SONAR-11459 Stop publishing modules and folders in the scanner report

24 files changed, 101 insertions, 774 deletions

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 611e42c7793..6588f2e3c0a 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
@@ -234,7 +234,7 @@ public class CpdExecutorTest {
       .setLines(lines);
     config.accept(fileBuilder);
     DefaultInputFile file = fileBuilder.build();
-    componentStore.put(file);
+    componentStore.put("foo", file);
     return file;
   }
 
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/tracking/SourceHashHolderTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/tracking/SourceHashHolderTest.java
index 6aa8686690f..590d4119282 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/tracking/SourceHashHolderTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/issue/tracking/SourceHashHolderTest.java
@@ -28,11 +28,9 @@ import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
 import org.mockito.Mockito;
-import org.sonar.api.CoreProperties;
-import org.sonar.api.batch.bootstrap.ProjectDefinition;
 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.DefaultInputProject;
 
 import static org.apache.commons.codec.digest.DigestUtils.md5Hex;
 import static org.assertj.core.api.Assertions.assertThat;
@@ -51,11 +49,10 @@ public class SourceHashHolderTest {
   DefaultInputFile file;
 
   private File ioFile;
-  private ProjectDefinition def;
+  private DefaultInputProject project;
 
   @Before
   public void setUp() throws Exception {
-    def = ProjectDefinition.create().setBaseDir(temp.newFolder()).setWorkDir(temp.newFolder());
     lastSnapshots = mock(ServerLineHashesLoader.class);
     file = mock(DefaultInputFile.class);
     ioFile = temp.newFile();
@@ -65,7 +62,8 @@ public class SourceHashHolderTest {
     when(file.lines()).thenReturn(1);
     when(file.charset()).thenReturn(StandardCharsets.UTF_8);
 
-    sourceHashHolder = new SourceHashHolder(new DefaultInputModule(def, 1), file, lastSnapshots);
+    project = mock(DefaultInputProject.class);
+    sourceHashHolder = new SourceHashHolder(project, file, lastSnapshots);
   }
 
   @Test
@@ -84,8 +82,8 @@ public class SourceHashHolderTest {
   public void should_lazy_load_reference_hashes_when_status_changed() throws Exception {
     final String source = "source";
     FileUtils.write(ioFile, source, StandardCharsets.UTF_8);
-    def.setKey("foo");
-    when(file.relativePath()).thenReturn("src/Foo.java");
+    when(project.getKeyWithBranch()).thenReturn("foo");
+    when(file.getProjectRelativePath()).thenReturn("src/Foo.java");
     String key = "foo:src/Foo.java";
     when(file.status()).thenReturn(InputFile.Status.CHANGED);
     when(lastSnapshots.getLineHashes(key)).thenReturn(new String[] {md5Hex(source)});
@@ -101,9 +99,8 @@ public class SourceHashHolderTest {
   public void should_lazy_load_reference_hashes_when_status_changed_on_branch() throws Exception {
     final String source = "source";
     FileUtils.write(ioFile, source, StandardCharsets.UTF_8);
-    def.setKey("foo");
-    def.setProperty(CoreProperties.PROJECT_BRANCH_PROPERTY, "myBranch");
-    when(file.relativePath()).thenReturn("src/Foo.java");
+    when(project.getKeyWithBranch()).thenReturn("foo:myBranch");
+    when(file.getProjectRelativePath()).thenReturn("src/Foo.java");
     String key = "foo:myBranch:src/Foo.java";
     when(file.status()).thenReturn(InputFile.Status.CHANGED);
     when(lastSnapshots.getLineHashes(key)).thenReturn(new String[] {md5Hex(source)});
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 21d88ed6f5d..62899cf17f1 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
@@ -73,7 +73,7 @@ public class BranchMediumTest {
   public void should_not_skip_report_for_unchanged_files_in_short_branch() {
     // sanity check, normally report gets generated
     AnalysisResult result = getResult(tester);
-    assertThat(getResult(tester).getReportComponent(result.inputFile(FILE_PATH).key())).isNotNull();
+    assertThat(getResult(tester).getReportComponent(result.inputFile(FILE_PATH))).isNotNull();
     int fileId = 2;
     assertThat(result.getReportReader().readChangesets(fileId)).isNotNull();
     assertThat(result.getReportReader().hasCoverage(fileId)).isTrue();
@@ -81,7 +81,7 @@ public class BranchMediumTest {
 
     // file is not skipped for short branches (need coverage, duplications coming soon)
     AnalysisResult result2 = getResult(tester.setBranchType(BranchType.SHORT));
-    assertThat(result2.getReportComponent(result2.inputFile(FILE_PATH).key())).isNotNull();
+    assertThat(result2.getReportComponent(result2.inputFile(FILE_PATH))).isNotNull();
     assertThat(result2.getReportReader().readChangesets(fileId)).isNull();
     assertThat(result2.getReportReader().hasCoverage(fileId)).isTrue();
     assertThat(result2.getReportReader().readFileSource(fileId)).isNull();
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/branch/DeprecatedBranchMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/branch/DeprecatedBranchMediumTest.java
index bcc46d488d4..41ea161bc72 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/branch/DeprecatedBranchMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/branch/DeprecatedBranchMediumTest.java
@@ -93,7 +93,7 @@ public class DeprecatedBranchMediumTest {
     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.scannerId()).getPath()).isEqualTo("src/sample.xoo");
+    assertThat(result.getReportReader().readComponent(inputfile.scannerId()).getProjectRelativePath()).isEqualTo("src/sample.xoo");
 
     assertThat(result.getReportReader().readMetadata().getDeprecatedBranch()).isEqualTo("branch");
 
@@ -125,14 +125,11 @@ public class DeprecatedBranchMediumTest {
       .execute();
 
     assertThat(result.inputFiles()).hasSize(1);
-    assertThat(result.inputFile("moduleA/src/sample.xoo").key()).isEqualTo("com.foo.project:moduleA:src/sample.xoo");
+    assertThat(result.inputFile("moduleA/src/sample.xoo").key()).isEqualTo("com.foo.project:moduleA/src/sample.xoo");
 
     // no branch in the report
     DefaultInputFile inputfile = (DefaultInputFile) result.inputFile("moduleA/src/sample.xoo");
-    assertThat(result.getReportReader().readComponent(inputfile.scannerId()).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().readComponent(inputfile.scannerId()).getProjectRelativePath()).isEqualTo("moduleA/src/sample.xoo");
 
     assertThat(result.getReportReader().readMetadata().getDeprecatedBranch()).isEqualTo("branch");
 
@@ -145,7 +142,7 @@ public class DeprecatedBranchMediumTest {
       .execute();
 
     assertThat(result.inputFiles()).hasSize(1);
-    assertThat(result.inputFile("moduleA/src/sample.xoo").key()).isEqualTo("com.foo.project:moduleA:src/sample.xoo");
+    assertThat(result.inputFile("moduleA/src/sample.xoo").key()).isEqualTo("com.foo.project:moduleA/src/sample.xoo");
   }
 
 }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/coverage/CoverageMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/coverage/CoverageMediumTest.java
index f230f2b8bf8..1417262c3f9 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/coverage/CoverageMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/coverage/CoverageMediumTest.java
@@ -330,14 +330,14 @@ public class CoverageMediumTest {
 
     Map<String, List<org.sonar.scanner.protocol.output.ScannerReport.Measure>> allMeasures = result.allMeasures();
 
-    assertThat(allMeasures.get("com.foo.project:module1:src/sample1.xoo")).extracting("metricKey", "intValue.value")
+    assertThat(allMeasures.get("com.foo.project:module1/src/sample1.xoo")).extracting("metricKey", "intValue.value")
       .contains(tuple(CoreMetrics.LINES_TO_COVER_KEY, 2),
         tuple(CoreMetrics.UNCOVERED_LINES_KEY, 2));
 
-    assertThat(allMeasures.get("com.foo.project:module1:src/sample1.xoo")).extracting("metricKey").doesNotContain(CoreMetrics.CONDITIONS_TO_COVER_KEY,
+    assertThat(allMeasures.get("com.foo.project:module1/src/sample1.xoo")).extracting("metricKey").doesNotContain(CoreMetrics.CONDITIONS_TO_COVER_KEY,
       CoreMetrics.UNCOVERED_CONDITIONS_KEY);
 
-    assertThat(allMeasures.get("com.foo.project:module1:src/sample2.xoo")).extracting("metricKey").doesNotContain(CoreMetrics.LINES_TO_COVER_KEY,
+    assertThat(allMeasures.get("com.foo.project:module1/src/sample2.xoo")).extracting("metricKey").doesNotContain(CoreMetrics.LINES_TO_COVER_KEY,
       CoreMetrics.CONDITIONS_TO_COVER_KEY,
       CoreMetrics.UNCOVERED_CONDITIONS_KEY, CoreMetrics.UNCOVERED_LINES_KEY);
   }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/cpd/CpdMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/cpd/CpdMediumTest.java
index 6ce98f526ac..e31dfbb1b4e 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/cpd/CpdMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/cpd/CpdMediumTest.java
@@ -125,7 +125,7 @@ public class CpdMediumTest {
     assertThat(cloneGroupFile1.getOriginPosition().getStartLine()).isEqualTo(1);
     assertThat(cloneGroupFile1.getOriginPosition().getEndLine()).isEqualTo(17);
     assertThat(cloneGroupFile1.getDuplicateList()).hasSize(1);
-    assertThat(cloneGroupFile1.getDuplicate(0).getOtherFileRef()).isEqualTo(result.getReportComponent((inputFile2).key()).getRef());
+    assertThat(cloneGroupFile1.getDuplicate(0).getOtherFileRef()).isEqualTo(result.getReportComponent(inputFile2).getRef());
 
     List<ScannerReport.Duplication> duplicationGroupsFile2 = result.duplicationsFor(inputFile2);
     assertThat(duplicationGroupsFile2).hasSize(1);
@@ -134,7 +134,7 @@ public class CpdMediumTest {
     assertThat(cloneGroupFile2.getOriginPosition().getStartLine()).isEqualTo(1);
     assertThat(cloneGroupFile2.getOriginPosition().getEndLine()).isEqualTo(17);
     assertThat(cloneGroupFile2.getDuplicateList()).hasSize(1);
-    assertThat(cloneGroupFile2.getDuplicate(0).getOtherFileRef()).isEqualTo(result.getReportComponent((inputFile1).key()).getRef());
+    assertThat(cloneGroupFile2.getDuplicate(0).getOtherFileRef()).isEqualTo(result.getReportComponent(inputFile1).getRef());
 
     assertThat(result.duplicationBlocksFor(inputFile1)).isEmpty();
   }
@@ -177,7 +177,7 @@ public class CpdMediumTest {
     assertThat(cloneGroupFile1.getOriginPosition().getStartLine()).isEqualTo(1);
     assertThat(cloneGroupFile1.getOriginPosition().getEndLine()).isEqualTo(17);
     assertThat(cloneGroupFile1.getDuplicateList()).hasSize(1);
-    assertThat(cloneGroupFile1.getDuplicate(0).getOtherFileRef()).isEqualTo(result.getReportComponent((inputFile2).key()).getRef());
+    assertThat(cloneGroupFile1.getDuplicate(0).getOtherFileRef()).isEqualTo(result.getReportComponent(inputFile2).getRef());
 
     List<ScannerReport.Duplication> duplicationGroupsFile2 = result.duplicationsFor(inputFile2);
     assertThat(duplicationGroupsFile2).hasSize(1);
@@ -186,7 +186,7 @@ public class CpdMediumTest {
     assertThat(cloneGroupFile2.getOriginPosition().getStartLine()).isEqualTo(1);
     assertThat(cloneGroupFile2.getOriginPosition().getEndLine()).isEqualTo(17);
     assertThat(cloneGroupFile2.getDuplicateList()).hasSize(1);
-    assertThat(cloneGroupFile2.getDuplicate(0).getOtherFileRef()).isEqualTo(result.getReportComponent((inputFile1).key()).getRef());
+    assertThat(cloneGroupFile2.getDuplicate(0).getOtherFileRef()).isEqualTo(result.getReportComponent(inputFile1).getRef());
 
     assertThat(result.duplicationBlocksFor(inputFile1)).isEmpty();
   }
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 a8e84a6faf2..705692a6777 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
@@ -25,7 +25,6 @@ import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.Random;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang.StringUtils;
@@ -34,10 +33,8 @@ import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
 import org.junit.rules.TemporaryFolder;
-import org.sonar.api.batch.fs.InputDir;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
-import org.sonar.api.scanner.fs.InputProject;
 import org.sonar.api.utils.MessageException;
 import org.sonar.api.utils.System2;
 import org.sonar.scanner.mediumtest.AnalysisResult;
@@ -112,19 +109,15 @@ public class FileSystemMediumTest {
     int ref = result.getReportReader().readMetadata().getRootComponentRef();
     assertThat(result.getReportReader().readComponent(ref).getName()).isEmpty();
     assertThat(result.inputFiles()).hasSize(1);
-    assertThat(result.inputDirs()).hasSize(1);
 
     DefaultInputFile file = (DefaultInputFile) result.inputFile("src/sample.xoo");
-    InputDir dir = result.inputDir("src");
     assertThat(file.type()).isEqualTo(InputFile.Type.MAIN);
     assertThat(file.relativePath()).isEqualTo("src/sample.xoo");
     assertThat(file.language()).isEqualTo("xoo");
-    assertThat(dir.relativePath()).isEqualTo("src");
 
-    // file and dirs were published, since language matched xoo
+    // file was published, since language matched xoo
     assertThat(file.isPublished()).isTrue();
-    assertThat(result.getReportComponent(dir.key())).isNotNull();
-    assertThat(result.getReportComponent(file.key())).isNotNull();
+    assertThat(result.getReportComponent(file.scannerId())).isNotNull();
   }
 
   @Test
@@ -290,7 +283,11 @@ public class FileSystemMediumTest {
     assertThat(logs.getAllAsString()).doesNotContain("'src/main/sample.java' generated metadata");
     assertThat(logs.getAllAsString()).doesNotContain("'src/test/sample.java' generated metadata");
     DefaultInputFile javaInputFile = (DefaultInputFile) result.inputFile("src/main/sample.java");
-    assertThat(result.getReportComponent(javaInputFile.key())).isNull();
+
+    thrown.expect(IllegalStateException.class);
+    thrown.expectMessage("Unable to find report for component");
+
+    result.getReportComponent(javaInputFile);
   }
 
   @Test
@@ -317,7 +314,7 @@ public class FileSystemMediumTest {
     assertThat(logs.getAllAsString()).contains("'src" + File.separator + "sample.unknown' indexed with language 'null'");
     assertThat(logs.getAllAsString()).contains("'src/sample.unknown' generated metadata");
     DefaultInputFile inputFile = (DefaultInputFile) result.inputFile("src/sample.unknown");
-    assertThat(result.getReportComponent(inputFile.key())).isNotNull();
+    assertThat(result.getReportComponent(inputFile)).isNotNull();
   }
 
   @Test
@@ -397,54 +394,9 @@ public class FileSystemMediumTest {
       .execute();
 
     DefaultInputFile file = (DefaultInputFile) result.inputFile("src/sample.xoo");
-    InputDir dir = result.inputDir("src");
 
     assertThat(file.isPublished()).isTrue();
-    assertThat(result.getReportComponent(dir.key())).isNotNull();
-    assertThat(result.getReportComponent(file.key())).isNotNull();
-  }
-
-  @Test
-  public void publishDirsWithIssues() throws IOException {
-    tester
-      .addRules(new XooRulesDefinition())
-      .addActiveRule("xoo", "OneIssuePerDirectory", null, "OneIssuePerDirectory", "MAJOR", null, "xoo");
-
-    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")
-      .put("sonar.projectDescription", "Description of Foo Project");
-
-    Path unknownRelative = Paths.get("src", "unknown", "file.notanalyzed");
-    Path unknown = baseDir.toPath().resolve(unknownRelative);
-    Files.createDirectories(unknown.getParent());
-    Files.write(unknown, "dummy content".getBytes());
-
-    Path emptyDirRelative = Paths.get("src", "emptydir");
-    Files.createDirectories(emptyDirRelative);
-
-    AnalysisResult result = tester.newAnalysis()
-      .properties(builder
-        .put("sonar.sources", "src")
-        .build())
-      .execute();
-
-    DefaultInputFile unknownInputFile = (DefaultInputFile) result.inputFile("src/unknown/file.notanalyzed");
-    InputProject project = result.project();
-
-    assertThat(unknownInputFile.isPublished()).isFalse();
-    assertThat(result.getReportComponent(project.key())).isNotNull();
-
-    // no issues on empty dir
-    InputDir emptyInputDir = result.inputDir(emptyDirRelative.toString());
-    assertThat(emptyInputDir).isNull();
-
-    // no issues on parent dir
-    InputDir parentInputDir = result.inputDir(unknownRelative.getParent().getParent().toString());
-    assertThat(parentInputDir).isNull();
+    assertThat(result.getReportComponent(file)).isNotNull();
   }
 
   @Test
@@ -462,10 +414,8 @@ public class FileSystemMediumTest {
       .execute();
 
     assertThat(result.inputFiles()).hasSize(1);
-    assertThat(result.inputDirs()).hasSize(1);
     assertThat(result.inputFile("src/sample.xoo").type()).isEqualTo(InputFile.Type.MAIN);
     assertThat(result.inputFile("src/sample.xoo").relativePath()).isEqualTo("src/sample.xoo");
-    assertThat(result.inputDir("src").relativePath()).isEqualTo("src");
   }
 
   @Test
@@ -487,7 +437,6 @@ public class FileSystemMediumTest {
       .execute();
 
     assertThat(result.inputFiles()).hasSize(100);
-    assertThat(result.inputDirs()).hasSize(1);
   }
 
   @Test
@@ -540,7 +489,6 @@ public class FileSystemMediumTest {
       .execute();
 
     assertThat(result.inputFiles()).hasSize(4);
-    assertThat(result.inputDirs()).hasSize(3);
   }
 
   @Test
@@ -680,7 +628,6 @@ public class FileSystemMediumTest {
       .execute();
 
     assertThat(result.inputFiles()).hasSize(4);
-    assertThat(result.inputDirs()).hasSize(4);
   }
 
   @Test
@@ -727,7 +674,6 @@ public class FileSystemMediumTest {
       .execute();
 
     assertThat(result.inputFiles()).hasSize(4);
-    assertThat(result.inputDirs()).hasSize(3);
   }
 
   @Test
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issues/IssuesOnDirMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issues/IssuesOnDirMediumTest.java
index ed76bba6c25..e09f0b42967 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issues/IssuesOnDirMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issues/IssuesOnDirMediumTest.java
@@ -70,7 +70,6 @@ public class IssuesOnDirMediumTest {
         .build())
       .execute();
 
-    assertThat(result.issuesFor(result.inputDir("src"))).hasSize(0);
     assertThat(result.issuesFor(result.project())).hasSize(2);
   }
 
@@ -97,7 +96,6 @@ public class IssuesOnDirMediumTest {
         .build())
       .execute();
 
-    assertThat(result.issuesFor(result.inputDir(""))).hasSize(0);
     assertThat(result.issuesFor(result.project())).hasSize(2);
   }
 
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issues/IssuesOnModuleMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issues/IssuesOnModuleMediumTest.java
index 48561c72e0a..5c8fa0d92e1 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issues/IssuesOnModuleMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/issues/IssuesOnModuleMediumTest.java
@@ -67,7 +67,7 @@ public class IssuesOnModuleMediumTest {
         .build())
       .execute();
 
-    assertThat(result.issuesFor(result.getReportComponent("com.foo.project"))).hasSize(1);
+    assertThat(result.issuesFor(result.project())).hasSize(1);
   }
 
 }
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 cb29125779c..2e58d577288 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
@@ -147,7 +147,7 @@ public class IssueModeAndReportsMediumTest {
     String logs = StringUtils.join(logTester.logs(LoggerLevel.INFO), "\n");
 
     assertThat(logs).contains("Performing issue tracking");
-    assertThat(logs).contains("6/6 components tracked");
+    assertThat(logs).contains("4/4 components tracked");
 
     // assert that original fields of a matched issue are kept
     assertThat(result.trackedIssues()).haveExactly(1, new Condition<TrackedIssue>() {
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/scm/ScmMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/scm/ScmMediumTest.java
index 5b42f3e016c..94f6030b3e6 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/scm/ScmMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/scm/ScmMediumTest.java
@@ -116,10 +116,9 @@ public class ScmMediumTest {
     ScannerReportReader reader = new ScannerReportReader(reportDir);
 
     Component project = reader.readComponent(reader.readMetadata().getRootComponentRef());
-    Component dir = reader.readComponent(project.getChildRef(0));
-    for (Integer fileRef : dir.getChildRefList()) {
+    for (Integer fileRef : project.getChildRefList()) {
       Component file = reader.readComponent(fileRef);
-      if (file.getPath().equals(path)) {
+      if (file.getProjectRelativePath().equals(path)) {
         return reader.readChangesets(file.getRef());
       }
     }
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 245fe2cefc1..3d45aa214d8 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
@@ -87,7 +87,7 @@ public class DefaultPostJobContextTest {
     assertThat(issue.inputComponent()).isNull();
 
     String moduleKey = "foo";
-    componentStore.put(new TestInputFileBuilder(moduleKey, "src/Foo.php").build());
+    componentStore.put(moduleKey, new TestInputFileBuilder(moduleKey, "src/Foo.php").build());
     assertThat(issue.inputComponent()).isNotNull();
 
   }
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 4b27f676ae9..e13bc24a9d0 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
@@ -21,12 +21,8 @@ package org.sonar.scanner.report;
 
 import java.io.File;
 import java.io.IOException;
-import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.Arrays;
 import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
 import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
@@ -35,10 +31,8 @@ import org.sonar.api.CoreProperties;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.fs.InputFile;
 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.DefaultInputProject;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.api.utils.DateUtils;
 import org.sonar.scanner.ProjectAnalysisInfo;
@@ -49,24 +43,17 @@ import org.sonar.scanner.protocol.output.ScannerReport.Component.FileStatus;
 import org.sonar.scanner.protocol.output.ScannerReport.ComponentLink.ComponentLinkType;
 import org.sonar.scanner.protocol.output.ScannerReportReader;
 import org.sonar.scanner.protocol.output.ScannerReportWriter;
-import org.sonar.scanner.scan.DefaultComponentTree;
-import org.sonar.scanner.scan.DefaultInputModuleHierarchy;
 import org.sonar.scanner.scan.branch.BranchConfiguration;
-import org.sonar.scanner.scan.branch.BranchType;
+import org.sonar.scanner.scan.filesystem.InputComponentStore;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
-import static org.sonar.api.batch.fs.internal.TestInputFileBuilder.newDefaultInputDir;
-import static org.sonar.api.batch.fs.internal.TestInputFileBuilder.newDefaultInputFile;
-import static org.sonar.api.batch.fs.internal.TestInputFileBuilder.newDefaultInputModule;
 
 public class ComponentsPublisherTest {
   @Rule
   public TemporaryFolder temp = new TemporaryFolder();
 
-  private DefaultComponentTree tree;
-  private InputModuleHierarchy moduleHierarchy;
   private File outputDir;
   private ScannerReportWriter writer;
   private ScannerReportReader reader;
@@ -75,7 +62,6 @@ public class ComponentsPublisherTest {
   @Before
   public void setUp() throws IOException {
     branchConfiguration = mock(BranchConfiguration.class);
-    tree = new DefaultComponentTree();
     outputDir = temp.newFolder();
     writer = new ScannerReportWriter(outputDir);
     reader = new ScannerReportReader(outputDir);
@@ -97,7 +83,9 @@ public class ComponentsPublisherTest {
       .setDescription("Root description")
       .setBaseDir(temp.newFolder())
       .setWorkDir(temp.newFolder());
-    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
+    DefaultInputProject project = new DefaultInputProject(rootDef, 1);
+
+    InputComponentStore store = new InputComponentStore(project, branchConfiguration);
 
     Path moduleBaseDir = temp.newFolder().toPath();
     ProjectDefinition module1Def = ProjectDefinition.create()
@@ -108,43 +96,25 @@ public class ComponentsPublisherTest {
       .setWorkDir(temp.newFolder());
     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));
-    when(moduleHierarchy.parent(module1)).thenReturn(root);
-    tree.index(module1, root);
-
-    DefaultInputDir dir = new DefaultInputDir("module1", "src", 3)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir, module1);
-
-    DefaultInputDir dir2 = new DefaultInputDir("module1", "src2", 17)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir2, module1);
+    DefaultInputFile file = new TestInputFileBuilder("foo", "module1/src/Foo.java", 4).setLines(2).setStatus(InputFile.Status.SAME).build();
+    store.put("module1", file);
 
-    DefaultInputFile file = new TestInputFileBuilder("module1", "src/Foo.java", 4).setLines(2).setStatus(InputFile.Status.SAME).build();
-    tree.index(file, dir);
+    DefaultInputFile file18 = new TestInputFileBuilder("foo", "module1/src2/Foo.java", 18).setLines(2).setStatus(InputFile.Status.SAME).build();
+    store.put("module1", file18);
 
-    DefaultInputFile file18 = new TestInputFileBuilder("module1", "src2/Foo.java", 18).setLines(2).setStatus(InputFile.Status.SAME).build();
-    tree.index(file18, dir2);
+    DefaultInputFile file2 = new TestInputFileBuilder("foo", "module1/src/Foo2.java", 5).setPublish(false).setLines(2).build();
+    store.put("module1", file2);
 
-    DefaultInputFile file2 = new TestInputFileBuilder("module1", "src/Foo2.java", 5).setPublish(false).setLines(2).build();
-    tree.index(file2, dir);
+    DefaultInputFile fileWithoutLang = new TestInputFileBuilder("foo", "module1/src/make", 6).setLines(10).setStatus(InputFile.Status.CHANGED).build();
+    store.put("module1", fileWithoutLang);
 
-    DefaultInputFile fileWithoutLang = new TestInputFileBuilder("module1", "src/make", 6).setLines(10).setStatus(InputFile.Status.CHANGED).build();
-    tree.index(fileWithoutLang, dir);
+    DefaultInputFile testFile = new TestInputFileBuilder("foo", "module1/test/FooTest.java", 7).setType(Type.TEST).setStatus(InputFile.Status.ADDED).setLines(4).build();
+    store.put("module1", testFile);
 
-    DefaultInputFile testFile = new TestInputFileBuilder("module1", "test/FooTest.java", 7).setType(Type.TEST).setStatus(InputFile.Status.ADDED).setLines(4).build();
-    tree.index(testFile, dir);
-
-    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree, branchConfiguration);
+    ComponentsPublisher publisher = new ComponentsPublisher(project, store);
     publisher.publish(writer);
 
     assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 1)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 2)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 3)).isTrue();
     assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 4)).isTrue();
     assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 6)).isTrue();
     assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 7)).isTrue();
@@ -161,11 +131,6 @@ public class ComponentsPublisherTest {
     assertThat(rootProtobuf.getVersion()).isEqualTo("1.0");
     assertThat(rootProtobuf.getLinkCount()).isEqualTo(0);
 
-    Component module1Protobuf = reader.readComponent(2);
-    assertThat(module1Protobuf.getKey()).isEqualTo("module1");
-    assertThat(module1Protobuf.getDescription()).isEqualTo("Module description");
-    assertThat(module1Protobuf.getVersion()).isEqualTo("1.0");
-
     assertThat(reader.readComponent(4).getStatus()).isEqualTo(FileStatus.SAME);
     assertThat(reader.readComponent(6).getStatus()).isEqualTo(FileStatus.CHANGED);
     assertThat(reader.readComponent(7).getStatus()).isEqualTo(FileStatus.ADDED);
@@ -183,12 +148,11 @@ public class ComponentsPublisherTest {
       .setWorkDir(temp.newFolder())
       .setProperty(CoreProperties.PROJECT_BRANCH_PROPERTY, "my_branch");
 
-    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
+    DefaultInputProject project = new DefaultInputProject(rootDef, 1);
 
-    moduleHierarchy = mock(InputModuleHierarchy.class);
-    when(moduleHierarchy.root()).thenReturn(root);
+    InputComponentStore store = new InputComponentStore(project, branchConfiguration);
 
-    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree, branchConfiguration);
+    ComponentsPublisher publisher = new ComponentsPublisher(project, store);
     publisher.publish(writer);
     Component rootProtobuf = reader.readComponent(1);
     assertThat(rootProtobuf.getKey()).isEqualTo("foo");
@@ -196,311 +160,48 @@ public class ComponentsPublisherTest {
   }
 
   @Test
-  public void should_write_relative_path_to_root_for_modules_in_flat_hierarchy() throws IOException {
-    Path rootBaseDir = temp.newFolder().toPath();
-    Path module1BaseDir = rootBaseDir.resolve("module1");
-    Path module2BaseDir = rootBaseDir.resolve("module2");
-    Files.createDirectories(module1BaseDir);
-    Files.createDirectories(module2BaseDir);
-
-    ProjectDefinition rootDef = ProjectDefinition.create()
-      .setKey("foo")
-      .setProperty(CoreProperties.PROJECT_VERSION_PROPERTY, "1.0")
-      .setName("Root project")
-      .setDescription("Root description")
-      .setBaseDir(rootBaseDir.toFile())
-      .setWorkDir(temp.newFolder());
-    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
-
-    ProjectDefinition module1Def = ProjectDefinition.create()
-      .setKey("module1k")
-      .setName("Module1")
-      .setDescription("Module description")
-      .setBaseDir(module1BaseDir.toFile())
-      .setWorkDir(temp.newFolder());
-    rootDef.addSubProject(module1Def);
-    DefaultInputModule module1 = new DefaultInputModule(module1Def, 2);
-
-    ProjectDefinition module2Def = ProjectDefinition.create()
-      .setKey("module2k")
-      .setName("Module2")
-      .setDescription("Module description")
-      .setBaseDir(module2BaseDir.toFile())
-      .setWorkDir(temp.newFolder());
-    module1Def.addSubProject(module2Def);
-    DefaultInputModule module2 = new DefaultInputModule(module2Def, 3);
-
-    Map<DefaultInputModule, DefaultInputModule> modules = new HashMap<>();
-    modules.put(module2, module1);
-    modules.put(module1, root);
-    moduleHierarchy = new DefaultInputModuleHierarchy(root, modules);
-    tree.index(module2, module1);
-    tree.index(module1, root);
-    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree, branchConfiguration);
-    publisher.publish(writer);
-
-    assertThat(reader.readComponent(2).getProjectRelativePath()).isEqualTo("module1");
-    assertThat(reader.readComponent(3).getProjectRelativePath()).isEqualTo("module2");
-  }
-
-  @Test
-  public void should_skip_dir_without_published_files() throws IOException {
-    ProjectAnalysisInfo projectAnalysisInfo = mock(ProjectAnalysisInfo.class);
-    when(projectAnalysisInfo.analysisDate()).thenReturn(DateUtils.parseDate("2012-12-12"));
-
-    Path moduleBaseDir = temp.newFolder().toPath();
-    ProjectDefinition rootDef = ProjectDefinition.create()
-      .setKey("foo")
-      .setProperty(CoreProperties.PROJECT_VERSION_PROPERTY, "1.0")
-      .setName("Root project")
-      .setDescription("Root description")
-      .setBaseDir(moduleBaseDir.toFile())
-      .setWorkDir(temp.newFolder());
-    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
-
-    moduleHierarchy = mock(InputModuleHierarchy.class);
-    when(moduleHierarchy.root()).thenReturn(root);
-    when(moduleHierarchy.children(root)).thenReturn(Collections.emptyList());
-
-    // dir with files
-    DefaultInputDir dir = new DefaultInputDir("module1", "src", 2)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir, root);
-
-    // dir without files and issues
-    DefaultInputDir dir2 = new DefaultInputDir("module1", "src2", 3)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir2, root);
-
-    // dir without files but has issues
-    DefaultInputDir dir3 = new DefaultInputDir("module1", "src3", 4)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir3, root);
-    writeIssue(4);
-
-    DefaultInputFile file = new TestInputFileBuilder("module1", "src/Foo.java", 5).setLines(2).setStatus(InputFile.Status.SAME).build();
-    tree.index(file, dir);
-
-    DefaultInputFile file2 = new TestInputFileBuilder("module1", "src2/Foo2.java", 6).setPublish(false).setLines(2).build();
-    tree.index(file2, dir2);
-
-    DefaultInputFile file3 = new TestInputFileBuilder("module1", "src2/Foo3.java", 7).setPublish(false).setLines(2).build();
-    tree.index(file3, dir3);
-
-    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree, branchConfiguration);
-    publisher.publish(writer);
-
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 1)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 2)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 5)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 4)).isTrue();
-
-    // file was not marked for publishing and directory doesn't contain issues, so directory won't be included as well
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 3)).isFalse();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 6)).isFalse();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 7)).isFalse();
-  }
-
-  @Test
-  public void should_skip_empty_modules_for_short_living_branches() throws IOException {
-    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")
-      .setBaseDir(temp.newFolder())
-      .setWorkDir(temp.newFolder());
-    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
-
-    ProjectDefinition emptyModuleDef = ProjectDefinition.create()
-      .setKey("modEmpty")
-      .setProperty(CoreProperties.PROJECT_VERSION_PROPERTY, "1.0")
-      .setName("Empty module")
-      .setDescription("Empty module")
-      .setBaseDir(temp.newFolder())
-      .setWorkDir(temp.newFolder());
-    DefaultInputModule emptyModule = new DefaultInputModule(emptyModuleDef, 2);
-
-    ProjectDefinition notEmptyModuleDef = ProjectDefinition.create()
-      .setKey("modNotEmpty")
-      .setProperty(CoreProperties.PROJECT_VERSION_PROPERTY, "1.0")
-      .setName("Module")
-      .setDescription("Module")
-      .setBaseDir(temp.newFolder())
-      .setWorkDir(temp.newFolder());
-    DefaultInputModule notEmptyModule = new DefaultInputModule(notEmptyModuleDef, 3);
-
-    moduleHierarchy = mock(InputModuleHierarchy.class);
-    when(moduleHierarchy.root()).thenReturn(root);
-    when(moduleHierarchy.isRoot(root)).thenReturn(true);
-    when(moduleHierarchy.children(root)).thenReturn(Arrays.asList(emptyModule, notEmptyModule));
-    when(moduleHierarchy.children(emptyModule)).thenReturn(Collections.emptyList());
-    when(moduleHierarchy.children(notEmptyModule)).thenReturn(Collections.emptyList());
-    when(branchConfiguration.branchType()).thenReturn(BranchType.SHORT);
-
-    // dir with files
-    DefaultInputDir dir = new DefaultInputDir("modNotEmpty", "src", 4);
-    tree.index(dir, notEmptyModule);
-
-    // Only an unchanged file, so module should also be skipped
-    DefaultInputFile file = new TestInputFileBuilder("modNotEmpty", "src/Foo.java", 5).setLines(2).setStatus(InputFile.Status.SAME).build();
-    tree.index(file, dir);
-
-    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree, branchConfiguration);
-    publisher.publish(writer);
-
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 1)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 2)).isFalse();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 3)).isFalse();
-  }
-
-  @Test
-  public void do_not_skip_unchanged_components_in_short_branches() throws IOException {
-    when(branchConfiguration.isShortOrPullRequest()).thenReturn(true);
-    ProjectAnalysisInfo projectAnalysisInfo = mock(ProjectAnalysisInfo.class);
-    when(projectAnalysisInfo.analysisDate()).thenReturn(DateUtils.parseDate("2012-12-12"));
-
-    Path moduleBaseDir = temp.newFolder().toPath();
-    ProjectDefinition rootDef = ProjectDefinition.create()
-      .setKey("foo")
-      .setProperty(CoreProperties.PROJECT_VERSION_PROPERTY, "1.0")
-      .setName("Root project")
-      .setDescription("Root description")
-      .setBaseDir(moduleBaseDir.toFile())
-      .setWorkDir(temp.newFolder());
-    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
-
-    moduleHierarchy = mock(InputModuleHierarchy.class);
-    when(moduleHierarchy.root()).thenReturn(root);
-    when(moduleHierarchy.children(root)).thenReturn(Collections.emptyList());
-
-    // dir with changed files
-    DefaultInputDir dir = new DefaultInputDir("module1", "src", 2)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir, root);
-
-    // dir without changed files or issues
-    DefaultInputDir dir2 = new DefaultInputDir("module1", "src2", 3)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir2, root);
-
-    // dir without changed files but has issues
-    DefaultInputDir dir3 = new DefaultInputDir("module1", "src3", 4)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir3, root);
-    writeIssue(4);
-
-    DefaultInputFile file = new TestInputFileBuilder("module1", "src/Foo.java", 5)
-      .setLines(2)
-      .setPublish(true)
-      .setStatus(InputFile.Status.ADDED)
-      .build();
-    tree.index(file, dir);
-
-    DefaultInputFile file2 = new TestInputFileBuilder("module1", "src2/Foo2.java", 6)
-      .setPublish(true)
-      .setStatus(InputFile.Status.SAME)
-      .setLines(2)
-      .build();
-    tree.index(file2, dir2);
-
-    DefaultInputFile file3 = new TestInputFileBuilder("module1", "src3/Foo3.java", 7)
-      .setPublish(true)
-      .setStatus(InputFile.Status.SAME)
-      .setLines(2)
-      .build();
-    tree.index(file3, dir3);
-
-    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree, branchConfiguration);
-    publisher.publish(writer);
-
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 1)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 2)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 4)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 5)).isTrue();
-
-    // do not skip, needed for computing overall coverage
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 3)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 6)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 7)).isTrue();
-  }
-
-  @Test
-  public void do_not_skip_unchanged_components_in_pull_requests() throws IOException {
+  public void publish_unchanged_components_even_in_short_branches() throws IOException {
     when(branchConfiguration.isShortOrPullRequest()).thenReturn(true);
     ProjectAnalysisInfo projectAnalysisInfo = mock(ProjectAnalysisInfo.class);
     when(projectAnalysisInfo.analysisDate()).thenReturn(DateUtils.parseDate("2012-12-12"));
 
-    Path moduleBaseDir = temp.newFolder().toPath();
+    Path baseDir = temp.newFolder().toPath();
     ProjectDefinition rootDef = ProjectDefinition.create()
       .setKey("foo")
       .setProperty(CoreProperties.PROJECT_VERSION_PROPERTY, "1.0")
       .setName("Root project")
       .setDescription("Root description")
-      .setBaseDir(moduleBaseDir.toFile())
+      .setBaseDir(baseDir.toFile())
       .setWorkDir(temp.newFolder());
-    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
-
-    moduleHierarchy = mock(InputModuleHierarchy.class);
-    when(moduleHierarchy.root()).thenReturn(root);
-    when(moduleHierarchy.children(root)).thenReturn(Collections.emptyList());
-
-    // dir with changed files
-    DefaultInputDir dir = new DefaultInputDir("module1", "src", 2)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir, root);
-
-    // dir without changed files or issues
-    DefaultInputDir dir2 = new DefaultInputDir("module1", "src2", 3)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir2, root);
+    DefaultInputProject project = new DefaultInputProject(rootDef, 1);
 
-    // dir without changed files but has issues
-    DefaultInputDir dir3 = new DefaultInputDir("module1", "src3", 4)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir3, root);
-    writeIssue(4);
+    InputComponentStore store = new InputComponentStore(project, branchConfiguration);
 
-    DefaultInputFile file = new TestInputFileBuilder("module1", "src/Foo.java", 5)
+    DefaultInputFile file = new TestInputFileBuilder("foo", "src/Foo.java", 5)
       .setLines(2)
       .setPublish(true)
       .setStatus(InputFile.Status.ADDED)
       .build();
-    tree.index(file, dir);
+    store.put("foo", file);
 
-    DefaultInputFile file2 = new TestInputFileBuilder("module1", "src2/Foo2.java", 6)
+    DefaultInputFile file2 = new TestInputFileBuilder("foo", "src2/Foo2.java", 6)
       .setPublish(true)
       .setStatus(InputFile.Status.SAME)
       .setLines(2)
       .build();
-    tree.index(file2, dir2);
+    store.put("foo", file2);
 
-    DefaultInputFile file3 = new TestInputFileBuilder("module1", "src3/Foo3.java", 7)
-      .setPublish(true)
-      .setStatus(InputFile.Status.SAME)
-      .setLines(2)
-      .build();
-    tree.index(file3, dir3);
-
-    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree, branchConfiguration);
+    ComponentsPublisher publisher = new ComponentsPublisher(project, store);
     publisher.publish(writer);
 
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 1)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 2)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 4)).isTrue();
     assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 5)).isTrue();
 
     // do not skip, needed for computing overall coverage
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 3)).isTrue();
     assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 6)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 7)).isTrue();
   }
 
   @Test
-  public void add_components_without_version_and_name() throws IOException {
+  public void publish_project_without_version_and_name() throws IOException {
     ProjectAnalysisInfo projectAnalysisInfo = mock(ProjectAnalysisInfo.class);
     when(projectAnalysisInfo.analysisDate()).thenReturn(DateUtils.parseDate("2012-12-12"));
 
@@ -509,47 +210,13 @@ public class ComponentsPublisherTest {
       .setDescription("Root description")
       .setBaseDir(temp.newFolder())
       .setWorkDir(temp.newFolder());
-    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
-
-    Path moduleBaseDir = temp.newFolder().toPath();
-    ProjectDefinition module1Def = ProjectDefinition.create()
-      .setKey("module1")
-      .setDescription("Module description")
-      .setBaseDir(moduleBaseDir.toFile())
-      .setWorkDir(temp.newFolder());
-    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)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir, module1);
-
-    DefaultInputFile file = new TestInputFileBuilder("module1", "src/Foo.java", 4).setLines(2).setStatus(InputFile.Status.SAME).build();
-    tree.index(file, dir);
-
-    DefaultInputFile fileWithoutLang = new TestInputFileBuilder("module1", "src/make", 5).setLines(10).setStatus(InputFile.Status.SAME).build();
-    tree.index(fileWithoutLang, dir);
+    DefaultInputProject project = new DefaultInputProject(rootDef, 1);
 
-    DefaultInputFile testFile = new TestInputFileBuilder("module1", "test/FooTest.java", 6).setType(Type.TEST).setStatus(InputFile.Status.SAME).setLines(4).build();
-    tree.index(testFile, dir);
-
-    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree, branchConfiguration);
+    InputComponentStore store = new InputComponentStore(project, branchConfiguration);
+    ComponentsPublisher publisher = new ComponentsPublisher(project, store);
     publisher.publish(writer);
 
     assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 1)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 2)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 3)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 4)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 5)).isTrue();
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 6)).isTrue();
-
-    // no such reference
-    assertThat(writer.hasComponentData(FileStructure.Domain.COMPONENT, 7)).isFalse();
 
     ScannerReportReader reader = new ScannerReportReader(outputDir);
     Component rootProtobuf = reader.readComponent(1);
@@ -558,16 +225,10 @@ public class ComponentsPublisherTest {
     assertThat(rootProtobuf.getDescription()).isEqualTo("Root description");
     assertThat(rootProtobuf.getVersion()).isEqualTo("");
     assertThat(rootProtobuf.getLinkCount()).isEqualTo(0);
-
-    Component module1Protobuf = reader.readComponent(2);
-    assertThat(module1Protobuf.getKey()).isEqualTo("module1");
-    assertThat(module1Protobuf.getName()).isEqualTo("");
-    assertThat(module1Protobuf.getDescription()).isEqualTo("Module description");
-    assertThat(module1Protobuf.getVersion()).isEqualTo("");
   }
 
   @Test
-  public void add_components_with_links_and_branch() throws Exception {
+  public void publish_project_with_links_and_branch() throws Exception {
     ProjectAnalysisInfo projectAnalysisInfo = mock(ProjectAnalysisInfo.class);
     when(projectAnalysisInfo.analysisDate()).thenReturn(DateUtils.parseDate("2012-12-12"));
 
@@ -577,156 +238,23 @@ public class ComponentsPublisherTest {
       .setProperty(CoreProperties.PROJECT_BRANCH_PROPERTY, "my_branch")
       .setName("Root project")
       .setProperty(CoreProperties.LINKS_HOME_PAGE, "http://home")
+      .setProperty(CoreProperties.LINKS_CI, "http://ci")
       .setDescription("Root description")
       .setBaseDir(temp.newFolder())
       .setWorkDir(temp.newFolder());
-    DefaultInputModule root = new DefaultInputModule(rootDef, 1);
-
-    Path moduleBaseDir = temp.newFolder().toPath();
-    ProjectDefinition module1Def = ProjectDefinition.create()
-      .setKey("module1")
-      .setName("Module1")
-      .setProperty(CoreProperties.LINKS_CI, "http://ci")
-      .setDescription("Module description")
-      .setBaseDir(moduleBaseDir.toFile())
-      .setWorkDir(temp.newFolder());
-    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));
-    when(moduleHierarchy.parent(module1)).thenReturn(root);
-    tree.index(module1, root);
+    DefaultInputProject project = new DefaultInputProject(rootDef, 1);
 
-    DefaultInputDir dir = new DefaultInputDir("module1", "src", 3)
-      .setModuleBaseDir(moduleBaseDir);
-    tree.index(dir, module1);
-
-    DefaultInputFile file = new TestInputFileBuilder("module1", "src/Foo.java", 4).setLines(2).setStatus(InputFile.Status.SAME).build();
-    tree.index(file, dir);
-
-    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree, branchConfiguration);
+    InputComponentStore store = new InputComponentStore(project, branchConfiguration);
+    ComponentsPublisher publisher = new ComponentsPublisher(project, store);
     publisher.publish(writer);
 
     ScannerReportReader reader = new ScannerReportReader(outputDir);
     Component rootProtobuf = reader.readComponent(1);
     assertThat(rootProtobuf.getVersion()).isEqualTo("1.0");
-    assertThat(rootProtobuf.getLinkCount()).isEqualTo(1);
+    assertThat(rootProtobuf.getLinkCount()).isEqualTo(2);
     assertThat(rootProtobuf.getLink(0).getType()).isEqualTo(ComponentLinkType.HOME);
     assertThat(rootProtobuf.getLink(0).getHref()).isEqualTo("http://home");
-
-    Component module1Protobuf = reader.readComponent(2);
-    assertThat(module1Protobuf.getVersion()).isEqualTo("1.0");
-    assertThat(module1Protobuf.getLinkCount()).isEqualTo(1);
-    assertThat(module1Protobuf.getLink(0).getType()).isEqualTo(ComponentLinkType.CI);
-    assertThat(module1Protobuf.getLink(0).getHref()).isEqualTo("http://ci");
-  }
-
-  @Test
-  public void add_components_with_correct_project_relative_path() throws Exception {
-    Map<DefaultInputModule, DefaultInputModule> parents = new HashMap<>();
-
-    DefaultInputModule root = newDefaultInputModule("foo", temp.newFolder());
-
-    DefaultInputFile file = newDefaultInputFile(root.getBaseDir(), root, "Foo.java");
-    tree.index(file, root);
-
-    DefaultInputDir dir1 = newDefaultInputDir(root, "dir1");
-    tree.index(dir1, root);
-
-    DefaultInputFile dir1_file = newDefaultInputFile(root.getBaseDir(), root, "dir1/Foo.java");
-    tree.index(dir1_file, dir1);
-
-    DefaultInputDir dir1_dir1 = newDefaultInputDir(root, "dir1/dir1");
-    tree.index(dir1_dir1, dir1);
-
-    DefaultInputFile dir1_dir1_file = newDefaultInputFile(root.getBaseDir(), root, "dir1/dir1/Foo.java");
-    tree.index(dir1_dir1_file, dir1_dir1);
-
-    // module in root
-
-    DefaultInputModule mod1 = newDefaultInputModule(root, "mod1");
-    parents.put(mod1, root);
-    tree.index(mod1, root);
-
-    DefaultInputFile mod1_file = newDefaultInputFile(root.getBaseDir(), mod1, "Foo.java");
-    tree.index(mod1_file, mod1);
-
-    DefaultInputDir mod1_dir2 = newDefaultInputDir(mod1, "dir2");
-    tree.index(mod1_dir2, mod1);
-
-    DefaultInputFile mod1_dir2_file = newDefaultInputFile(root.getBaseDir(), mod1, "dir2/Foo.java");
-    tree.index(mod1_dir2_file, mod1_dir2);
-
-    // module in module
-
-    DefaultInputModule mod1_mod2 = newDefaultInputModule(mod1, "mod2");
-    parents.put(mod1_mod2, mod1);
-    tree.index(mod1_mod2, mod1);
-
-    DefaultInputFile mod1_mod2_file = newDefaultInputFile(root.getBaseDir(), mod1_mod2, "Foo.java");
-    tree.index(mod1_mod2_file, mod1_mod2);
-
-    DefaultInputDir mod1_mod2_dir = newDefaultInputDir(mod1_mod2, "dir");
-    tree.index(mod1_mod2_dir, mod1_mod2);
-
-    DefaultInputFile mod1_mod2_dir_file = newDefaultInputFile(root.getBaseDir(), mod1_mod2, "dir/Foo.java");
-    tree.index(mod1_mod2_dir_file, mod1_mod2_dir);
-
-    moduleHierarchy = new DefaultInputModuleHierarchy(root, parents);
-
-    ComponentsPublisher publisher = new ComponentsPublisher(moduleHierarchy, tree, branchConfiguration);
-    publisher.publish(writer);
-
-    ScannerReportReader reader = new ScannerReportReader(outputDir);
-
-    // project root
-    assertThat(reader.readComponent(root.scannerId()).getPath()).isEmpty();
-    assertThat(reader.readComponent(root.scannerId()).getProjectRelativePath()).isEmpty();
-
-    // file in root
-    assertThat(reader.readComponent(file.scannerId()).getPath()).isEqualTo("Foo.java");
-    assertThat(reader.readComponent(file.scannerId()).getProjectRelativePath()).isEqualTo("Foo.java");
-
-    // dir in root
-    assertThat(reader.readComponent(dir1.scannerId()).getPath()).isEqualTo("dir1");
-    assertThat(reader.readComponent(dir1.scannerId()).getProjectRelativePath()).isEqualTo("dir1");
-
-    // file in dir in root
-    assertThat(reader.readComponent(dir1_file.scannerId()).getPath()).isEqualTo("dir1/Foo.java");
-    assertThat(reader.readComponent(dir1_file.scannerId()).getProjectRelativePath()).isEqualTo("dir1/Foo.java");
-
-    // dir in dir in root
-    assertThat(reader.readComponent(dir1_dir1.scannerId()).getPath()).isEqualTo("dir1/dir1");
-    assertThat(reader.readComponent(dir1_dir1.scannerId()).getProjectRelativePath()).isEqualTo("dir1/dir1");
-
-    // module in root
-    assertThat(reader.readComponent(mod1.scannerId()).getPath()).isEqualTo("mod1");
-    assertThat(reader.readComponent(mod1.scannerId()).getProjectRelativePath()).isEqualTo("mod1");
-
-    // dir in module in root
-    assertThat(reader.readComponent(mod1_dir2.scannerId()).getPath()).isEqualTo("dir2");
-    assertThat(reader.readComponent(mod1_dir2.scannerId()).getProjectRelativePath()).isEqualTo("mod1/dir2");
-
-    // file in dir in module in root
-    assertThat(reader.readComponent(mod1_dir2_file.scannerId()).getPath()).isEqualTo("dir2/Foo.java");
-    assertThat(reader.readComponent(mod1_dir2_file.scannerId()).getProjectRelativePath()).isEqualTo("mod1/dir2/Foo.java");
-
-    // module in module
-    assertThat(reader.readComponent(mod1_mod2.scannerId()).getPath()).isEqualTo("mod2");
-    assertThat(reader.readComponent(mod1_mod2.scannerId()).getProjectRelativePath()).isEqualTo("mod1/mod2");
-
-    // file in module in module
-    assertThat(reader.readComponent(mod1_mod2_file.scannerId()).getPath()).isEqualTo("Foo.java");
-    assertThat(reader.readComponent(mod1_mod2_file.scannerId()).getProjectRelativePath()).isEqualTo("mod1/mod2/Foo.java");
-
-    // dir in module in module
-    assertThat(reader.readComponent(mod1_mod2_dir.scannerId()).getPath()).isEqualTo("dir");
-    assertThat(reader.readComponent(mod1_mod2_dir.scannerId()).getProjectRelativePath()).isEqualTo("mod1/mod2/dir");
-
-    // file in dir in module in module
-    assertThat(reader.readComponent(mod1_mod2_dir_file.scannerId()).getPath()).isEqualTo("dir/Foo.java");
-    assertThat(reader.readComponent(mod1_mod2_dir_file.scannerId()).getProjectRelativePath()).isEqualTo("mod1/mod2/dir/Foo.java");
+    assertThat(rootProtobuf.getLink(1).getType()).isEqualTo(ComponentLinkType.CI);
+    assertThat(rootProtobuf.getLink(1).getHref()).isEqualTo("http://ci");
   }
 }
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 d2cc7ac178d..93663f7f57b 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
@@ -59,7 +59,7 @@ public class CoveragePublisherTest {
     inputFile = new TestInputFileBuilder(moduleKey, "src/Foo.php").setLines(5).build();
     DefaultInputProject rootModule = TestInputFileBuilder.newDefaultInputProject(moduleKey, temp.newFolder());
     InputComponentStore componentCache = new InputComponentStore(rootModule, mock(BranchConfiguration.class));
-    componentCache.put(inputFile);
+    componentCache.put(moduleKey, inputFile);
 
     measureCache = mock(MeasureCache.class);
     when(measureCache.byMetric(anyString(), anyString())).thenReturn(null);
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 08cb3b61e3c..7583eac0971 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
@@ -70,7 +70,7 @@ public class MeasuresPublisherTest {
     project = TestInputFileBuilder.newDefaultInputProject(projectKey, temp.newFolder());
     inputFile = new TestInputFileBuilder(projectKey, "src/Foo.php").setPublish(true).build();
     InputComponentStore componentCache = new InputComponentStore(project, mock(BranchConfiguration.class));
-    componentCache.put(inputFile);
+    componentCache.put(projectKey, inputFile);
     measureCache = mock(MeasureCache.class);
     when(measureCache.byComponentKey(anyString())).thenReturn(Collections.<DefaultMeasure<?>>emptyList());
     publisher = new MeasuresPublisher(componentCache, measureCache, mock(TestPlanBuilder.class));
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 f6840f3b175..da37398e387 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
@@ -59,7 +59,7 @@ public class SourcePublisherTest {
 
     DefaultInputProject rootProject = TestInputFileBuilder.newDefaultInputProject(moduleKey, baseDir);
     InputComponentStore componentStore = new InputComponentStore(rootProject, mock(BranchConfiguration.class));
-    componentStore.put(inputFile);
+    componentStore.put(moduleKey, inputFile);
 
     publisher = new SourcePublisher(componentStore);
     File outputDir = temp.newFolder();
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/DefaultComponentTreeTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/DefaultComponentTreeTest.java
deleted file mode 100644
index 930f5ee8086..00000000000
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/DefaultComponentTreeTest.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2019 SonarSource SA
- * mailto:info 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;
-
-import java.io.IOException;
-import org.junit.Before;
-import org.junit.Rule;
-import org.junit.Test;
-import org.junit.rules.TemporaryFolder;
-import org.sonar.api.batch.bootstrap.ProjectDefinition;
-import org.sonar.api.batch.fs.internal.DefaultInputModule;
-import org.sonar.api.batch.fs.internal.DefaultInputProject;
-
-import static org.assertj.core.api.Assertions.assertThat;
-
-public class DefaultComponentTreeTest {
-
-  @Rule
-  public TemporaryFolder temp = new TemporaryFolder();
-
-  private DefaultComponentTree tree;
-
-  @Before
-  public void setUp() {
-    tree = new DefaultComponentTree();
-  }
-
-  @Test
-  public void test() throws IOException {
-    DefaultInputProject root = new DefaultInputProject(ProjectDefinition.create().setKey("root").setBaseDir(temp.newFolder()).setWorkDir(temp.newFolder()));
-    DefaultInputModule mod1 = new DefaultInputModule(ProjectDefinition.create().setKey("mod1").setBaseDir(temp.newFolder()).setWorkDir(temp.newFolder()));
-    DefaultInputModule mod2 = new DefaultInputModule(ProjectDefinition.create().setKey("mod2").setBaseDir(temp.newFolder()).setWorkDir(temp.newFolder()));
-    DefaultInputModule mod3 = new DefaultInputModule(ProjectDefinition.create().setKey("mod3").setBaseDir(temp.newFolder()).setWorkDir(temp.newFolder()));
-    DefaultInputModule mod4 = new DefaultInputModule(ProjectDefinition.create().setKey("mod4").setBaseDir(temp.newFolder()).setWorkDir(temp.newFolder()));
-
-    tree.index(mod1, root);
-    tree.index(mod2, mod1);
-    tree.index(mod3, root);
-    tree.index(mod4, root);
-
-    assertThat(tree.getChildren(root)).containsOnly(mod1, mod3, mod4);
-    assertThat(tree.getChildren(mod4)).isEmpty();
-    assertThat(tree.getChildren(mod1)).containsOnly(mod2);
-
-    assertThat(tree.getParent(mod4)).isEqualTo(root);
-    assertThat(tree.getParent(mod2)).isEqualTo(mod1);
-    assertThat(tree.getParent(mod1)).isEqualTo(root);
-    assertThat(tree.getParent(root)).isNull();
-  }
-}
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/ModuleIndexerTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/ModuleIndexerTest.java
index 2f54bfea404..2c2b51fd0ca 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/ModuleIndexerTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/ModuleIndexerTest.java
@@ -33,15 +33,13 @@ import static org.mockito.Mockito.when;
 
 public class ModuleIndexerTest {
   private ModuleIndexer indexer;
-  private DefaultComponentTree tree;
   private DefaultInputModuleHierarchy moduleHierarchy;
   private InputComponentStore componentStore;
 
   public void createIndexer(DefaultInputProject rootProject) {
     componentStore = new InputComponentStore(rootProject, mock(BranchConfiguration.class));
-    tree = new DefaultComponentTree();
     moduleHierarchy = mock(DefaultInputModuleHierarchy.class);
-    indexer = new ModuleIndexer(tree, componentStore, moduleHierarchy);
+    indexer = new ModuleIndexer(componentStore, moduleHierarchy);
   }
 
   @Test
@@ -80,6 +78,5 @@ public class ModuleIndexerTest {
     DefaultInputModule rootModule = moduleHierarchy.root();
     assertThat(rootModule).isNotNull();
     assertThat(moduleHierarchy.children(rootModule)).hasSize(3);
-    assertThat(tree.getChildren(rootModule)).hasSize(3);
   }
 }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputComponentStoreTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputComponentStoreTest.java
index 5170bf0745e..a9d30ff3bed 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputComponentStoreTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputComponentStoreTest.java
@@ -60,15 +60,15 @@ public class InputComponentStoreTest {
     DefaultInputProject rootProject = TestInputFileBuilder.newDefaultInputProject(rootDef);
     DefaultInputModule subModule = TestInputFileBuilder.newDefaultInputModule(moduleDef);
 
-    InputComponentStore cache = new InputComponentStore(rootProject, mock(BranchConfiguration.class));
-    cache.put(subModule);
+    InputComponentStore store = new InputComponentStore(rootProject, mock(BranchConfiguration.class));
+    store.put(subModule);
 
     DefaultInputFile fooFile = new TestInputFileBuilder(rootModuleKey, "src/main/java/Foo.java")
       .setModuleBaseDir(rootBaseDir.toPath())
       .setPublish(true)
       .build();
-    cache.put(fooFile);
-    cache.put(new TestInputFileBuilder(subModuleKey, "src/main/java/Bar.java")
+    store.put(rootProject.key(), fooFile);
+    store.put(subModuleKey, new TestInputFileBuilder(rootModuleKey, "src/main/java/Bar.java")
       .setLanguage("bla")
       .setPublish(false)
       .setType(Type.MAIN)
@@ -78,28 +78,20 @@ public class InputComponentStoreTest {
       .setModuleBaseDir(temp.newFolder().toPath())
       .build());
 
-    DefaultInputFile loadedFile = (DefaultInputFile) cache.getFile(subModuleKey, "src/main/java/Bar.java");
+    DefaultInputFile loadedFile = (DefaultInputFile) store.getFile(subModuleKey, "src/main/java/Bar.java");
     assertThat(loadedFile.relativePath()).isEqualTo("src/main/java/Bar.java");
     assertThat(loadedFile.charset()).isEqualTo(StandardCharsets.UTF_8);
 
-    assertThat(cache.filesByModule(rootModuleKey)).hasSize(1);
-    assertThat(cache.filesByModule(subModuleKey)).hasSize(1);
-    assertThat(cache.allFiles()).hasSize(2);
-    for (InputPath inputPath : cache.allFiles()) {
+    assertThat(store.filesByModule(rootModuleKey)).hasSize(1);
+    assertThat(store.filesByModule(subModuleKey)).hasSize(1);
+    assertThat(store.allFiles()).hasSize(2);
+    for (InputPath inputPath : store.allFiles()) {
       assertThat(inputPath.relativePath()).startsWith("src/main/java/");
     }
 
     List<InputFile> toPublish = new LinkedList<>();
-    cache.allFilesToPublish().forEach(toPublish::add);
+    store.allFilesToPublish().forEach(toPublish::add);
     assertThat(toPublish).containsExactly(fooFile);
-
-    cache.remove(fooFile);
-    assertThat(cache.allFiles()).hasSize(1);
-
-    cache.removeModule(rootModuleKey);
-    assertThat(cache.filesByModule(rootModuleKey)).hasSize(0);
-    assertThat(cache.filesByModule(subModuleKey)).hasSize(1);
-    assertThat(cache.allFiles()).hasSize(1);
   }
 
   static class InputComponentStoreTester extends InputComponentStore {
@@ -111,7 +103,7 @@ public class InputComponentStoreTest {
       DefaultInputFile file = new TestInputFileBuilder(moduleKey, relpath)
         .setLanguage(language)
         .build();
-      put(file);
+      put(moduleKey, file);
       return file;
     }
   }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputFileBuilderTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputFileBuilderTest.java
index 32ba8fbc390..840cd7d9257 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputFileBuilderTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputFileBuilderTest.java
@@ -53,21 +53,17 @@ public class InputFileBuilderTest {
   public void setUp() throws IOException {
     baseDir = temp.newFolder().toPath();
     workDir = temp.newFolder().toPath();
-    DefaultInputModule root = new DefaultInputModule(ProjectDefinition.create()
+    DefaultInputProject project = new DefaultInputProject(ProjectDefinition.create()
       .setBaseDir(baseDir.toFile())
       .setWorkDir(workDir.toFile())
+      .setProperty(CoreProperties.ENCODING_PROPERTY, StandardCharsets.UTF_8.name())
       .setKey("root"), 0);
     Path moduleBaseDir = baseDir.resolve("module1");
     Files.createDirectories(moduleBaseDir);
-    DefaultInputProject project = new DefaultInputProject(ProjectDefinition.create()
-      .setBaseDir(baseDir.toFile())
-      .setWorkDir(workDir.toFile())
-      .setProperty(CoreProperties.ENCODING_PROPERTY, StandardCharsets.UTF_8.name())
-      .setKey("module1"), 0);
     DefaultInputModule module = new DefaultInputModule(ProjectDefinition.create()
       .setBaseDir(moduleBaseDir.toFile())
       .setWorkDir(workDir.toFile())
-      .setKey("module1"), 0);
+      .setKey("module1"), 1);
 
     MetadataGenerator metadataGenerator = mock(MetadataGenerator.class);
     ScannerComponentIdGenerator idGenerator = new ScannerComponentIdGenerator();
@@ -82,11 +78,10 @@ public class InputFileBuilderTest {
     Path filePath = baseDir.resolve("module1/src/File1.xoo");
     DefaultInputFile inputFile = builder.create(Type.MAIN, filePath, null);
 
-    assertThat(inputFile.moduleKey()).isEqualTo("module1");
     assertThat(inputFile.absolutePath()).isEqualTo(filePath.toString().replaceAll("\\\\", "/"));
     assertThat(inputFile.relativePath()).isEqualTo("src/File1.xoo");
     assertThat(inputFile.path()).isEqualTo(filePath);
-    assertThat(inputFile.key()).isEqualTo("module1:src/File1.xoo");
+    assertThat(inputFile.key()).isEqualTo("root:module1/src/File1.xoo");
     assertThat(inputFile.isPublished()).isFalse();
 
     sensorStrategy.setGlobal(true);
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/ModuleInputComponentStoreTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/ModuleInputComponentStoreTest.java
index dcd265010d1..523d875470d 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/ModuleInputComponentStoreTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/ModuleInputComponentStoreTest.java
@@ -114,7 +114,9 @@ public class ModuleInputComponentStoreTest {
   }
 
   private ModuleInputComponentStore newModuleInputComponentStore() {
-    return new ModuleInputComponentStore(mock(InputModule.class), componentStore, mock(SensorStrategy.class));
+    InputModule module = mock(InputModule.class);
+    when(module.key()).thenReturn("moduleKey");
+    return new ModuleInputComponentStore(module, componentStore, mock(SensorStrategy.class));
   }
 
   @Test
@@ -132,9 +134,6 @@ public class ModuleInputComponentStoreTest {
     store.inputFile(relativePath);
     verify(inputComponentStore).getFile(any(String.class), eq(relativePath));
 
-    store.inputDir(relativePath);
-    verify(inputComponentStore).getDir(any(String.class), eq(relativePath));
-
     store.languages();
     verify(inputComponentStore).getLanguages(any(String.class));
   }
@@ -154,9 +153,6 @@ public class ModuleInputComponentStoreTest {
     store.inputFile(relativePath);
     verify(inputComponentStore).getFile(relativePath);
 
-    store.inputDir(relativePath);
-    verify(inputComponentStore).getDir(relativePath);
-
     store.languages();
     verify(inputComponentStore).getLanguages();
   }
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 d813051b339..36f422d95bf 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
@@ -23,7 +23,6 @@ import java.io.File;
 import java.io.IOException;
 import java.io.StringWriter;
 import java.text.SimpleDateFormat;
-import java.util.Arrays;
 import java.util.Collections;
 import java.util.TimeZone;
 import org.apache.commons.io.IOUtils;
@@ -34,9 +33,7 @@ import org.junit.rules.TemporaryFolder;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
 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.DefaultInputProject;
 import org.sonar.api.batch.fs.internal.InputModuleHierarchy;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
@@ -48,7 +45,6 @@ import org.sonar.api.platform.Server;
 import org.sonar.api.rule.RuleKey;
 import org.sonar.scanner.issue.IssueCache;
 import org.sonar.scanner.issue.tracking.TrackedIssue;
-import org.sonar.scanner.scan.DefaultComponentTree;
 import org.sonar.scanner.scan.branch.BranchConfiguration;
 import org.sonar.scanner.scan.filesystem.InputComponentStore;
 
@@ -81,39 +77,20 @@ public class JSONReportTest {
     SIMPLE_DATE_FORMAT.setTimeZone(TimeZone.getTimeZone("GMT+02:00"));
     when(server.getVersion()).thenReturn("3.6");
 
-    DefaultComponentTree inputComponentTree = new DefaultComponentTree();
     ProjectDefinition def = ProjectDefinition.create().setBaseDir(projectBaseDir).setWorkDir(temp.newFolder()).setKey("struts");
     DefaultInputProject project = new DefaultInputProject(def, 1);
-    DefaultInputModule rootModule = new DefaultInputModule(def, 1);
     InputComponentStore inputComponentStore = new InputComponentStore(project, mock(BranchConfiguration.class));
 
-    DefaultInputModule moduleA = new DefaultInputModule(ProjectDefinition.create().setKey("struts-core").setBaseDir(temp.newFolder()).setWorkDir(temp.newFolder()));
-    inputComponentTree.index(moduleA, rootModule);
-    DefaultInputModule moduleB = new DefaultInputModule(ProjectDefinition.create().setKey("struts-ui").setBaseDir(temp.newFolder()).setWorkDir(temp.newFolder()));
-    inputComponentTree.index(moduleB, rootModule);
-
-    DefaultInputDir inputDir = new DefaultInputDir("struts", "src/main/java/org/apache/struts", TestInputFileBuilder.nextBatchId())
-      .setModuleBaseDir(projectBaseDir.toPath());
     DefaultInputFile inputFile = new TestInputFileBuilder("struts", "src/main/java/org/apache/struts/Action.java")
       .setModuleBaseDir(projectBaseDir.toPath()).build();
     inputFile.setStatus(InputFile.Status.CHANGED);
     inputFile.setPublished(true);
-    inputComponentStore.put(inputFile);
-    inputComponentStore.put(inputDir);
-
-    inputComponentTree.index(inputDir, rootModule);
-    inputComponentTree.index(inputFile, inputDir);
-
-    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");
+    inputComponentStore.put("struts", inputFile);
 
     RulesBuilder builder = new RulesBuilder();
     builder.add(RuleKey.of("squid", "AvoidCycles")).setName("Avoid Cycles");
     rules = builder.build();
-    jsonReport = new JSONReport(moduleHierarchy, settings.asConfig(), fs, server, rules, issueCache, rootModule, inputComponentStore, inputComponentTree);
+    jsonReport = new JSONReport(settings.asConfig(), fs, server, rules, issueCache, project, inputComponentStore);
   }
 
   @Test
diff --git a/sonar-scanner-engine/src/test/resources/org/sonar/scanner/scan/report/JSONReportTest/report-without-resolved-issues.json b/sonar-scanner-engine/src/test/resources/org/sonar/scanner/scan/report/JSONReportTest/report-without-resolved-issues.json
index b5af45efe6c..8238d2eae85 100644
--- a/sonar-scanner-engine/src/test/resources/org/sonar/scanner/scan/report/JSONReportTest/report-without-resolved-issues.json
+++ b/sonar-scanner-engine/src/test/resources/org/sonar/scanner/scan/report/JSONReportTest/report-without-resolved-issues.json
@@ -4,23 +4,9 @@
   "components": [
     {"key": "struts"},
     {
-      "key": "struts-core",
-      "path": "core"
-    },
-    {
-      "key": "struts-ui",
-      "path": "ui"
-    },
-    {
       "key": "struts:src/main/java/org/apache/struts/Action.java",
       "path": "src/main/java/org/apache/struts/Action.java",
-      "moduleKey": "struts",
       "status": "CHANGED"
-    },
-    {
-      "key": "struts:src/main/java/org/apache/struts",
-      "path": "src/main/java/org/apache/struts",
-      "moduleKey": "struts"
     }
   ],
   "rules": [],
diff --git a/sonar-scanner-engine/src/test/resources/org/sonar/scanner/scan/report/JSONReportTest/report.json b/sonar-scanner-engine/src/test/resources/org/sonar/scanner/scan/report/JSONReportTest/report.json
index a78fbca71e5..f80eadc890c 100644
--- a/sonar-scanner-engine/src/test/resources/org/sonar/scanner/scan/report/JSONReportTest/report.json
+++ b/sonar-scanner-engine/src/test/resources/org/sonar/scanner/scan/report/JSONReportTest/report.json
@@ -24,23 +24,9 @@
       "key": "struts"
     },
     {
-      "key": "struts-core",
-      "path": "core"
-    },
-    {
-      "key": "struts-ui",
-      "path": "ui"
-    },
-    {
       "key": "struts:src/main/java/org/apache/struts/Action.java",
       "path": "src/main/java/org/apache/struts/Action.java",
-      "moduleKey": "struts",
       "status": "CHANGED"
-    },
-    {
-      "key": "struts:src/main/java/org/apache/struts",
-      "path": "src/main/java/org/apache/struts",
-      "moduleKey": "struts"
     }
   ],
   "rules": [