Extract implementation from plugin API - Scanner FS

sonar-application/build.gradle

@@ -203,8 +203,8 @@ zip.doFirst {
 }
 // Check the size of the archive
 zip.doLast {
-  def minLength = 198000000
-  def maxLength = 208000000
+  def minLength = 185000000
+  def maxLength = 199000000
   def length = archiveFile.get().asFile.length()
   if (length < minLength)
     throw new GradleException("$archiveName size ($length) too small. Min is $minLength")

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/InputFile.java

@@ -25,12 +25,11 @@ import java.io.InputStream;
 import java.nio.charset.Charset;
 import java.nio.file.Path;
 import javax.annotation.CheckForNull;
-import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.api.batch.sensor.SensorDescriptor;
 
 /**
  * This layer over {@link java.io.File} adds information for code analyzers.
- * For unit testing purpose, use {@link TestInputFileBuilder} and initialize
+ * For unit testing purpose, use TestInputFileBuilder and initialize
  * the needed fields:
  * 
  * <pre>

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultIndexedFile.java

@@ -45,14 +45,6 @@ public class DefaultIndexedFile extends DefaultInputComponent implements Indexed
   private final Path absolutePath;
   private final SensorStrategy sensorStrategy;
 
-  /**
-   * Testing purposes only!
-   */
-  public DefaultIndexedFile(String projectKey, Path baseDir, String relativePath, @Nullable String language) {
-    this(baseDir.resolve(relativePath), projectKey, relativePath, relativePath, Type.MAIN, language, TestInputFileBuilder.nextBatchId(),
-      new SensorStrategy());
-  }
-
   public DefaultIndexedFile(Path absolutePath, String projectKey, String projectRelativePath, String moduleRelativePath, Type type, @Nullable String language, int batchId,
     SensorStrategy sensorStrategy) {
     super(batchId);

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultInputFile.java

@@ -49,7 +49,7 @@ import static org.sonar.api.utils.Preconditions.checkState;
 
 /**
  * @since 4.2
- * To create {@link InputFile} in tests, use {@link TestInputFileBuilder}.
+ * To create {@link InputFile} in tests, use TestInputFileBuilder.
  */
 public class DefaultInputFile extends DefaultInputComponent implements InputFile {
 

sonar-plugin-api/src/main/java/org/sonar/api/batch/sensor/Sensor.java

@@ -22,7 +22,6 @@ package org.sonar.api.batch.sensor;
 import org.sonar.api.ExtensionPoint;
 import org.sonar.api.batch.InstantiationStrategy;
 import org.sonar.api.batch.ScannerSide;
-import org.sonar.api.batch.sensor.internal.SensorContextTester;
 import org.sonar.api.scanner.sensor.ProjectSensor;
 import org.sonarsource.api.sonarlint.SonarLintSide;
 
@@ -33,7 +32,7 @@ import org.sonarsource.api.sonarlint.SonarLintSide;
  * <p>
  * For example the Cobertura Sensor parses Cobertura report and saves the first-level of measures on files.
  * 
- * For testing purpose you can use {@link SensorContextTester}
+ * For testing purpose you can use SensorContextTester
  * @since 5.1
  * @since 7.6 use {@link ProjectSensor} instead to make your Sensor run only once per analysis, and no more once per module
  */

sonar-plugin-api/src/main/java/org/sonar/api/batch/sensor/SensorContext.java

@@ -30,7 +30,6 @@ import org.sonar.api.batch.sensor.coverage.NewCoverage;
 import org.sonar.api.batch.sensor.cpd.NewCpdTokens;
 import org.sonar.api.batch.sensor.error.NewAnalysisError;
 import org.sonar.api.batch.sensor.highlighting.NewHighlighting;
-import org.sonar.api.batch.sensor.internal.SensorContextTester;
 import org.sonar.api.batch.sensor.issue.ExternalIssue;
 import org.sonar.api.batch.sensor.issue.Issue;
 import org.sonar.api.batch.sensor.issue.NewExternalIssue;
@@ -48,7 +47,7 @@ import org.sonar.api.utils.Version;
 
 /**
  * See {@link Sensor#execute(SensorContext)}
- * In order to write unit tests you can use {@link SensorContextTester}
+ * In order to write unit tests you can use SensorContextTester
  * @since 5.1
  */
 public interface SensorContext {

sonar-plugin-api/src/main/java/org/sonar/api/scanner/sensor/ProjectSensor.java

@@ -23,7 +23,6 @@ import org.sonar.api.ExtensionPoint;
 import org.sonar.api.scanner.ScannerSide;
 import org.sonar.api.batch.sensor.SensorContext;
 import org.sonar.api.batch.sensor.SensorDescriptor;
-import org.sonar.api.batch.sensor.internal.SensorContextTester;
 import org.sonarsource.api.sonarlint.SonarLintSide;
 
 /**
@@ -32,7 +31,7 @@ import org.sonarsource.api.sonarlint.SonarLintSide;
  * <p>
  * For example the Cobertura Sensor parses Cobertura report and saves the first-level of measures on files.
  * 
- * For testing purpose you can use {@link SensorContextTester}
+ * For testing purpose you can use  SensorContextTester
  * @since 7.6
  */
 @ScannerSide

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/AbstractProjectOrModule.java

@@ -0,0 +1,161 @@
+/*
+ * 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.fs;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.LinkOption;
+import java.nio.file.Path;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+import javax.annotation.CheckForNull;
+import javax.annotation.concurrent.Immutable;
+import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang.SystemUtils;
+import org.sonar.api.CoreProperties;
+import org.sonar.api.batch.bootstrap.ProjectDefinition;
+import org.sonar.api.utils.log.Logger;
+import org.sonar.api.utils.log.Loggers;
+
+@Immutable
+public abstract class AbstractProjectOrModule extends DefaultInputComponent {
+  private static final Logger LOGGER = Loggers.get(AbstractProjectOrModule.class);
+  private final Path baseDir;
+  private final Path workDir;
+  private final String name;
+  private final String originalName;
+  private final String description;
+  private final String keyWithBranch;
+  private final String branch;
+  private final Map<String, String> properties;
+
+  private final String key;
+  private final ProjectDefinition definition;
+  private final Charset encoding;
+
+  public AbstractProjectOrModule(ProjectDefinition definition, int scannerComponentId) {
+    super(scannerComponentId);
+    this.baseDir = initBaseDir(definition);
+    this.workDir = initWorkingDir(definition);
+    this.name = definition.getName();
+    this.originalName = definition.getOriginalName();
+    this.description = definition.getDescription();
+    this.keyWithBranch = definition.getKeyWithBranch();
+    this.branch = definition.getBranch();
+    this.properties = Collections.unmodifiableMap(new HashMap<>(definition.properties()));
+
+    this.definition = definition;
+    this.key = definition.getKey();
+    this.encoding = initEncoding(definition);
+  }
+
+  private static Charset initEncoding(ProjectDefinition module) {
+    String encodingStr = module.properties().get(CoreProperties.ENCODING_PROPERTY);
+    Charset result;
+    if (StringUtils.isNotEmpty(encodingStr)) {
+      result = Charset.forName(StringUtils.trim(encodingStr));
+    } else {
+      result = Charset.defaultCharset();
+    }
+    return result;
+  }
+
+  private static Path initBaseDir(ProjectDefinition module) {
+    Path result;
+    try {
+      result = module.getBaseDir().toPath().toRealPath(LinkOption.NOFOLLOW_LINKS);
+    } catch (IOException e) {
+      throw new IllegalStateException("Unable to resolve module baseDir", e);
+    }
+    return result;
+  }
+
+  private static Path initWorkingDir(ProjectDefinition module) {
+    File workingDirAsFile = module.getWorkDir();
+    Path workingDir = workingDirAsFile.getAbsoluteFile().toPath().normalize();
+    if (SystemUtils.IS_OS_WINDOWS) {
+      try {
+        Files.createDirectories(workingDir);
+        Files.setAttribute(workingDir, "dos:hidden", true, LinkOption.NOFOLLOW_LINKS);
+      } catch (IOException e) {
+        LOGGER.warn("Failed to set working directory hidden: {}", e.getMessage());
+      }
+    }
+    return workingDir;
+  }
+
+  /**
+   * Module key without branch
+   */
+  @Override
+  public String key() {
+    return key;
+  }
+
+  @Override
+  public boolean isFile() {
+    return false;
+  }
+
+  public ProjectDefinition definition() {
+    return definition;
+  }
+
+  public Path getBaseDir() {
+    return baseDir;
+  }
+
+  public Path getWorkDir() {
+    return workDir;
+  }
+
+  public String getKeyWithBranch() {
+    return keyWithBranch;
+  }
+
+  @CheckForNull
+  public String getBranch() {
+    return branch;
+  }
+
+  public Map<String, String> properties() {
+    return properties;
+  }
+
+  @CheckForNull
+  public String getOriginalName() {
+    return originalName;
+  }
+
+  public String getName() {
+    return name;
+  }
+
+  public String getDescription() {
+    return description;
+  }
+
+  public Charset getEncoding() {
+    return encoding;
+  }
+}

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultFileSystem.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/DefaultFileSystem.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs;
 
 import java.io.File;
 import java.io.IOException;
@@ -39,6 +39,9 @@ import org.sonar.api.batch.fs.InputDir;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.scan.filesystem.PathResolver;
 import org.sonar.api.utils.PathUtils;
+import org.sonar.scanner.fs.predicates.DefaultFilePredicates;
+import org.sonar.scanner.fs.predicates.FileExtensionPredicate;
+import org.sonar.scanner.fs.predicates.OptimizedFilePredicateAdapter;
 
 /**
  * @since 4.2

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/DefaultIndexedFile.java

@@ -0,0 +1,158 @@
+/*
+ * 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.fs;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import javax.annotation.CheckForNull;
+import javax.annotation.Nullable;
+import javax.annotation.concurrent.Immutable;
+import org.sonar.api.batch.fs.IndexedFile;
+import org.sonar.api.batch.fs.InputFile.Type;
+import org.sonar.api.utils.PathUtils;
+
+/**
+ * @since 6.3
+ */
+@Immutable
+public class DefaultIndexedFile extends DefaultInputComponent implements IndexedFile {
+  private final String projectRelativePath;
+  private final String moduleRelativePath;
+  private final String projectKey;
+  private final String language;
+  private final Type type;
+  private final Path absolutePath;
+  private final SensorStrategy sensorStrategy;
+
+  /**
+   * Testing purposes only!
+   */
+  public DefaultIndexedFile(String projectKey, Path baseDir, String relativePath, @Nullable String language) {
+    this(baseDir.resolve(relativePath), projectKey, relativePath, relativePath, Type.MAIN, language, TestInputFileBuilder.nextBatchId(),
+      new SensorStrategy());
+  }
+
+  public DefaultIndexedFile(Path absolutePath, String projectKey, String projectRelativePath, String moduleRelativePath, Type type, @Nullable String language, int batchId,
+    SensorStrategy sensorStrategy) {
+    super(batchId);
+    this.projectKey = projectKey;
+    this.projectRelativePath = PathUtils.sanitize(projectRelativePath);
+    this.moduleRelativePath = PathUtils.sanitize(moduleRelativePath);
+    this.type = type;
+    this.language = language;
+    this.sensorStrategy = sensorStrategy;
+    this.absolutePath = absolutePath;
+  }
+
+  @Override
+  public String relativePath() {
+    return sensorStrategy.isGlobal() ? projectRelativePath : moduleRelativePath;
+  }
+
+  public String getModuleRelativePath() {
+    return moduleRelativePath;
+  }
+
+  public String getProjectRelativePath() {
+    return projectRelativePath;
+  }
+
+  @Override
+  public String absolutePath() {
+    return PathUtils.sanitize(path().toString());
+  }
+
+  @Override
+  public File file() {
+    return path().toFile();
+  }
+
+  @Override
+  public Path path() {
+    return absolutePath;
+  }
+
+  @Override
+  public InputStream inputStream() throws IOException {
+    return Files.newInputStream(path());
+  }
+
+  @CheckForNull
+  @Override
+  public String language() {
+    return language;
+  }
+
+  @Override
+  public Type type() {
+    return type;
+  }
+
+  /**
+   * Component key (without branch).
+   */
+  @Override
+  public String key() {
+    return new StringBuilder().append(projectKey).append(":").append(projectRelativePath).toString();
+  }
+
+  @Override
+  public boolean equals(Object o) {
+    if (this == o) {
+      return true;
+    }
+
+    if (!(o instanceof DefaultIndexedFile)) {
+      return false;
+    }
+
+    DefaultIndexedFile that = (DefaultIndexedFile) o;
+    return projectRelativePath.equals(that.projectRelativePath);
+  }
+
+  @Override
+  public int hashCode() {
+    return projectRelativePath.hashCode();
+  }
+
+  @Override
+  public String toString() {
+    return projectRelativePath;
+  }
+
+  @Override
+  public boolean isFile() {
+    return true;
+  }
+
+  @Override
+  public String filename() {
+    return path().getFileName().toString();
+  }
+
+  @Override
+  public URI uri() {
+    return path().toUri();
+  }
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/DefaultInputComponent.java

@@ -0,0 +1,72 @@
+/*
+ * 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.fs;
+
+import java.util.HashSet;
+import java.util.Set;
+import org.sonar.api.batch.fs.InputComponent;
+import org.sonar.api.batch.measure.Metric;
+
+/**
+ * @since 5.2
+ */
+public abstract class DefaultInputComponent implements InputComponent {
+  private int id;
+  private Set<String> storedMetricKeys = new HashSet<>();
+
+  public DefaultInputComponent(int scannerId) {
+    this.id = scannerId;
+  }
+
+  @Override
+  public boolean equals(Object o) {
+    if (this == o) {
+      return true;
+    }
+    if (o == null || this.getClass() != o.getClass()) {
+      return false;
+    }
+
+    DefaultInputComponent that = (DefaultInputComponent) o;
+    return key().equals(that.key());
+  }
+
+  public int scannerId() {
+    return id;
+  }
+
+  @Override
+  public int hashCode() {
+    return key().hashCode();
+  }
+
+  @Override
+  public String toString() {
+    return "[key=" + key() + "]";
+  }
+
+  public void setHasMeasureFor(Metric metric) {
+    storedMetricKeys.add(metric.key());
+  }
+
+  public boolean hasMeasureFor(Metric metric) {
+    return storedMetricKeys.contains(metric.key());
+  }
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/DefaultInputDir.java

@@ -0,0 +1,122 @@
+/*
+ * 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.fs;
+
+import java.io.File;
+import java.net.URI;
+import java.nio.file.Path;
+import org.apache.commons.lang.StringUtils;
+import org.sonar.api.batch.fs.InputDir;
+import org.sonar.api.utils.PathUtils;
+
+/**
+ * @since 4.5
+ */
+public class DefaultInputDir extends DefaultInputComponent implements InputDir {
+
+  private final String relativePath;
+  private final String moduleKey;
+  private Path moduleBaseDir;
+
+  public DefaultInputDir(String moduleKey, String relativePath) {
+    super(-1);
+    this.moduleKey = moduleKey;
+    this.relativePath = PathUtils.sanitize(relativePath);
+  }
+
+  @Override
+  public String relativePath() {
+    return relativePath;
+  }
+
+  @Override
+  public String absolutePath() {
+    return PathUtils.sanitize(path().toString());
+  }
+
+  @Override
+  public File file() {
+    return path().toFile();
+  }
+
+  @Override
+  public Path path() {
+    if (moduleBaseDir == null) {
+      throw new IllegalStateException("Can not return the java.nio.file.Path because module baseDir is not set (see method setModuleBaseDir(java.io.File))");
+    }
+    return moduleBaseDir.resolve(relativePath);
+  }
+
+  public String moduleKey() {
+    return moduleKey;
+  }
+
+  @Override
+  public String key() {
+    StringBuilder sb = new StringBuilder().append(moduleKey).append(":");
+    if (StringUtils.isEmpty(relativePath)) {
+      sb.append("/");
+    } else {
+      sb.append(relativePath);
+    }
+    return sb.toString();
+  }
+
+  /**
+   * For testing purpose. Will be automatically set when dir is added to {@link DefaultFileSystem}
+   */
+  public DefaultInputDir setModuleBaseDir(Path moduleBaseDir) {
+    this.moduleBaseDir = moduleBaseDir.normalize();
+    return this;
+  }
+
+  @Override
+  public boolean isFile() {
+    return false;
+  }
+
+  @Override
+  public boolean equals(Object o) {
+    if (this == o) {
+      return true;
+    }
+    if (o == null || this.getClass() != o.getClass()) {
+      return false;
+    }
+
+    DefaultInputDir that = (DefaultInputDir) o;
+    return moduleKey.equals(that.moduleKey) && relativePath.equals(that.relativePath);
+  }
+
+  @Override
+  public int hashCode() {
+    return moduleKey.hashCode() + relativePath.hashCode() * 13;
+  }
+
+  @Override
+  public String toString() {
+    return "[moduleKey=" + moduleKey + ", relative=" + relativePath + ", basedir=" + moduleBaseDir + "]";
+  }
+
+  @Override
+  public URI uri() {
+    return path().toUri();
+  }
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/DefaultInputFile.java

@@ -0,0 +1,440 @@
+/*
+ * 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.fs;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collection;
+import java.util.Optional;
+import java.util.Set;
+import java.util.function.Consumer;
+import java.util.stream.Collectors;
+import javax.annotation.CheckForNull;
+import javax.annotation.Nullable;
+import org.apache.commons.io.ByteOrderMark;
+import org.apache.commons.io.input.BOMInputStream;
+import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.fs.TextPointer;
+import org.sonar.api.batch.fs.TextRange;
+import org.sonar.api.batch.fs.internal.Metadata;
+
+import static org.sonar.api.utils.Preconditions.checkArgument;
+import static org.sonar.api.utils.Preconditions.checkState;
+
+/**
+ * @since 4.2
+ * To create {@link InputFile} in tests, use {@link TestInputFileBuilder}.
+ */
+public class DefaultInputFile extends DefaultInputComponent implements InputFile {
+
+  private static final int DEFAULT_BUFFER_SIZE = 1024 * 4;
+
+  private final DefaultIndexedFile indexedFile;
+  private final String contents;
+  private final Consumer<DefaultInputFile> metadataGenerator;
+
+  private boolean published;
+  private boolean excludedForCoverage;
+  private boolean excludedForDuplication;
+  private boolean ignoreAllIssues;
+  // Lazy init to save memory
+  private BitSet noSonarLines;
+  private Status status;
+  private Charset charset;
+  private Metadata metadata;
+  private Collection<int[]> ignoreIssuesOnlineRanges;
+  private BitSet executableLines;
+
+  public DefaultInputFile(DefaultIndexedFile indexedFile, Consumer<DefaultInputFile> metadataGenerator) {
+    this(indexedFile, metadataGenerator, null);
+  }
+
+  // For testing
+  public DefaultInputFile(DefaultIndexedFile indexedFile, Consumer<DefaultInputFile> metadataGenerator, @Nullable String contents) {
+    super(indexedFile.scannerId());
+    this.indexedFile = indexedFile;
+    this.metadataGenerator = metadataGenerator;
+    this.metadata = null;
+    this.published = false;
+    this.excludedForCoverage = false;
+    this.contents = contents;
+  }
+
+  public void checkMetadata() {
+    if (metadata == null) {
+      metadataGenerator.accept(this);
+    }
+  }
+
+  @Override
+  public InputStream inputStream() throws IOException {
+    return contents != null ? new ByteArrayInputStream(contents.getBytes(charset()))
+      : new BOMInputStream(Files.newInputStream(path()),
+      ByteOrderMark.UTF_8, ByteOrderMark.UTF_16LE, ByteOrderMark.UTF_16BE, ByteOrderMark.UTF_32LE, ByteOrderMark.UTF_32BE);
+  }
+
+  @Override
+  public String contents() throws IOException {
+    if (contents != null) {
+      return contents;
+    } else {
+      ByteArrayOutputStream result = new ByteArrayOutputStream();
+      try (InputStream inputStream = inputStream()) {
+        byte[] buffer = new byte[DEFAULT_BUFFER_SIZE];
+        int length;
+        while ((length = inputStream.read(buffer)) != -1) {
+          result.write(buffer, 0, length);
+        }
+      }
+      return result.toString(charset().name());
+    }
+  }
+
+  public DefaultInputFile setPublished(boolean published) {
+    this.published = published;
+    return this;
+  }
+
+  public boolean isPublished() {
+    return published;
+  }
+
+  public DefaultInputFile setExcludedForCoverage(boolean excludedForCoverage) {
+    this.excludedForCoverage = excludedForCoverage;
+    return this;
+  }
+
+  public boolean isExcludedForCoverage() {
+    return excludedForCoverage;
+  }
+
+  public DefaultInputFile setExcludedForDuplication(boolean excludedForDuplication) {
+    this.excludedForDuplication = excludedForDuplication;
+    return this;
+  }
+
+  public boolean isExcludedForDuplication() {
+    return excludedForDuplication;
+  }
+
+  /**
+   * @deprecated since 6.6
+   */
+  @Deprecated
+  @Override
+  public String relativePath() {
+    return indexedFile.relativePath();
+  }
+
+  public String getModuleRelativePath() {
+    return indexedFile.getModuleRelativePath();
+  }
+
+  public String getProjectRelativePath() {
+    return indexedFile.getProjectRelativePath();
+  }
+
+  @Override
+  public String absolutePath() {
+    return indexedFile.absolutePath();
+  }
+
+  @Override
+  public File file() {
+    return indexedFile.file();
+  }
+
+  @Override
+  public Path path() {
+    return indexedFile.path();
+  }
+
+  @CheckForNull
+  @Override
+  public String language() {
+    return indexedFile.language();
+  }
+
+  @Override
+  public Type type() {
+    return indexedFile.type();
+  }
+
+  /**
+   * Component key (without branch).
+   */
+  @Override
+  public String key() {
+    return indexedFile.key();
+  }
+
+  @Override
+  public int hashCode() {
+    return indexedFile.hashCode();
+  }
+
+  @Override
+  public String toString() {
+    return indexedFile.toString();
+  }
+
+  /**
+   * {@link #setStatus(Status)}
+   */
+  @Override
+  public Status status() {
+    checkMetadata();
+    return status;
+  }
+
+  @Override
+  public int lines() {
+    checkMetadata();
+    return metadata.lines();
+  }
+
+  @Override
+  public boolean isEmpty() {
+    checkMetadata();
+    return metadata.isEmpty();
+  }
+
+  @Override
+  public Charset charset() {
+    checkMetadata();
+    return charset;
+  }
+
+  public int lastValidOffset() {
+    checkMetadata();
+    return metadata.lastValidOffset();
+  }
+
+  /**
+   * Digest hash of the file.
+   */
+  public String hash() {
+    checkMetadata();
+    return metadata.hash();
+  }
+
+  public int nonBlankLines() {
+    checkMetadata();
+    return metadata.nonBlankLines();
+  }
+
+  public int[] originalLineStartOffsets() {
+    checkMetadata();
+    checkState(metadata.originalLineStartOffsets() != null, "InputFile is not properly initialized.");
+    checkState(metadata.originalLineStartOffsets().length == metadata.lines(),
+      "InputFile is not properly initialized. 'originalLineStartOffsets' property length should be equal to 'lines'");
+    return metadata.originalLineStartOffsets();
+  }
+
+  public int[] originalLineEndOffsets() {
+    checkMetadata();
+    checkState(metadata.originalLineEndOffsets() != null, "InputFile is not properly initialized.");
+    checkState(metadata.originalLineEndOffsets().length == metadata.lines(),
+      "InputFile is not properly initialized. 'originalLineEndOffsets' property length should be equal to 'lines'");
+    return metadata.originalLineEndOffsets();
+  }
+
+  @Override
+  public TextPointer newPointer(int line, int lineOffset) {
+    checkMetadata();
+    DefaultTextPointer textPointer = new DefaultTextPointer(line, lineOffset);
+    checkValid(textPointer, "pointer");
+    return textPointer;
+  }
+
+  @Override
+  public TextRange newRange(TextPointer start, TextPointer end) {
+    checkMetadata();
+    checkValid(start, "start pointer");
+    checkValid(end, "end pointer");
+    return newRangeValidPointers(start, end, false);
+  }
+
+  @Override
+  public TextRange newRange(int startLine, int startLineOffset, int endLine, int endLineOffset) {
+    checkMetadata();
+    TextPointer start = newPointer(startLine, startLineOffset);
+    TextPointer end = newPointer(endLine, endLineOffset);
+    return newRangeValidPointers(start, end, false);
+  }
+
+  @Override
+  public TextRange selectLine(int line) {
+    checkMetadata();
+    TextPointer startPointer = newPointer(line, 0);
+    TextPointer endPointer = newPointer(line, lineLength(line));
+    return newRangeValidPointers(startPointer, endPointer, true);
+  }
+
+  public void validate(TextRange range) {
+    checkMetadata();
+    checkValid(range.start(), "start pointer");
+    checkValid(range.end(), "end pointer");
+  }
+
+  /**
+   * Create Range from global offsets. Used for backward compatibility with older API.
+   */
+  public TextRange newRange(int startOffset, int endOffset) {
+    checkMetadata();
+    return newRangeValidPointers(newPointer(startOffset), newPointer(endOffset), false);
+  }
+
+  public TextPointer newPointer(int globalOffset) {
+    checkMetadata();
+    checkArgument(globalOffset >= 0, "%s is not a valid offset for a file", globalOffset);
+    checkArgument(globalOffset <= lastValidOffset(), "%s is not a valid offset for file %s. Max offset is %s", globalOffset, this, lastValidOffset());
+    int line = findLine(globalOffset);
+    int startLineOffset = originalLineStartOffsets()[line - 1];
+    // In case the global offset is between \r and \n, move the pointer to a valid location
+    return new DefaultTextPointer(line, Math.min(globalOffset, originalLineEndOffsets()[line - 1]) - startLineOffset);
+  }
+
+  public DefaultInputFile setStatus(Status status) {
+    this.status = status;
+    return this;
+  }
+
+  public DefaultInputFile setCharset(Charset charset) {
+    this.charset = charset;
+    return this;
+  }
+
+  private void checkValid(TextPointer pointer, String owner) {
+    checkArgument(pointer.line() >= 1, "%s is not a valid line for a file", pointer.line());
+    checkArgument(pointer.line() <= this.metadata.lines(), "%s is not a valid line for %s. File %s has %s line(s)", pointer.line(), owner, this, metadata.lines());
+    checkArgument(pointer.lineOffset() >= 0, "%s is not a valid line offset for a file", pointer.lineOffset());
+    int lineLength = lineLength(pointer.line());
+    checkArgument(pointer.lineOffset() <= lineLength,
+      "%s is not a valid line offset for %s. File %s has %s character(s) at line %s", pointer.lineOffset(), owner, this, lineLength, pointer.line());
+  }
+
+  private int lineLength(int line) {
+    return originalLineEndOffsets()[line - 1] - originalLineStartOffsets()[line - 1];
+  }
+
+  private static TextRange newRangeValidPointers(TextPointer start, TextPointer end, boolean acceptEmptyRange) {
+    checkArgument(acceptEmptyRange ? (start.compareTo(end) <= 0) : (start.compareTo(end) < 0),
+      "Start pointer %s should be before end pointer %s", start, end);
+    return new DefaultTextRange(start, end);
+  }
+
+  private int findLine(int globalOffset) {
+    return Math.abs(Arrays.binarySearch(originalLineStartOffsets(), globalOffset) + 1);
+  }
+
+  public DefaultInputFile setMetadata(Metadata metadata) {
+    this.metadata = metadata;
+    return this;
+  }
+
+  @Override
+  public boolean equals(Object obj) {
+    if (obj == null) {
+      return false;
+    }
+
+    if (this.getClass() != obj.getClass()) {
+      return false;
+    }
+
+    DefaultInputFile that = (DefaultInputFile) obj;
+    return this.getProjectRelativePath().equals(that.getProjectRelativePath());
+  }
+
+  @Override
+  public boolean isFile() {
+    return true;
+  }
+
+  @Override
+  public String filename() {
+    return indexedFile.filename();
+  }
+
+  @Override
+  public URI uri() {
+    return indexedFile.uri();
+  }
+
+  public void noSonarAt(Set<Integer> noSonarLines) {
+    if (this.noSonarLines == null) {
+      this.noSonarLines = new BitSet(lines());
+    }
+    noSonarLines.forEach(l -> this.noSonarLines.set(l - 1));
+  }
+
+  public boolean hasNoSonarAt(int line) {
+    if (this.noSonarLines == null) {
+      return false;
+    }
+    return this.noSonarLines.get(line - 1);
+  }
+
+  public boolean isIgnoreAllIssues() {
+    return ignoreAllIssues;
+  }
+
+  public void setIgnoreAllIssues(boolean ignoreAllIssues) {
+    this.ignoreAllIssues = ignoreAllIssues;
+  }
+
+  public void addIgnoreIssuesOnLineRanges(Collection<int[]> lineRanges) {
+    if (this.ignoreIssuesOnlineRanges == null) {
+      this.ignoreIssuesOnlineRanges = new ArrayList<>();
+    }
+    this.ignoreIssuesOnlineRanges.addAll(lineRanges);
+  }
+
+  public boolean isIgnoreAllIssuesOnLine(@Nullable Integer line) {
+    if (line == null || ignoreIssuesOnlineRanges == null) {
+      return false;
+    }
+    return ignoreIssuesOnlineRanges.stream().anyMatch(r -> r[0] <= line && line <= r[1]);
+  }
+
+  public void setExecutableLines(Set<Integer> executableLines) {
+    checkState(this.executableLines == null, "Executable lines have already been saved for file: {}", this.toString());
+    this.executableLines = new BitSet(lines());
+    executableLines.forEach(l -> this.executableLines.set(l - 1));
+  }
+
+  public Optional<Set<Integer>> getExecutableLines() {
+    if (this.executableLines == null) {
+      return Optional.empty();
+    }
+    return Optional.of(this.executableLines.stream().map(i -> i + 1).boxed().collect(Collectors.toSet()));
+  }
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/DefaultInputModule.java

@@ -0,0 +1,81 @@
+/*
+ * 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.fs;
+
+import java.io.File;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+import javax.annotation.CheckForNull;
+import javax.annotation.concurrent.Immutable;
+import org.sonar.api.batch.bootstrap.ProjectDefinition;
+import org.sonar.api.batch.fs.InputModule;
+import org.sonar.api.scan.filesystem.PathResolver;
+
+import static org.sonar.api.config.internal.MultivalueProperty.parseAsCsv;
+
+@Immutable
+public class DefaultInputModule extends AbstractProjectOrModule implements InputModule {
+
+  private final List<Path> sourceDirsOrFiles;
+  private final List<Path> testDirsOrFiles;
+
+  /**
+   * For testing only!
+   */
+  public DefaultInputModule(ProjectDefinition definition) {
+    this(definition, 0);
+  }
+
+  public DefaultInputModule(ProjectDefinition definition, int scannerComponentId) {
+    super(definition, scannerComponentId);
+
+    this.sourceDirsOrFiles = initSources(definition, ProjectDefinition.SOURCES_PROPERTY);
+    this.testDirsOrFiles = initSources(definition, ProjectDefinition.TESTS_PROPERTY);
+  }
+
+  @CheckForNull
+  private List<Path> initSources(ProjectDefinition module, String propertyKey) {
+    if (!module.properties().containsKey(propertyKey)) {
+      return null;
+    }
+    List<Path> result = new ArrayList<>();
+    PathResolver pathResolver = new PathResolver();
+    String srcPropValue = module.properties().get(propertyKey);
+    if (srcPropValue != null) {
+      for (String sourcePath : parseAsCsv(propertyKey, srcPropValue)) {
+        File dirOrFile = pathResolver.relativeFile(getBaseDir().toFile(), sourcePath);
+        if (dirOrFile.exists()) {
+          result.add(dirOrFile.toPath());
+        }
+      }
+    }
+    return result;
+  }
+
+  public Optional<List<Path>> getSourceDirsOrFiles() {
+    return Optional.ofNullable(sourceDirsOrFiles);
+  }
+
+  public Optional<List<Path>> getTestDirsOrFiles() {
+    return Optional.ofNullable(testDirsOrFiles);
+  }
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/DefaultInputProject.java

@@ -0,0 +1,39 @@
+/*
+ * 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.fs;
+
+import javax.annotation.concurrent.Immutable;
+import org.sonar.api.batch.bootstrap.ProjectDefinition;
+import org.sonar.api.scanner.fs.InputProject;
+
+@Immutable
+public class DefaultInputProject extends AbstractProjectOrModule implements InputProject {
+
+  /**
+   * For testing only!
+   */
+  public DefaultInputProject(ProjectDefinition definition) {
+    super(definition, 0);
+  }
+
+  public DefaultInputProject(ProjectDefinition definition, int scannerComponentId) {
+    super(definition, scannerComponentId);
+  }
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/DefaultTextPointer.java

@@ -0,0 +1,74 @@
+/*
+ * 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.fs;
+
+import org.sonar.api.batch.fs.TextPointer;
+
+/**
+ * @since 5.2
+ */
+public class DefaultTextPointer implements TextPointer {
+
+  private final int line;
+  private final int lineOffset;
+
+  public DefaultTextPointer(int line, int lineOffset) {
+    this.line = line;
+    this.lineOffset = lineOffset;
+  }
+
+  @Override
+  public int line() {
+    return line;
+  }
+
+  @Override
+  public int lineOffset() {
+    return lineOffset;
+  }
+
+  @Override
+  public String toString() {
+    return "[line=" + line + ", lineOffset=" + lineOffset + "]";
+  }
+
+  @Override
+  public boolean equals(Object obj) {
+    if (!(obj instanceof DefaultTextPointer)) {
+      return false;
+    }
+    DefaultTextPointer other = (DefaultTextPointer) obj;
+    return other.line == this.line && other.lineOffset == this.lineOffset;
+  }
+
+  @Override
+  public int hashCode() {
+    return 37 * this.line + lineOffset;
+  }
+
+  @Override
+  public int compareTo(TextPointer o) {
+    if (this.line == o.line()) {
+      return Integer.compare(this.lineOffset, o.lineOffset());
+    }
+    return Integer.compare(this.line, o.line());
+  }
+
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/DefaultTextRange.java

@@ -0,0 +1,74 @@
+/*
+ * 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.fs;
+
+import org.sonar.api.batch.fs.TextPointer;
+import org.sonar.api.batch.fs.TextRange;
+
+/**
+ * @since 5.2
+ */
+public class DefaultTextRange implements TextRange {
+
+  private final TextPointer start;
+  private final TextPointer end;
+
+  public DefaultTextRange(TextPointer start, TextPointer end) {
+    this.start = start;
+    this.end = end;
+  }
+
+  @Override
+  public TextPointer start() {
+    return start;
+  }
+
+  @Override
+  public TextPointer end() {
+    return end;
+  }
+
+  @Override
+  public boolean overlap(TextRange another) {
+    // [A,B] and [C,D]
+    // B > C && D > A
+    return this.end.compareTo(another.start()) > 0 && another.end().compareTo(this.start) > 0;
+  }
+
+  @Override
+  public String toString() {
+    return "Range[from " + start + " to " + end + "]";
+  }
+
+  @Override
+  public boolean equals(Object obj) {
+    if (!(obj instanceof DefaultTextRange)) {
+      return false;
+    }
+    DefaultTextRange other = (DefaultTextRange) obj;
+    return start.equals(other.start) && end.equals(other.end);
+  }
+
+  @Override
+  public int hashCode() {
+    return start.hashCode() * 17 + end.hashCode();
+  }
+
+}

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/FileMetadata.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/FileMetadata.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs;
 
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -29,11 +29,12 @@ import java.nio.charset.StandardCharsets;
 import javax.annotation.Nullable;
 import javax.annotation.concurrent.Immutable;
 import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.internal.charhandler.CharHandler;
-import org.sonar.api.batch.fs.internal.charhandler.FileHashComputer;
-import org.sonar.api.batch.fs.internal.charhandler.LineCounter;
-import org.sonar.api.batch.fs.internal.charhandler.LineHashComputer;
-import org.sonar.api.batch.fs.internal.charhandler.LineOffsetCounter;
+import org.sonar.api.batch.fs.internal.Metadata;
+import org.sonar.scanner.fs.charhandler.CharHandler;
+import org.sonar.scanner.fs.charhandler.FileHashComputer;
+import org.sonar.scanner.fs.charhandler.LineCounter;
+import org.sonar.scanner.fs.charhandler.LineHashComputer;
+import org.sonar.scanner.fs.charhandler.LineOffsetCounter;
 
 /**
  * Computes hash of files. Ends of Lines are ignored, so files with

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/InputModuleHierarchy.java

@@ -0,0 +1,42 @@
+/*
+ * 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.fs;
+
+import java.util.Collection;
+import javax.annotation.CheckForNull;
+import javax.annotation.concurrent.Immutable;
+
+@Immutable
+public interface InputModuleHierarchy {
+  DefaultInputModule root();
+
+  boolean isRoot(DefaultInputModule module);
+
+  Collection<DefaultInputModule> children(DefaultInputModule module);
+
+  @CheckForNull
+  DefaultInputModule parent(DefaultInputModule module);
+
+  @CheckForNull
+  String relativePath(DefaultInputModule module);
+
+  @CheckForNull
+  String relativePathToRoot(DefaultInputModule module);
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/PathPattern.java

@@ -0,0 +1,136 @@
+/*
+ * 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.fs;
+
+import java.nio.file.Path;
+import javax.annotation.concurrent.ThreadSafe;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.lang.StringUtils;
+import org.sonar.api.utils.PathUtils;
+import org.sonar.api.utils.WildcardPattern;
+import org.sonar.api.utils.log.Logger;
+import org.sonar.api.utils.log.Loggers;
+
+@ThreadSafe
+public abstract class PathPattern {
+
+  private static final Logger LOG = Loggers.get(PathPattern.class);
+
+  /**
+   * @deprecated since 6.6
+   */
+  @Deprecated
+  private static final String ABSOLUTE_PATH_PATTERN_PREFIX = "file:";
+  final WildcardPattern pattern;
+
+  PathPattern(String pattern) {
+    this.pattern = WildcardPattern.create(pattern);
+  }
+
+  public abstract boolean match(Path absolutePath, Path relativePath);
+
+  public abstract boolean match(Path absolutePath, Path relativePath, boolean caseSensitiveFileExtension);
+
+  public static PathPattern create(String s) {
+    String trimmed = StringUtils.trim(s);
+    if (StringUtils.startsWithIgnoreCase(trimmed, ABSOLUTE_PATH_PATTERN_PREFIX)) {
+      LOG.warn("Using absolute path pattern is deprecated. Please use relative path instead of '" + trimmed + "'");
+      return new AbsolutePathPattern(StringUtils.substring(trimmed, ABSOLUTE_PATH_PATTERN_PREFIX.length()));
+    }
+    return new RelativePathPattern(trimmed);
+  }
+
+  public static PathPattern[] create(String[] s) {
+    PathPattern[] result = new PathPattern[s.length];
+    for (int i = 0; i < s.length; i++) {
+      result[i] = create(s[i]);
+    }
+    return result;
+  }
+
+  /**
+   * @deprecated since 6.6
+   */
+  @Deprecated
+  private static class AbsolutePathPattern extends PathPattern {
+    private AbsolutePathPattern(String pattern) {
+      super(pattern);
+    }
+
+    @Override
+    public boolean match(Path absolutePath, Path relativePath) {
+      return match(absolutePath, relativePath, true);
+    }
+
+    @Override
+    public boolean match(Path absolutePath, Path relativePath, boolean caseSensitiveFileExtension) {
+      String path = PathUtils.sanitize(absolutePath.toString());
+      if (!caseSensitiveFileExtension) {
+        String extension = sanitizeExtension(FilenameUtils.getExtension(path));
+        if (StringUtils.isNotBlank(extension)) {
+          path = StringUtils.removeEndIgnoreCase(path, extension);
+          path = path + extension;
+        }
+      }
+      return pattern.match(path);
+    }
+
+    @Override
+    public String toString() {
+      return ABSOLUTE_PATH_PATTERN_PREFIX + pattern.toString();
+    }
+  }
+
+  /**
+   * Path relative to module basedir
+   */
+  private static class RelativePathPattern extends PathPattern {
+    private RelativePathPattern(String pattern) {
+      super(pattern);
+    }
+
+    @Override
+    public boolean match(Path absolutePath, Path relativePath) {
+      return match(absolutePath, relativePath, true);
+    }
+
+    @Override
+    public boolean match(Path absolutePath, Path relativePath, boolean caseSensitiveFileExtension) {
+      String path = PathUtils.sanitize(relativePath.toString());
+      if (!caseSensitiveFileExtension) {
+        String extension = sanitizeExtension(FilenameUtils.getExtension(path));
+        if (StringUtils.isNotBlank(extension)) {
+          path = StringUtils.removeEndIgnoreCase(path, extension);
+          path = path + extension;
+        }
+      }
+      return path != null && pattern.match(path);
+    }
+
+    @Override
+    public String toString() {
+      return pattern.toString();
+    }
+  }
+
+  static String sanitizeExtension(String suffix) {
+    return StringUtils.lowerCase(StringUtils.removeStart(suffix, "."));
+  }
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/SensorStrategy.java

@@ -0,0 +1,41 @@
+/*
+ * 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.fs;
+
+import org.sonar.api.batch.fs.InputFile;
+
+/**
+ * A shared, mutable object in the project container.
+ * It's used during the execution of sensors to decide whether
+ * sensors should be executed once for the entire project, or per-module.
+ * It is also injected into each InputFile to change the behavior of {@link InputFile#relativePath()}
+ */
+public class SensorStrategy {
+
+  private boolean global = true;
+
+  public boolean isGlobal() {
+    return global;
+  }
+
+  public void setGlobal(boolean global) {
+    this.global = global;
+  }
+}

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/TestInputFileBuilder.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/TestInputFileBuilder.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs;
 
 import java.io.File;
 import java.io.IOException;
@@ -31,6 +31,7 @@ import javax.annotation.CheckForNull;
 import javax.annotation.Nullable;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.fs.internal.Metadata;
 import org.sonar.api.utils.PathUtils;
 
 /**

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/charhandler/CharHandler.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/charhandler/CharHandler.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal.charhandler;
+package org.sonar.scanner.fs.charhandler;
 
 public abstract class CharHandler {
 

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/charhandler/FileHashComputer.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/charhandler/FileHashComputer.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal.charhandler;
+package org.sonar.scanner.fs.charhandler;
 
 import java.nio.ByteBuffer;
 import java.nio.CharBuffer;
@@ -26,7 +26,6 @@ import java.nio.charset.CharsetEncoder;
 import java.nio.charset.CodingErrorAction;
 import java.nio.charset.StandardCharsets;
 import java.security.MessageDigest;
-
 import org.apache.commons.codec.binary.Hex;
 import org.apache.commons.codec.digest.DigestUtils;
 

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/charhandler/IntArrayList.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/charhandler/IntArrayList.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal.charhandler;
+package org.sonar.scanner.fs.charhandler;
 
 import java.util.Arrays;
 import java.util.Collection;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/charhandler/LineCounter.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/charhandler/LineCounter.java

@@ -17,10 +17,9 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal.charhandler;
+package org.sonar.scanner.fs.charhandler;
 
 import java.nio.charset.Charset;
-
 import org.sonar.api.CoreProperties;
 import org.sonar.api.utils.log.Logger;
 import org.sonar.api.utils.log.Loggers;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/charhandler/LineHashComputer.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/charhandler/LineHashComputer.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal.charhandler;
+package org.sonar.scanner.fs.charhandler;
 
 import java.io.File;
 import java.nio.ByteBuffer;
@@ -27,19 +27,18 @@ import java.nio.charset.CharsetEncoder;
 import java.nio.charset.CodingErrorAction;
 import java.nio.charset.StandardCharsets;
 import java.security.MessageDigest;
-
 import org.apache.commons.codec.digest.DigestUtils;
-import org.sonar.api.batch.fs.internal.FileMetadata.LineHashConsumer;
+import org.sonar.scanner.fs.FileMetadata;
 
 public class LineHashComputer extends CharHandler {
   private final MessageDigest lineMd5Digest = DigestUtils.getMd5Digest();
   private final CharsetEncoder encoder;
   private final StringBuilder sb = new StringBuilder();
-  private final LineHashConsumer consumer;
+  private final FileMetadata.LineHashConsumer consumer;
   private final File file;
   private int line = 1;
 
-  public LineHashComputer(LineHashConsumer consumer, File f) {
+  public LineHashComputer(FileMetadata.LineHashConsumer consumer, File f) {
     this.consumer = consumer;
     this.file = f;
     this.encoder = StandardCharsets.UTF_8.newEncoder()

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/charhandler/LineOffsetCounter.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/charhandler/LineOffsetCounter.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal.charhandler;
+package org.sonar.scanner.fs.charhandler;
 
 public class LineOffsetCounter extends CharHandler {
   private long currentOriginalLineStartOffset = 0;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/charhandler/package-info.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/charhandler/package-info.java

@@ -18,7 +18,7 @@
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
 @ParametersAreNonnullByDefault
-package org.sonar.api.batch.fs.internal.charhandler;
+package org.sonar.scanner.fs.charhandler;
 
 import javax.annotation.ParametersAreNonnullByDefault;
 

sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/package-info.java

@@ -0,0 +1,24 @@
+/*
+ * 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.
+ */
+@ParametersAreNonnullByDefault
+package org.sonar.scanner.fs;
+
+import javax.annotation.ParametersAreNonnullByDefault;
+

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/AbsolutePathPredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/AbsolutePathPredicate.java

@@ -17,17 +17,16 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
-
-import org.sonar.api.batch.fs.FileSystem.Index;
-import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.scan.filesystem.PathResolver;
-import org.sonar.api.utils.PathUtils;
+package org.sonar.scanner.fs.predicates;
 
 import java.io.File;
 import java.nio.file.Path;
 import java.util.Arrays;
 import java.util.Collections;
+import org.sonar.api.batch.fs.FileSystem.Index;
+import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.scan.filesystem.PathResolver;
+import org.sonar.api.utils.PathUtils;
 
 /**
  * @since 4.2

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/AbstractFilePredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/AbstractFilePredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import java.util.stream.StreamSupport;
 import org.sonar.api.batch.fs.FileSystem.Index;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/AndPredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/AndPredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import java.util.ArrayList;
 import java.util.Collection;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultFilePredicates.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/DefaultFilePredicates.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import java.io.File;
 import java.net.URI;
@@ -30,9 +30,10 @@ import org.sonar.api.batch.fs.FilePredicate;
 import org.sonar.api.batch.fs.FilePredicates;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.InputFile.Status;
+import org.sonar.scanner.fs.PathPattern;
 
 /**
- * Factory of {@link org.sonar.api.batch.fs.FilePredicate}
+ * Factory of {@link FilePredicate}
  *
  * @since 4.2
  */

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/FalsePredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/FalsePredicate.java

@@ -17,14 +17,13 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
+import java.util.Collections;
 import org.sonar.api.batch.fs.FilePredicate;
 import org.sonar.api.batch.fs.FileSystem.Index;
 import org.sonar.api.batch.fs.InputFile;
 
-import java.util.Collections;
-
 class FalsePredicate extends AbstractFilePredicate {
 
   static final FilePredicate FALSE = new FalsePredicate();

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/FileExtensionPredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/FileExtensionPredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import java.util.Locale;
 import org.sonar.api.batch.fs.FileSystem;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/FilenamePredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/FilenamePredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import org.sonar.api.batch.fs.FileSystem;
 import org.sonar.api.batch.fs.InputFile;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/LanguagePredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/LanguagePredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import org.sonar.api.batch.fs.InputFile;
 

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/NotPredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/NotPredicate.java

@@ -17,12 +17,14 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import java.util.Arrays;
 import java.util.List;
 import org.sonar.api.batch.fs.FilePredicate;
 import org.sonar.api.batch.fs.InputFile;
+import org.sonar.scanner.fs.predicates.AbstractFilePredicate;
+import org.sonar.scanner.fs.predicates.OperatorPredicate;
 
 /**
  * @since 4.2

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/OperatorPredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/OperatorPredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import java.util.List;
 import org.sonar.api.batch.fs.FilePredicate;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/OptimizedFilePredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/OptimizedFilePredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import org.sonar.api.batch.fs.FilePredicate;
 import org.sonar.api.batch.fs.FileSystem;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/OptimizedFilePredicateAdapter.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/OptimizedFilePredicateAdapter.java

@@ -17,12 +17,12 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import org.sonar.api.batch.fs.FilePredicate;
 import org.sonar.api.batch.fs.InputFile;
 
-class OptimizedFilePredicateAdapter extends AbstractFilePredicate {
+public class OptimizedFilePredicateAdapter extends AbstractFilePredicate {
 
   private FilePredicate unoptimizedPredicate;
 

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/OrPredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/OrPredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import java.util.ArrayList;
 import java.util.Collection;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/PathPatternPredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/PathPatternPredicate.java

@@ -17,10 +17,11 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import java.nio.file.Paths;
 import org.sonar.api.batch.fs.InputFile;
+import org.sonar.scanner.fs.PathPattern;
 
 /**
  * @since 4.2

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/RelativePathPredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/RelativePathPredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import java.util.Collections;
 import javax.annotation.Nullable;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/StatusPredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/StatusPredicate.java

@@ -17,10 +17,11 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import javax.annotation.Nullable;
 import org.sonar.api.batch.fs.InputFile;
+import org.sonar.scanner.fs.predicates.AbstractFilePredicate;
 
 /**
  * @deprecated since 7.8

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/TruePredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/TruePredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import org.sonar.api.batch.fs.FilePredicate;
 import org.sonar.api.batch.fs.FileSystem.Index;

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/TypePredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/TypePredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import org.sonar.api.batch.fs.InputFile;
 

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/URIPredicate.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/fs/predicates/URIPredicate.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.fs.internal;
+package org.sonar.scanner.fs.predicates;
 
 import java.net.URI;
 import java.nio.file.Path;

sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/AbstractDefaultIssue.java

@@ -0,0 +1,122 @@
+/*
+ * 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.issue;
+
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+import javax.annotation.Nullable;
+import org.sonar.api.batch.fs.InputComponent;
+import org.sonar.api.batch.fs.internal.DefaultInputDir;
+import org.sonar.api.batch.fs.internal.DefaultInputModule;
+import org.sonar.api.batch.fs.internal.DefaultInputProject;
+import org.sonar.api.batch.sensor.internal.DefaultStorable;
+import org.sonar.api.batch.sensor.internal.SensorStorage;
+import org.sonar.api.batch.sensor.issue.Issue.Flow;
+import org.sonar.api.batch.sensor.issue.IssueLocation;
+import org.sonar.api.batch.sensor.issue.NewIssueLocation;
+import org.sonar.api.utils.PathUtils;
+
+import static java.util.Collections.unmodifiableList;
+import static java.util.stream.Collectors.toList;
+import static org.sonar.api.utils.Preconditions.checkArgument;
+import static org.sonar.api.utils.Preconditions.checkState;
+
+public abstract class AbstractDefaultIssue<T extends AbstractDefaultIssue> extends DefaultStorable {
+  protected IssueLocation primaryLocation;
+  protected List<List<IssueLocation>> flows = new ArrayList<>();
+  protected DefaultInputProject project;
+
+  protected AbstractDefaultIssue(DefaultInputProject project) {
+    this(project, null);
+  }
+
+  public AbstractDefaultIssue(DefaultInputProject project, @Nullable SensorStorage storage) {
+    super(storage);
+    this.project = project;
+  }
+
+  public IssueLocation primaryLocation() {
+    return primaryLocation;
+  }
+
+  public List<Flow> flows() {
+    return this.flows.stream()
+      .<Flow>map(l -> () -> unmodifiableList(new ArrayList<>(l)))
+      .collect(toList());
+  }
+
+  public NewIssueLocation newLocation() {
+    return new DefaultIssueLocation();
+  }
+
+  public T at(NewIssueLocation primaryLocation) {
+    checkArgument(primaryLocation != null, "Cannot use a location that is null");
+    checkState(this.primaryLocation == null, "at() already called");
+    this.primaryLocation = rewriteLocation((DefaultIssueLocation) primaryLocation);
+    checkArgument(this.primaryLocation.inputComponent() != null, "Cannot use a location with no input component");
+    return (T) this;
+  }
+
+  public T addLocation(NewIssueLocation secondaryLocation) {
+    flows.add(Collections.singletonList(rewriteLocation((DefaultIssueLocation) secondaryLocation)));
+    return (T) this;
+  }
+
+  public T addFlow(Iterable<NewIssueLocation> locations) {
+    List<IssueLocation> flowAsList = new ArrayList<>();
+    for (NewIssueLocation issueLocation : locations) {
+      flowAsList.add(rewriteLocation((DefaultIssueLocation) issueLocation));
+    }
+    flows.add(flowAsList);
+    return (T) this;
+  }
+
+  private DefaultIssueLocation rewriteLocation(DefaultIssueLocation location) {
+    InputComponent component = location.inputComponent();
+    Optional<Path> dirOrModulePath = Optional.empty();
+
+    if (component instanceof DefaultInputDir) {
+      DefaultInputDir dirComponent = (DefaultInputDir) component;
+      dirOrModulePath = Optional.of(project.getBaseDir().relativize(dirComponent.path()));
+    } else if (component instanceof DefaultInputModule && !Objects.equals(project.key(), component.key())) {
+      DefaultInputModule moduleComponent = (DefaultInputModule) component;
+      dirOrModulePath = Optional.of(project.getBaseDir().relativize(moduleComponent.getBaseDir()));
+    }
+
+    if (dirOrModulePath.isPresent()) {
+      String path = PathUtils.sanitize(dirOrModulePath.get().toString());
+      DefaultIssueLocation fixedLocation = new DefaultIssueLocation();
+      fixedLocation.on(project);
+      StringBuilder fullMessage = new StringBuilder();
+      if (path != null && !path.isEmpty()) {
+        fullMessage.append("[").append(path).append("] ");
+      }
+      fullMessage.append(location.message());
+      fixedLocation.message(fullMessage.toString());
+      return fixedLocation;
+    } else {
+      return location;
+    }
+  }
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/DefaultIssue.java

@@ -0,0 +1,93 @@
+/*
+ * 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.issue;
+
+import javax.annotation.Nullable;
+import org.sonar.api.batch.fs.internal.DefaultInputProject;
+import org.sonar.api.batch.rule.Severity;
+import org.sonar.api.batch.sensor.internal.SensorStorage;
+import org.sonar.api.batch.sensor.issue.Issue;
+import org.sonar.api.batch.sensor.issue.IssueLocation;
+import org.sonar.api.batch.sensor.issue.NewIssue;
+import org.sonar.api.rule.RuleKey;
+
+import static java.lang.String.format;
+import static java.util.Objects.requireNonNull;
+import static org.sonar.api.utils.Preconditions.checkArgument;
+import static org.sonar.api.utils.Preconditions.checkState;
+
+public class DefaultIssue extends AbstractDefaultIssue<DefaultIssue> implements Issue, NewIssue {
+  private RuleKey ruleKey;
+  private Double gap;
+  private Severity overriddenSeverity;
+
+  public DefaultIssue(DefaultInputProject project) {
+    this(project, null);
+  }
+
+  public DefaultIssue(DefaultInputProject project, @Nullable SensorStorage storage) {
+    super(project, storage);
+  }
+
+  public DefaultIssue forRule(RuleKey ruleKey) {
+    this.ruleKey = ruleKey;
+    return this;
+  }
+
+  public RuleKey ruleKey() {
+    return this.ruleKey;
+  }
+
+  @Override
+  public DefaultIssue gap(@Nullable Double gap) {
+    checkArgument(gap == null || gap >= 0, format("Gap must be greater than or equal 0 (got %s)", gap));
+    this.gap = gap;
+    return this;
+  }
+
+  @Override
+  public DefaultIssue overrideSeverity(@Nullable Severity severity) {
+    this.overriddenSeverity = severity;
+    return this;
+  }
+
+  @Override
+  public Severity overriddenSeverity() {
+    return this.overriddenSeverity;
+  }
+
+  @Override
+  public Double gap() {
+    return this.gap;
+  }
+
+  @Override
+  public IssueLocation primaryLocation() {
+    return primaryLocation;
+  }
+
+  @Override
+  public void doSave() {
+    requireNonNull(this.ruleKey, "ruleKey is mandatory on issue");
+    checkState(primaryLocation != null, "Primary location is mandatory on every issue");
+    storage.store(this);
+  }
+
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/DefaultIssueLocation.java

@@ -0,0 +1,92 @@
+/*
+ * 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.issue;
+
+import javax.annotation.Nullable;
+import org.sonar.api.batch.fs.InputComponent;
+import org.sonar.api.batch.fs.TextRange;
+import org.sonar.api.batch.fs.internal.DefaultInputFile;
+import org.sonar.api.batch.sensor.issue.IssueLocation;
+import org.sonar.api.batch.sensor.issue.NewIssueLocation;
+
+import static java.util.Objects.requireNonNull;
+import static org.apache.commons.lang.StringUtils.abbreviate;
+import static org.apache.commons.lang.StringUtils.trim;
+import static org.sonar.api.utils.Preconditions.checkArgument;
+import static org.sonar.api.utils.Preconditions.checkState;
+
+public class DefaultIssueLocation implements NewIssueLocation, IssueLocation {
+
+  private InputComponent component;
+  private TextRange textRange;
+  private String message;
+
+  @Override
+  public DefaultIssueLocation on(InputComponent component) {
+    checkArgument(component != null, "Component can't be null");
+    checkState(this.component == null, "on() already called");
+    this.component = component;
+    return this;
+  }
+
+  @Override
+  public DefaultIssueLocation at(TextRange location) {
+    checkState(this.component != null, "at() should be called after on()");
+    checkState(this.component.isFile(), "at() should be called only for an InputFile.");
+    DefaultInputFile file = (DefaultInputFile) this.component;
+    file.validate(location);
+    this.textRange = location;
+    return this;
+  }
+
+  @Override
+  public DefaultIssueLocation message(String message) {
+    requireNonNull(message, "Message can't be null");
+    if (message.contains("\u0000")) {
+      throw new IllegalArgumentException(unsupportedCharacterError(message, component));
+    }
+    this.message = abbreviate(trim(message), MESSAGE_MAX_SIZE);
+    return this;
+  }
+
+  private static String unsupportedCharacterError(String message, @Nullable InputComponent component) {
+    String error = "Character \\u0000 is not supported in issue message '" + message + "'";
+    if (component != null) {
+      error += ", on component: " + component.toString();
+    }
+    return error;
+  }
+
+  @Override
+  public InputComponent inputComponent() {
+    return this.component;
+  }
+
+  @Override
+  public TextRange textRange() {
+    return textRange;
+  }
+
+  @Override
+  public String message() {
+    return this.message;
+  }
+
+}

sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/scanner/IssueExclusionsLoader.java

@@ -24,10 +24,10 @@ import java.util.List;
 import javax.annotation.CheckForNull;
 import org.apache.commons.lang.StringUtils;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
-import org.sonar.api.batch.fs.internal.charhandler.CharHandler;
 import org.sonar.api.notifications.AnalysisWarnings;
 import org.sonar.api.utils.log.Logger;
 import org.sonar.api.utils.log.Loggers;
+import org.sonar.scanner.fs.charhandler.CharHandler;
 import org.sonar.scanner.issue.ignore.IgnoreIssuesFilter;
 import org.sonar.scanner.issue.ignore.pattern.BlockIssuePattern;
 import org.sonar.scanner.issue.ignore.pattern.IssueExclusionPatternInitializer;

sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/scanner/IssueExclusionsRegexpScanner.java

@@ -26,9 +26,9 @@ import java.util.Set;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
-import org.sonar.api.batch.fs.internal.charhandler.CharHandler;
 import org.sonar.api.utils.log.Logger;
 import org.sonar.api.utils.log.Loggers;
+import org.sonar.scanner.fs.charhandler.CharHandler;
 import org.sonar.scanner.issue.ignore.pattern.LineRange;
 import org.sonar.scanner.issue.ignore.scanner.IssueExclusionsLoader.DoubleRegexpMatcher;
 

sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectScanContainer.java

@@ -24,7 +24,6 @@ import javax.annotation.Nullable;
 import org.sonar.api.SonarEdition;
 import org.sonar.api.SonarRuntime;
 import org.sonar.api.batch.fs.internal.DefaultInputModule;
-import org.sonar.api.batch.fs.internal.FileMetadata;
 import org.sonar.api.batch.fs.internal.InputModuleHierarchy;
 import org.sonar.api.batch.fs.internal.SensorStrategy;
 import org.sonar.api.batch.rule.CheckFactory;
@@ -67,6 +66,7 @@ import org.sonar.scanner.cpd.CpdSettings;
 import org.sonar.scanner.cpd.index.SonarCpdBlockIndex;
 import org.sonar.scanner.deprecated.test.TestPlanBuilder;
 import org.sonar.scanner.deprecated.test.TestableBuilder;
+import org.sonar.scanner.fs.FileMetadata;
 import org.sonar.scanner.issue.IssueFilters;
 import org.sonar.scanner.issue.IssuePublisher;
 import org.sonar.scanner.issue.ignore.EnforceIssuesFilter;

sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/AdditionalFilePredicates.java

@@ -20,7 +20,7 @@
 package org.sonar.scanner.scan.filesystem;
 
 import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.internal.AbstractFilePredicate;
+import org.sonar.scanner.fs.predicates.AbstractFilePredicate;
 
 /**
  * Additional {@link org.sonar.api.batch.fs.FilePredicate}s that are

sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/DefaultModuleFileSystem.java

@@ -20,8 +20,8 @@
 package org.sonar.scanner.scan.filesystem;
 
 import com.google.common.annotations.VisibleForTesting;
-import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.batch.fs.internal.DefaultInputModule;
+import org.sonar.scanner.fs.DefaultFileSystem;
 
 public class DefaultModuleFileSystem extends DefaultFileSystem {
 

sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/DefaultProjectFileSystem.java

@@ -20,8 +20,8 @@
 package org.sonar.scanner.scan.filesystem;
 
 import com.google.common.annotations.VisibleForTesting;
-import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.batch.fs.internal.DefaultInputProject;
+import org.sonar.scanner.fs.DefaultFileSystem;
 
 public class DefaultProjectFileSystem extends DefaultFileSystem {
 

sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/InputComponentStore.java

@@ -35,10 +35,10 @@ import java.util.stream.Stream;
 import javax.annotation.CheckForNull;
 import org.sonar.api.batch.fs.InputComponent;
 import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.DefaultInputModule;
-import org.sonar.api.batch.fs.internal.FileExtensionPredicate;
+import org.sonar.scanner.fs.DefaultFileSystem;
+import org.sonar.scanner.fs.predicates.FileExtensionPredicate;
 import org.sonar.scanner.scan.branch.BranchConfiguration;
 
 /**

sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/MetadataGenerator.java

@@ -24,10 +24,10 @@ import java.io.InputStream;
 import java.nio.charset.Charset;
 import org.sonar.api.batch.fs.InputFile.Type;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
-import org.sonar.api.batch.fs.internal.FileMetadata;
 import org.sonar.api.batch.fs.internal.Metadata;
 import org.sonar.api.utils.log.Logger;
 import org.sonar.api.utils.log.Loggers;
+import org.sonar.scanner.fs.FileMetadata;
 import org.sonar.scanner.issue.ignore.scanner.IssueExclusionsLoader;
 
 public class MetadataGenerator {

sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleInputComponentStore.java

@@ -23,8 +23,8 @@ import java.util.SortedSet;
 import org.sonar.api.batch.ScannerSide;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.InputModule;
-import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.batch.fs.internal.SensorStrategy;
+import org.sonar.scanner.fs.DefaultFileSystem;
 
 @ScannerSide
 public class ModuleInputComponentStore extends DefaultFileSystem.Cache {

sonar-plugin-api/src/main/java/org/sonar/api/batch/sensor/internal/InMemorySensorStorage.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/sensor/InMemorySensorStorage.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.sensor.internal;
+package org.sonar.scanner.sensor;
 
 import java.util.ArrayList;
 import java.util.Collection;
@@ -30,6 +30,7 @@ import org.sonar.api.batch.sensor.coverage.internal.DefaultCoverage;
 import org.sonar.api.batch.sensor.cpd.internal.DefaultCpdTokens;
 import org.sonar.api.batch.sensor.error.AnalysisError;
 import org.sonar.api.batch.sensor.highlighting.internal.DefaultHighlighting;
+import org.sonar.api.batch.sensor.internal.SensorStorage;
 import org.sonar.api.batch.sensor.issue.ExternalIssue;
 import org.sonar.api.batch.sensor.issue.Issue;
 import org.sonar.api.batch.sensor.issue.internal.DefaultExternalIssue;

sonar-plugin-api/src/main/java/org/sonar/api/batch/sensor/internal/SensorContextTester.java → sonar-scanner-engine/src/main/java/org/sonar/scanner/sensor/SensorContextTester.java

@@ -17,7 +17,7 @@
  * along with this program; if not, write to the Free Software Foundation,
  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  */
-package org.sonar.api.batch.sensor.internal;
+package org.sonar.scanner.sensor;
 
 import java.io.File;
 import java.io.Serializable;
@@ -39,7 +39,6 @@ import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.InputModule;
 import org.sonar.api.batch.fs.TextRange;
-import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.DefaultInputModule;
 import org.sonar.api.batch.fs.internal.DefaultInputProject;
@@ -86,6 +85,7 @@ import org.sonar.api.measures.Metric;
 import org.sonar.api.scanner.fs.InputProject;
 import org.sonar.api.utils.System2;
 import org.sonar.api.utils.Version;
+import org.sonar.scanner.fs.DefaultFileSystem;
 
 import static java.util.Collections.unmodifiableMap;