12")));
-    root.setId(1).setUuid("PROJECT_UUID");
-    resourceCache.add(root, null).setInputComponent(new DefaultInputModule("foo"));
-
-    Project module1 = new Project("module1").setDescription("Module description");
-    module1.setParent(root);
-    module1.setId(2).setUuid("MODULE_UUID");
-    resourceCache.add(module1, root).setInputComponent(new DefaultInputModule("module1"));
-    rootDef.addSubProject(ProjectDefinition.create().setKey("module1"));
-
-    Directory dir = Directory.create("src");
-    dir.setEffectiveKey("module1:src");
-    dir.setId(3).setUuid("DIR_UUID");
-    resourceCache.add(dir, module1).setInputComponent(new DefaultInputDir("foo", "src"));
-
-    org.sonar.api.resources.File file = org.sonar.api.resources.File.create("src/Foo.java", FakeJava.INSTANCE, false);
-    file.setEffectiveKey("module1:src/Foo.java");
-    file.setId(4).setUuid("FILE_UUID");
-    resourceCache.add(file, dir).setInputComponent(new TestInputFileBuilder("module1", "src/Foo.java").setLines(2).build());
-
-    org.sonar.api.resources.File fileWithoutLang = org.sonar.api.resources.File.create("src/make", null, false);
-    fileWithoutLang.setEffectiveKey("module1:src/make");
-    fileWithoutLang.setId(5).setUuid("FILE_WITHOUT_LANG_UUID");
-    resourceCache.add(fileWithoutLang, dir).setInputComponent(new TestInputFileBuilder("module1", "src/make").setLines(10).build());
-
-    org.sonar.api.resources.File testFile = org.sonar.api.resources.File.create("test/FooTest.java", FakeJava.INSTANCE, true);
-    testFile.setEffectiveKey("module1:test/FooTest.java");
-    testFile.setId(6).setUuid("TEST_FILE_UUID");
-    resourceCache.add(testFile, dir).setInputComponent(new TestInputFileBuilder("module1", "test/FooTest.java").setLines(4).build());
-
-    ImmutableProjectReactor reactor = new ImmutableProjectReactor(rootDef);
-
-    ComponentsPublisher publisher = new ComponentsPublisher(reactor, resourceCache);
-
-    File outputDir = temp.newFolder();
-    ScannerReportWriter writer = new ScannerReportWriter(outputDir);
+    ProjectAnalysisInfo projectAnalysisInfo = mock(ProjectAnalysisInfo.class);
+    when(projectAnalysisInfo.analysisDate()).thenReturn(DateUtils.parseDate("2012-12-12"));
+
+    ProjectDefinition rootDef = ProjectDefinition.create()
+      .setKey("foo")
+      .setDescription("Root description");
+    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
+
+    ProjectDefinition module1Def = ProjectDefinition.create()
+      .setKey("module1")
+      .setDescription("Module description");
+    rootDef.addSubProject(module1Def);
+    DefaultInputModule module1 = new DefaultInputModule(module1Def, 2);
+
+    moduleHierarchy = mock(InputModuleHierarchy.class);
+    when(moduleHierarchy.root()).thenReturn(root);
+    when(moduleHierarchy.children(root)).thenReturn(Collections.singleton(module1));
+    tree.index(module1, root);
+
+    DefaultInputDir dir = new DefaultInputDir("module1", "src", 3);
+    tree.index(dir, module1);
+
+    DefaultInputFile file = new TestInputFileBuilder("module1", "src/Foo.java", 4).setLines(2).build();
+    tree.index(file, dir);
+
+    DefaultInputFile fileWithoutLang = new TestInputFileBuilder("module1", "src/make", 5).setLines(10).build();
+    tree.index(fileWithoutLang, dir);
+
+    DefaultInputFile testFile = new TestInputFileBuilder("module1", "test/FooTest.java", 6).setType(Type.TEST).setLines(4).build();
+    tree.index(testFile, dir);
+
+    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree);
     publisher.publish(writer);
 
     assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 1)).isTrue();
@@ -188,40 +191,38 @@ public class ComponentsPublisherTest {
 
   @Test
   public void add_components_with_links_and_branch() throws Exception {
-    // inputs
-    ProjectDefinition rootDef = ProjectDefinition.create().setKey("foo");
-    rootDef.properties().put(CoreProperties.PROJECT_VERSION_PROPERTY, "1.0");
-    Project root = new Project("foo:my_branch").setName("Root project")
-      .setAnalysisDate(DateUtils.parseDate(("2012-12-12")));
-    root.setId(1).setUuid("PROJECT_UUID");
-    resourceCache.add(root, null).setInputComponent(new DefaultInputModule("foo"));
-    rootDef.properties().put(CoreProperties.LINKS_HOME_PAGE, "http://home");
-    rootDef.properties().put(CoreProperties.PROJECT_BRANCH_PROPERTY, "my_branch");
-
-    Project module1 = new Project("module1:my_branch").setName("Module1");
-    module1.setParent(root);
-    module1.setId(2).setUuid("MODULE_UUID");
-    resourceCache.add(module1, root).setInputComponent(new DefaultInputModule("module1"));
-    ProjectDefinition moduleDef = ProjectDefinition.create().setKey("module1");
-    moduleDef.properties().put(CoreProperties.LINKS_CI, "http://ci");
-    rootDef.addSubProject(moduleDef);
-
-    Directory dir = Directory.create("src");
-    dir.setEffectiveKey("module1:my_branch:my_branch:src");
-    dir.setId(3).setUuid("DIR_UUID");
-    resourceCache.add(dir, module1).setInputComponent(new DefaultInputDir("foo", "src"));
-
-    org.sonar.api.resources.File file = org.sonar.api.resources.File.create("src/Foo.java", FakeJava.INSTANCE, false);
-    file.setEffectiveKey("module1:my_branch:my_branch:src/Foo.java");
-    file.setId(4).setUuid("FILE_UUID");
-    resourceCache.add(file, dir).setInputComponent(new TestInputFileBuilder("module1", "src/Foo.java").setLines(2).build());
-
-    ImmutableProjectReactor reactor = new ImmutableProjectReactor(rootDef);
-
-    ComponentsPublisher publisher = new ComponentsPublisher(reactor, resourceCache);
-
-    File outputDir = temp.newFolder();
-    ScannerReportWriter writer = new ScannerReportWriter(outputDir);
+    ProjectAnalysisInfo projectAnalysisInfo = mock(ProjectAnalysisInfo.class);
+    when(projectAnalysisInfo.analysisDate()).thenReturn(DateUtils.parseDate("2012-12-12"));
+
+    ProjectDefinition rootDef = ProjectDefinition.create()
+      .setKey("foo")
+      .setProperty(CoreProperties.PROJECT_VERSION_PROPERTY, "1.0")
+      .setProperty(CoreProperties.PROJECT_BRANCH_PROPERTY, "my_branch")
+      .setName("Root project")
+      .setProperty(CoreProperties.LINKS_HOME_PAGE, "http://home")
+      .setDescription("Root description");
+    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
+
+    ProjectDefinition module1Def = ProjectDefinition.create()
+      .setKey("module1")
+      .setName("Module1")
+      .setProperty(CoreProperties.LINKS_CI, "http://ci")
+      .setDescription("Module description");
+    rootDef.addSubProject(module1Def);
+    DefaultInputModule module1 = new DefaultInputModule(module1Def, 2);
+
+    moduleHierarchy = mock(InputModuleHierarchy.class);
+    when(moduleHierarchy.root()).thenReturn(root);
+    when(moduleHierarchy.children(root)).thenReturn(Collections.singleton(module1));
+    tree.index(module1, root);
+
+    DefaultInputDir dir = new DefaultInputDir("module1", "src", 3);
+    tree.index(dir, module1);
+
+    DefaultInputFile file = new TestInputFileBuilder("module1", "src/Foo.java", 4).setLines(2).build();
+    tree.index(file, dir);
+
+    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree);
     publisher.publish(writer);
 
     ScannerReportReader reader = new ScannerReportReader(outputDir);
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/CoveragePublisherTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/CoveragePublisherTest.java
index 067169696e4..2f141e94fbf 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/CoveragePublisherTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/CoveragePublisherTest.java
@@ -20,21 +20,20 @@
 package org.sonar.scanner.report;
 
 import java.io.File;
-import java.util.Date;
 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.batch.fs.internal.DefaultInputModule;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.api.batch.sensor.measure.internal.DefaultMeasure;
 import org.sonar.api.measures.CoreMetrics;
-import org.sonar.api.resources.Project;
 import org.sonar.core.util.CloseableIterator;
-import org.sonar.scanner.index.BatchComponentCache;
 import org.sonar.scanner.protocol.output.ScannerReport.LineCoverage;
 import org.sonar.scanner.protocol.output.ScannerReportReader;
 import org.sonar.scanner.protocol.output.ScannerReportWriter;
+import org.sonar.scanner.scan.filesystem.InputComponentStore;
 import org.sonar.scanner.scan.measure.MeasureCache;
 
 import static org.assertj.core.api.Assertions.assertThat;
@@ -50,18 +49,19 @@ public class CoveragePublisherTest {
   private MeasureCache measureCache;
   private CoveragePublisher publisher;
 
-  private org.sonar.api.resources.Resource sampleFile;
+  private InputComponentStore componentCache;
+  private DefaultInputFile inputFile;
 
   @Before
   public void prepare() {
-    Project p = new Project("foo").setAnalysisDate(new Date(1234567L));
-    BatchComponentCache resourceCache = new BatchComponentCache();
-    sampleFile = org.sonar.api.resources.File.create("src/Foo.php").setEffectiveKey("foo:src/Foo.php");
-    resourceCache.add(p, null).setInputComponent(new DefaultInputModule("foo"));
-    resourceCache.add(sampleFile, null).setInputComponent(new TestInputFileBuilder("foo", "src/Foo.php").setLines(5).build());
+    inputFile = new TestInputFileBuilder("foo", "src/Foo.php").setLines(5).build();
+    componentCache = new InputComponentStore();
+    componentCache.put(new DefaultInputModule("foo"));
+    componentCache.put(inputFile);
+
     measureCache = mock(MeasureCache.class);
     when(measureCache.byMetric(anyString(), anyString())).thenReturn(null);
-    publisher = new CoveragePublisher(resourceCache, measureCache);
+    publisher = new CoveragePublisher(componentCache, measureCache);
   }
 
   @Test
@@ -81,7 +81,7 @@ public class CoveragePublisherTest {
 
     publisher.publish(writer);
 
-    try (CloseableIterator<LineCoverage> it = new ScannerReportReader(outputDir).readComponentCoverage(2)) {
+    try (CloseableIterator<LineCoverage> it = new ScannerReportReader(outputDir).readComponentCoverage(inputFile.batchId())) {
       assertThat(it.next()).isEqualTo(LineCoverage.newBuilder()
         .setLine(2)
         .setHits(true)
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/MeasuresPublisherTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/MeasuresPublisherTest.java
index 6ee89c3e5b9..f6caf2f6bbd 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/MeasuresPublisherTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/MeasuresPublisherTest.java
@@ -20,25 +20,25 @@
 package org.sonar.scanner.report;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.Collections;
-import java.util.Date;
 import org.apache.commons.lang.exception.ExceptionUtils;
 import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
 import org.junit.rules.TemporaryFolder;
+import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.DefaultInputModule;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.api.batch.sensor.measure.internal.DefaultMeasure;
 import org.sonar.api.measures.CoreMetrics;
-import org.sonar.api.resources.Project;
 import org.sonar.core.util.CloseableIterator;
 import org.sonar.scanner.deprecated.test.TestPlanBuilder;
-import org.sonar.scanner.index.BatchComponentCache;
 import org.sonar.scanner.protocol.output.ScannerReport;
 import org.sonar.scanner.protocol.output.ScannerReportReader;
 import org.sonar.scanner.protocol.output.ScannerReportWriter;
+import org.sonar.scanner.scan.filesystem.InputComponentStore;
 import org.sonar.scanner.scan.measure.MeasureCache;
 
 import static java.util.Arrays.asList;
@@ -61,18 +61,22 @@ public class MeasuresPublisherTest {
   private MeasureCache measureCache;
   private MeasuresPublisher publisher;
 
-  private org.sonar.api.resources.Resource sampleFile;
+  private InputComponentStore componentCache;
+  private File outputDir;
+  private ScannerReportWriter writer;
+  private DefaultInputFile inputFile;
 
   @Before
-  public void prepare() {
-    Project p = new Project("foo").setAnalysisDate(new Date(1234567L));
-    BatchComponentCache resourceCache = new BatchComponentCache();
-    sampleFile = org.sonar.api.resources.File.create("src/Foo.php").setEffectiveKey(FILE_KEY);
-    resourceCache.add(p, null).setInputComponent(new DefaultInputModule("foo"));
-    resourceCache.add(sampleFile, null).setInputComponent(new TestInputFileBuilder("foo", "src/Foo.php").build());
+  public void prepare() throws IOException {
+    inputFile = new TestInputFileBuilder("foo", "src/Foo.php").build();
+    componentCache = new InputComponentStore();
+    componentCache.put(new DefaultInputModule("foo"));
+    componentCache.put(inputFile);
     measureCache = mock(MeasureCache.class);
     when(measureCache.byComponentKey(anyString())).thenReturn(Collections.<DefaultMeasure<?>>emptyList());
-    publisher = new MeasuresPublisher(resourceCache, measureCache, mock(TestPlanBuilder.class));
+    publisher = new MeasuresPublisher(componentCache, measureCache, mock(TestPlanBuilder.class));
+    outputDir = temp.newFolder();
+    writer = new ScannerReportWriter(outputDir);
   }
 
   @Test
@@ -84,15 +88,11 @@ public class MeasuresPublisherTest {
       .withValue("foo bar");
     when(measureCache.byComponentKey(FILE_KEY)).thenReturn(asList(measure, stringMeasure));
 
-    File outputDir = temp.newFolder();
-    ScannerReportWriter writer = new ScannerReportWriter(outputDir);
-
     publisher.publish(writer);
-
     ScannerReportReader reader = new ScannerReportReader(outputDir);
 
     assertThat(reader.readComponentMeasures(1)).hasSize(0);
-    try (CloseableIterator<ScannerReport.Measure> componentMeasures = reader.readComponentMeasures(2)) {
+    try (CloseableIterator<ScannerReport.Measure> componentMeasures = reader.readComponentMeasures(inputFile.batchId())) {
       assertThat(componentMeasures).hasSize(2);
     }
   }
@@ -102,9 +102,6 @@ public class MeasuresPublisherTest {
     DefaultMeasure<Integer> measure = new DefaultMeasure<Integer>().forMetric(CoreMetrics.LINES_TO_COVER);
     when(measureCache.byComponentKey(FILE_KEY)).thenReturn(Collections.singletonList(measure));
 
-    File outputDir = temp.newFolder();
-    ScannerReportWriter writer = new ScannerReportWriter(outputDir);
-
     try {
       publisher.publish(writer);
       fail();
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/MetadataPublisherTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/MetadataPublisherTest.java
index 95dc51a8aef..6e5ee36b182 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/MetadataPublisherTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/MetadataPublisherTest.java
@@ -29,14 +29,15 @@ import org.sonar.api.CoreProperties;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.config.MapSettings;
 import org.sonar.api.config.Settings;
-import org.sonar.api.resources.Project;
-import org.sonar.scanner.index.BatchComponentCache;
+import org.sonar.api.batch.fs.internal.DefaultInputModule;
+import org.sonar.api.batch.fs.internal.InputModuleHierarchy;
+import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
+import org.sonar.scanner.ProjectAnalysisInfo;
 import org.sonar.scanner.protocol.output.ScannerReport;
 import org.sonar.scanner.protocol.output.ScannerReportReader;
 import org.sonar.scanner.protocol.output.ScannerReportWriter;
 import org.sonar.scanner.rule.ModuleQProfiles;
 import org.sonar.scanner.rule.QProfile;
-import org.sonar.scanner.scan.ImmutableProjectReactor;
 
 import static java.util.Arrays.asList;
 import static org.assertj.core.api.Assertions.assertThat;
@@ -50,22 +51,24 @@ public class MetadataPublisherTest {
   public TemporaryFolder temp = new TemporaryFolder();
 
   private ProjectDefinition projectDef;
-  private Project project;
+  private DefaultInputModule rootModule;
   private MetadataPublisher underTest;
   private Settings settings;
   private ModuleQProfiles qProfiles;
+  private ProjectAnalysisInfo projectAnalysisInfo;
+  private InputModuleHierarchy inputModuleHierarchy;
 
   @Before
   public void prepare() {
     projectDef = ProjectDefinition.create().setKey("foo");
-    project = new Project("foo").setAnalysisDate(new Date(1234567L));
-    BatchComponentCache componentCache = new BatchComponentCache();
-    org.sonar.api.resources.Resource sampleFile = org.sonar.api.resources.File.create("src/Foo.php").setEffectiveKey("foo:src/Foo.php");
-    componentCache.add(project, null);
-    componentCache.add(sampleFile, project);
+    rootModule = new DefaultInputModule(projectDef, TestInputFileBuilder.batchId++);
+    projectAnalysisInfo = mock(ProjectAnalysisInfo.class);
+    when(projectAnalysisInfo.analysisDate()).thenReturn(new Date(1234567L));
+    inputModuleHierarchy = mock(InputModuleHierarchy.class);
+    when(inputModuleHierarchy.root()).thenReturn(rootModule);
     settings = new MapSettings();
     qProfiles = mock(ModuleQProfiles.class);
-    underTest = new MetadataPublisher(componentCache, new ImmutableProjectReactor(projectDef), settings, qProfiles);
+    underTest = new MetadataPublisher(projectAnalysisInfo, inputModuleHierarchy, settings, qProfiles);
   }
 
   @Test
@@ -101,8 +104,7 @@ public class MetadataPublisherTest {
     settings.setProperty(CoreProperties.CPD_CROSS_PROJECT, "true");
     settings.setProperty(CoreProperties.PROJECT_BRANCH_PROPERTY, "myBranch");
     projectDef.properties().put(CoreProperties.PROJECT_BRANCH_PROPERTY, "myBranch");
-    project.setKey("foo:myBranch");
-    project.setEffectiveKey("foo:myBranch");
+    projectDef.setKey("foo");
 
     File outputDir = temp.newFolder();
     ScannerReportWriter writer = new ScannerReportWriter(outputDir);
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/SourcePublisherTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/SourcePublisherTest.java
index 0ecc47a1088..8044f49d440 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/SourcePublisherTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/report/SourcePublisherTest.java
@@ -22,19 +22,17 @@ package org.sonar.scanner.report;
 import java.io.File;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
-import java.util.Date;
 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.batch.fs.internal.DefaultInputModule;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
-import org.sonar.api.resources.Project;
-import org.sonar.api.resources.Qualifiers;
-import org.sonar.scanner.index.BatchComponentCache;
 import org.sonar.scanner.protocol.output.ScannerReportWriter;
 import org.sonar.scanner.report.SourcePublisher;
+import org.sonar.scanner.scan.filesystem.InputComponentStore;
 
 import static org.assertj.core.api.Assertions.assertThat;
 
@@ -42,31 +40,25 @@ public class SourcePublisherTest {
 
   @Rule
   public TemporaryFolder temp = new TemporaryFolder();
-
   private SourcePublisher publisher;
-
   private File sourceFile;
-
   private ScannerReportWriter writer;
-
-  private org.sonar.api.resources.File sampleFile;
+  private DefaultInputFile inputFile;
+  private InputComponentStore componentStore;
 
   @Before
   public void prepare() throws IOException {
-    Project p = new Project("foo").setAnalysisDate(new Date(1234567L));
-    BatchComponentCache resourceCache = new BatchComponentCache();
-    sampleFile = org.sonar.api.resources.File.create("src/Foo.php");
-    sampleFile.setEffectiveKey("foo:src/Foo.php");
-    resourceCache.add(p, null).setInputComponent(new DefaultInputModule("foo"));
     File baseDir = temp.newFolder();
     sourceFile = new File(baseDir, "src/Foo.php");
-    resourceCache.add(sampleFile, null).setInputComponent(
-      new TestInputFileBuilder("foo", "src/Foo.php")
+    inputFile = new TestInputFileBuilder("foo", "src/Foo.php")
       .setLines(5)
       .setModuleBaseDir(baseDir.toPath())
       .setCharset(StandardCharsets.ISO_8859_1)
-      .build());
-    publisher = new SourcePublisher(resourceCache);
+      .build();
+    componentStore = new InputComponentStore();
+    componentStore.put(new DefaultInputModule("foo"));
+    componentStore.put(inputFile);
+    publisher = new SourcePublisher(componentStore);
     File outputDir = temp.newFolder();
     writer = new ScannerReportWriter(outputDir);
   }
@@ -77,7 +69,7 @@ public class SourcePublisherTest {
 
     publisher.publish(writer);
 
-    File out = writer.getSourceFile(2);
+    File out = writer.getSourceFile(inputFile.batchId());
     assertThat(FileUtils.readFileToString(out, StandardCharsets.UTF_8)).isEqualTo("");
   }
 
@@ -87,18 +79,18 @@ public class SourcePublisherTest {
 
     publisher.publish(writer);
 
-    File out = writer.getSourceFile(2);
+    File out = writer.getSourceFile(inputFile.batchId());
     assertThat(FileUtils.readFileToString(out, StandardCharsets.UTF_8)).isEqualTo("1\n2\n3\n4\n");
   }
 
   @Test
   public void publishTestSource() throws Exception {
     FileUtils.write(sourceFile, "1\n2\n3\n4\n", StandardCharsets.ISO_8859_1);
-    sampleFile.setQualifier(Qualifiers.UNIT_TEST_FILE);
+    // sampleFile.setQualifier(Qualifiers.UNIT_TEST_FILE);
 
     publisher.publish(writer);
 
-    File out = writer.getSourceFile(2);
+    File out = writer.getSourceFile(inputFile.batchId());
     assertThat(FileUtils.readFileToString(out, StandardCharsets.UTF_8)).isEqualTo("1\n2\n3\n4\n");
   }
 
@@ -108,7 +100,7 @@ public class SourcePublisherTest {
 
     publisher.publish(writer);
 
-    File out = writer.getSourceFile(2);
+    File out = writer.getSourceFile(inputFile.batchId());
     assertThat(FileUtils.readFileToString(out, StandardCharsets.UTF_8)).isEqualTo("1\n2\n3\n4\n5");
   }
 
@@ -118,7 +110,7 @@ public class SourcePublisherTest {
 
     publisher.publish(writer);
 
-    File out = writer.getSourceFile(2);
+    File out = writer.getSourceFile(inputFile.batchId());
     assertThat(FileUtils.readFileToString(out, StandardCharsets.UTF_8)).isEqualTo("\n2\n3\n4\n5");
   }
 }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/ComponentIndexerTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/ComponentIndexerTest.java
deleted file mode 100644
index 0db12d01f39..00000000000
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/ComponentIndexerTest.java
+++ /dev/null
@@ -1,146 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2016 SonarSource SA
- * mailto:contact AT sonarsource DOT com
- *
- * This program 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.
- *
- * This program 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.scanner.scan.filesystem;
-
-import java.io.File;
-import java.io.IOException;
-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.ArgumentMatcher;
-import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.InputFile.Status;
-import org.sonar.api.batch.fs.internal.DefaultFileSystem;
-import org.sonar.api.batch.fs.internal.DefaultInputFile;
-import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
-import org.sonar.api.resources.AbstractLanguage;
-import org.sonar.api.resources.Directory;
-import org.sonar.api.resources.Languages;
-import org.sonar.api.resources.Project;
-import org.sonar.api.resources.Qualifiers;
-import org.sonar.api.resources.Resource;
-import org.sonar.scanner.FakeJava;
-import org.sonar.scanner.analysis.DefaultAnalysisMode;
-import org.sonar.scanner.index.BatchComponent;
-import org.sonar.scanner.index.BatchComponentCache;
-import org.sonar.scanner.index.DefaultIndex;
-import org.sonar.scanner.repository.ProjectRepositories;
-import org.sonar.scanner.scan.filesystem.ComponentIndexer;
-import org.sonar.scanner.scan.filesystem.DefaultModuleFileSystem;
-import org.sonar.scanner.scan.filesystem.FileIndexer;
-import org.sonar.scanner.scan.filesystem.ModuleFileSystemInitializer;
-
-import static org.mockito.Matchers.any;
-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 {
-
-  @Rule
-  public TemporaryFolder temp = new TemporaryFolder();
-  private File baseDir;
-  private DefaultFileSystem fs;
-  private DefaultIndex sonarIndex;
-  private AbstractLanguage cobolLanguage;
-  private Project project;
-  private ModuleFileSystemInitializer initializer;
-  private DefaultAnalysisMode mode;
-
-  @Before
-  public void prepare() throws IOException {
-    baseDir = temp.newFolder();
-    fs = new DefaultFileSystem(baseDir.toPath());
-    sonarIndex = mock(DefaultIndex.class);
-    project = new Project("myProject");
-    initializer = mock(ModuleFileSystemInitializer.class);
-    mode = mock(DefaultAnalysisMode.class);
-    when(initializer.baseDir()).thenReturn(baseDir);
-    when(initializer.workingDir()).thenReturn(temp.newFolder());
-    cobolLanguage = new AbstractLanguage("cobol") {
-      @Override
-      public String[] getFileSuffixes() {
-        return new String[] {"cbl"};
-      }
-    };
-  }
-
-  @Test
-  public void should_index_java_files() throws IOException {
-    Languages languages = new Languages(FakeJava.INSTANCE);
-    ComponentIndexer indexer = createIndexer(languages);
-    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(project, null, mock(FileIndexer.class), initializer, indexer, mode, new ProjectRepositories());
-    fs.add(newInputFile("src/main/java/foo/bar/Foo.java", "", "foo/bar/Foo.java", "java", false, Status.ADDED));
-    fs.add(newInputFile("src/main/java2/foo/bar/Foo.java", "", "foo/bar/Foo.java", "java", false, Status.ADDED));
-    // should index even if filter is applied
-    fs.add(newInputFile("src/test/java/foo/bar/FooTest.java", "", "foo/bar/FooTest.java", "java", true, Status.SAME));
-
-    fs.index();
-
-    verify(sonarIndex).index(org.sonar.api.resources.File.create("src/main/java/foo/bar/Foo.java", FakeJava.INSTANCE, false));
-    verify(sonarIndex).index(org.sonar.api.resources.File.create("src/main/java2/foo/bar/Foo.java", FakeJava.INSTANCE, false));
-    verify(sonarIndex).index(argThat(new ArgumentMatcher<org.sonar.api.resources.File>() {
-      @Override
-      public boolean matches(Object arg0) {
-        org.sonar.api.resources.File javaFile = (org.sonar.api.resources.File) arg0;
-        return javaFile.getKey().equals("src/test/java/foo/bar/FooTest.java")
-          && javaFile.getPath().equals("src/test/java/foo/bar/FooTest.java")
-          && javaFile.getQualifier().equals(Qualifiers.UNIT_TEST_FILE);
-      }
-    }));
-  }
-
-  private ComponentIndexer createIndexer(Languages languages) {
-    BatchComponentCache resourceCache = mock(BatchComponentCache.class);
-    when(resourceCache.get(any(Resource.class)))
-      .thenReturn(new BatchComponent(2, org.sonar.api.resources.File.create("foo.php"), new BatchComponent(1, Directory.create("src"), null)));
-    return new ComponentIndexer(project, languages, sonarIndex, resourceCache);
-  }
-
-  @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, mode, new ProjectRepositories());
-    fs.add(newInputFile("src/foo/bar/Foo.cbl", "", "foo/bar/Foo.cbl", "cobol", false, Status.ADDED));
-    fs.add(newInputFile("src2/foo/bar/Foo.cbl", "", "foo/bar/Foo.cbl", "cobol", false, Status.ADDED));
-    fs.add(newInputFile("src/test/foo/bar/FooTest.cbl", "", "foo/bar/FooTest.cbl", "cobol", true, Status.ADDED));
-
-    fs.index();
-
-    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, InputFile.Status status) throws IOException {
-    File file = new File(baseDir, path);
-    FileUtils.write(file, content);
-    return new TestInputFileBuilder("foo", path)
-      .setLanguage(languageKey)
-      .setType(unitTest ? InputFile.Type.TEST : InputFile.Type.MAIN)
-      .setStatus(status)
-      .build();
-  }
-
-}
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputPathCacheTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputComponentStoreTest.java
index a08039430a0..131eb7d6c6e 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputPathCacheTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputComponentStoreTest.java
@@ -19,8 +19,6 @@
  */
 package org.sonar.scanner.scan.filesystem;
 
-import org.junit.After;
-import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
@@ -29,30 +27,21 @@ 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.TestInputFileBuilder;
-import org.sonar.scanner.scan.filesystem.InputPathCache;
+import org.sonar.scanner.scan.filesystem.InputComponentStore;
 import java.nio.charset.StandardCharsets;
 
 import static org.assertj.core.api.Assertions.assertThat;
 
-public class InputPathCacheTest {
-
+public class InputComponentStoreTest {
   @Rule
   public TemporaryFolder temp = new TemporaryFolder();
 
-  @Before
-  public void start() {
-  }
-
-  @After
-  public void stop() {
-  }
-
   @Test
   public void should_add_input_file() throws Exception {
-    InputPathCache cache = new InputPathCache();
-    DefaultInputFile fooFile = new TestInputFileBuilder("foo", "src/main/java/Foo.java").setModuleBaseDir(temp.newFolder().toPath()).build();
-    cache.put("struts", fooFile);
-    cache.put("struts-core", new TestInputFileBuilder("foo", "src/main/java/Bar.java")
+    InputComponentStore cache = new InputComponentStore();
+    DefaultInputFile fooFile = new TestInputFileBuilder("struts", "src/main/java/Foo.java").setModuleBaseDir(temp.newFolder().toPath()).build();
+    cache.put(fooFile);
+    cache.put(new TestInputFileBuilder("struts-core", "src/main/java/Bar.java")
       .setLanguage("bla")
       .setType(Type.MAIN)
       .setStatus(Status.ADDED)
@@ -72,7 +61,7 @@ public class InputPathCacheTest {
       assertThat(inputPath.relativePath()).startsWith("src/main/java/");
     }
 
-    cache.remove("struts", fooFile);
+    cache.remove(fooFile);
     assertThat(cache.allFiles()).hasSize(1);
 
     cache.removeModule("struts");
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/MetadataGeneratorProviderTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/MetadataGeneratorProviderTest.java
index 26542931d04..73f0dc3c8f7 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/MetadataGeneratorProviderTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/MetadataGeneratorProviderTest.java
@@ -23,6 +23,7 @@ import org.junit.Test;
 import org.mockito.Mockito;
 import org.sonar.api.batch.fs.internal.FileMetadata;
 
+import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.mock;
 
 public class MetadataGeneratorProviderTest {
@@ -31,7 +32,6 @@ public class MetadataGeneratorProviderTest {
     StatusDetectionFactory statusDetectionFactory = mock(StatusDetectionFactory.class, Mockito.RETURNS_MOCKS);
 
     MetadataGeneratorProvider factory = new MetadataGeneratorProvider();
-    MetadataGenerator builder = factory.provide(statusDetectionFactory, new FileMetadata());
-    //TODO
+    assertThat(factory.provide(statusDetectionFactory, new FileMetadata())).isNotNull();
   }
 }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/report/ConsoleReportTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/report/ConsoleReportTest.java
index eba14f3a7b1..a176c309830 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/report/ConsoleReportTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/report/ConsoleReportTest.java
@@ -33,7 +33,7 @@ import org.sonar.api.rule.Severity;
 import org.sonar.api.utils.log.LogTester;
 import org.sonar.scanner.issue.IssueCache;
 import org.sonar.scanner.issue.tracking.TrackedIssue;
-import org.sonar.scanner.scan.filesystem.InputPathCache;
+import org.sonar.scanner.scan.filesystem.InputComponentStore;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.mock;
@@ -46,14 +46,14 @@ public class ConsoleReportTest {
 
   private Settings settings;
   private IssueCache issueCache;
-  private InputPathCache inputPathCache;
+  private InputComponentStore inputPathCache;
   private ConsoleReport report;
 
   @Before
   public void prepare() {
     settings = new MapSettings();
     issueCache = mock(IssueCache.class);
-    inputPathCache = mock(InputPathCache.class);
+    inputPathCache = mock(InputComponentStore.class);
     report = new ConsoleReport(settings, issueCache, inputPathCache);
   }
 
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/report/JSONReportTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/report/JSONReportTest.java
index c75da60b841..2918d4fd5e6 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/report/JSONReportTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/report/JSONReportTest.java
@@ -36,6 +36,8 @@ import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.batch.fs.internal.DefaultInputDir;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
+import org.sonar.api.batch.fs.internal.DefaultInputModule;
+import org.sonar.api.batch.fs.internal.InputModuleHierarchy;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.api.batch.rule.Rules;
 import org.sonar.api.batch.rule.internal.RulesBuilder;
@@ -43,14 +45,12 @@ import org.sonar.api.config.Settings;
 import org.sonar.api.config.MapSettings;
 import org.sonar.api.issue.Issue;
 import org.sonar.api.platform.Server;
-import org.sonar.api.resources.Project;
-import org.sonar.api.resources.Resource;
 import org.sonar.api.rule.RuleKey;
 import org.sonar.scanner.issue.IssueCache;
 import org.sonar.scanner.issue.tracking.TrackedIssue;
 import org.sonar.scanner.protocol.input.ScannerInput;
 import org.sonar.scanner.repository.user.UserRepositoryLoader;
-import org.sonar.scanner.scan.filesystem.InputPathCache;
+import org.sonar.scanner.scan.filesystem.InputComponentStore;
 
 import static net.javacrumbs.jsonunit.assertj.JsonAssert.assertThatJson;
 import static org.assertj.core.api.Assertions.assertThat;
@@ -66,37 +66,43 @@ public class JSONReportTest {
   public TemporaryFolder temp = new TemporaryFolder();
 
   JSONReport jsonReport;
-  Resource resource = mock(Resource.class);
   DefaultFileSystem fs;
   Server server = mock(Server.class);
   Rules rules = mock(Rules.class);
   Settings settings = new MapSettings();
   IssueCache issueCache = mock(IssueCache.class);
   private UserRepositoryLoader userRepository;
+  private InputModuleHierarchy moduleHierarchy;
 
   @Before
   public void before() throws Exception {
+    moduleHierarchy = mock(InputModuleHierarchy.class);
+    userRepository = mock(UserRepositoryLoader.class);
     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");
-    userRepository = mock(UserRepositoryLoader.class);
-    DefaultInputDir inputDir = new DefaultInputDir("struts", "src/main/java/org/apache/struts");
+
+    DefaultInputDir inputDir = new DefaultInputDir("struts", "src/main/java/org/apache/struts", TestInputFileBuilder.batchId++);
     DefaultInputFile inputFile = new TestInputFileBuilder("struts", "src/main/java/org/apache/struts/Action.java").build();
     inputFile.setStatus(InputFile.Status.CHANGED);
-    InputPathCache fileCache = mock(InputPathCache.class);
+    InputComponentStore fileCache = mock(InputComponentStore.class);
     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");
-    Project moduleB = new Project("struts-ui");
-    moduleB.setParent(rootModule).setPath("ui");
+
+    DefaultInputModule rootModule = new DefaultInputModule("struts");
+    DefaultInputModule moduleA = new DefaultInputModule("struts-core");
+    DefaultInputModule moduleB = new DefaultInputModule("struts-ui");
+
+    when(moduleHierarchy.children(rootModule)).thenReturn(Arrays.asList(moduleA, moduleB));
+    when(moduleHierarchy.parent(moduleA)).thenReturn(rootModule);
+    when(moduleHierarchy.parent(moduleB)).thenReturn(rootModule);
+    when(moduleHierarchy.relativePath(moduleA)).thenReturn("core");
+    when(moduleHierarchy.relativePath(moduleB)).thenReturn("ui");
 
     RulesBuilder builder = new RulesBuilder();
     builder.add(RuleKey.of("squid", "AvoidCycles")).setName("Avoid Cycles");
     rules = builder.build();
-    jsonReport = new JSONReport(settings, fs, server, rules, issueCache, rootModule, fileCache, userRepository);
+    jsonReport = new JSONReport(moduleHierarchy, settings, fs, server, rules, issueCache, rootModule, fileCache, userRepository);
   }
 
   @Test
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scm/DefaultBlameOutputTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scm/DefaultBlameOutputTest.java
index 02867cc63ee..673c717601c 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scm/DefaultBlameOutputTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scm/DefaultBlameOutputTest.java
@@ -21,42 +21,24 @@ package org.sonar.scanner.scm;
 
 import java.util.Arrays;
 import java.util.Date;
-import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
-import org.sonar.api.batch.fs.InputComponent;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.api.batch.scm.BlameLine;
-import org.sonar.scanner.index.BatchComponent;
-import org.sonar.scanner.index.BatchComponentCache;
 import org.sonar.scanner.scm.DefaultBlameOutput;
 
-import static org.mockito.Matchers.any;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
-
 public class DefaultBlameOutputTest {
 
   @Rule
   public ExpectedException thrown = ExpectedException.none();
 
-  private BatchComponentCache componentCache;
-
-  @Before
-  public void prepare() {
-    componentCache = mock(BatchComponentCache.class);
-    BatchComponent component = mock(BatchComponent.class);
-    when(component.batchId()).thenReturn(1);
-    when(componentCache.get(any(InputComponent.class))).thenReturn(component);
-  }
-
   @Test
   public void shouldNotFailIfNotSameNumberOfLines() {
     InputFile file = new TestInputFileBuilder("foo", "src/main/java/Foo.java").setLines(10).build();
 
-    new DefaultBlameOutput(null, null, Arrays.asList(file)).blameResult(file, Arrays.asList(new BlameLine().revision("1").author("guy")));
+    new DefaultBlameOutput(null, Arrays.asList(file)).blameResult(file, Arrays.asList(new BlameLine().revision("1").author("guy")));
   }
 
   @Test
@@ -66,7 +48,7 @@ public class DefaultBlameOutputTest {
     thrown.expect(IllegalArgumentException.class);
     thrown.expectMessage("It was not expected to blame file src/main/java/Foo.java");
 
-    new DefaultBlameOutput(null, null, Arrays.<InputFile>asList(new TestInputFileBuilder("foo", "src/main/java/Foo2.java").build()))
+    new DefaultBlameOutput(null, Arrays.<InputFile>asList(new TestInputFileBuilder("foo", "src/main/java/Foo2.java").build()))
       .blameResult(file, Arrays.asList(new BlameLine().revision("1").author("guy")));
   }
 
@@ -77,7 +59,7 @@ public class DefaultBlameOutputTest {
     thrown.expect(IllegalArgumentException.class);
     thrown.expectMessage("Blame date is null for file src/main/java/Foo.java at line 1");
 
-    new DefaultBlameOutput(null, componentCache, Arrays.<InputFile>asList(file))
+    new DefaultBlameOutput(null, Arrays.<InputFile>asList(file))
       .blameResult(file, Arrays.asList(new BlameLine().revision("1").author("guy")));
   }
 
@@ -88,7 +70,7 @@ public class DefaultBlameOutputTest {
     thrown.expect(IllegalArgumentException.class);
     thrown.expectMessage("Blame revision is blank for file src/main/java/Foo.java at line 1");
 
-    new DefaultBlameOutput(null, componentCache, Arrays.<InputFile>asList(file))
+    new DefaultBlameOutput(null, Arrays.<InputFile>asList(file))
       .blameResult(file, Arrays.asList(new BlameLine().date(new Date()).author("guy")));
   }
 
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/sensor/DefaultSensorStorageTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/sensor/DefaultSensorStorageTest.java
index b2ed93632e8..4d11247c5d4 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/sensor/DefaultSensorStorageTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/sensor/DefaultSensorStorageTest.java
@@ -38,12 +38,10 @@ import org.sonar.api.config.MapSettings;
 import org.sonar.api.config.Settings;
 import org.sonar.api.measures.CoreMetrics;
 import org.sonar.api.resources.File;
-import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.utils.KeyValueFormat;
 import org.sonar.core.metric.ScannerMetrics;
 import org.sonar.scanner.cpd.index.SonarCpdBlockIndex;
-import org.sonar.scanner.index.BatchComponentCache;
 import org.sonar.scanner.issue.ModuleIssues;
 import org.sonar.scanner.protocol.output.ScannerReportWriter;
 import org.sonar.scanner.report.ReportPublisher;
@@ -71,7 +69,6 @@ public class DefaultSensorStorageTest {
   private ModuleIssues moduleIssues;
   private MeasureCache measureCache;
   private ContextPropertiesCache contextPropertiesCache = new ContextPropertiesCache();
-  private BatchComponentCache componentCache;
 
   @Before
   public void prepare() throws Exception {
@@ -83,11 +80,10 @@ public class DefaultSensorStorageTest {
     measureCache = mock(MeasureCache.class);
     CoverageExclusions coverageExclusions = mock(CoverageExclusions.class);
     when(coverageExclusions.isExcluded(any(InputFile.class))).thenReturn(false);
-    componentCache = new BatchComponentCache();
     ReportPublisher reportPublisher = mock(ReportPublisher.class);
     when(reportPublisher.getWriter()).thenReturn(new ScannerReportWriter(temp.newFolder()));
     underTest = new DefaultSensorStorage(metricFinder,
-      moduleIssues, settings, coverageExclusions, componentCache, reportPublisher, measureCache,
+      moduleIssues, settings, coverageExclusions, reportPublisher, measureCache,
       mock(SonarCpdBlockIndex.class), contextPropertiesCache, new ScannerMetrics());
   }
 
@@ -110,7 +106,6 @@ public class DefaultSensorStorageTest {
 
     ArgumentCaptor<DefaultMeasure> argumentCaptor = ArgumentCaptor.forClass(DefaultMeasure.class);
     Resource sonarFile = File.create("src/Foo.php").setEffectiveKey("foo:src/Foo.php");
-    componentCache.add(sonarFile, null).setInputComponent(file);
     when(measureCache.put(eq(file.key()), eq(CoreMetrics.NCLOC_KEY), argumentCaptor.capture())).thenReturn(null);
     underTest.store(new DefaultMeasure()
       .on(file)
@@ -126,7 +121,6 @@ public class DefaultSensorStorageTest {
   public void shouldSaveProjectMeasureToSensorContext() {
     String projectKey = "myProject";
     DefaultInputModule module = new DefaultInputModule(projectKey);
-    componentCache.add(new Project(projectKey), null).setInputComponent(module);
 
     ArgumentCaptor<DefaultMeasure> argumentCaptor = ArgumentCaptor.forClass(DefaultMeasure.class);
     when(measureCache.put(eq(module.key()), eq(CoreMetrics.NCLOC_KEY), argumentCaptor.capture())).thenReturn(null);
@@ -143,10 +137,8 @@ public class DefaultSensorStorageTest {
 
   @Test(expected = UnsupportedOperationException.class)
   public void duplicateHighlighting() throws Exception {
-    Resource sonarFile = File.create("src/Foo.java").setEffectiveKey("foo:src/Foo.java");
     InputFile inputFile = new TestInputFileBuilder("foo", "src/Foo.java")
       .setModuleBaseDir(temp.newFolder().toPath()).build();
-    componentCache.add(sonarFile, null).setInputComponent(inputFile);
     DefaultHighlighting h = new DefaultHighlighting(null)
       .onFile(inputFile);
     underTest.store(h);
@@ -155,10 +147,8 @@ public class DefaultSensorStorageTest {
 
   @Test(expected = UnsupportedOperationException.class)
   public void duplicateSymbolTable() throws Exception {
-    Resource sonarFile = File.create("src/Foo.java").setEffectiveKey("foo:src/Foo.java");
     InputFile inputFile = new TestInputFileBuilder("foo", "src/Foo.java")
       .setModuleBaseDir(temp.newFolder().toPath()).build();
-    componentCache.add(sonarFile, null).setInputComponent(inputFile);
     DefaultSymbolTable st = new DefaultSymbolTable(null)
       .onFile(inputFile);
     underTest.store(st);