Revert "SONAR-21195 Refactor file indexing into two distinct steps"

This reverts commit 42d16dafde01b19bc7fcb99084e087fdc9b8e95e.

24 files changed, 355 insertions, 992 deletions

diff --git a/sonar-scanner-engine/src/it/java/org/sonar/scanner/mediumtest/ScannerMediumTester.java b/sonar-scanner-engine/src/it/java/org/sonar/scanner/mediumtest/ScannerMediumTester.java
index 1916d3e6d00..ebf0dc20efa 100644
--- a/sonar-scanner-engine/src/it/java/org/sonar/scanner/mediumtest/ScannerMediumTester.java
+++ b/sonar-scanner-engine/src/it/java/org/sonar/scanner/mediumtest/ScannerMediumTester.java
@@ -35,7 +35,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Optional;
 import java.util.Properties;
-import java.util.Set;
 import javax.annotation.CheckForNull;
 import javax.annotation.Nullable;
 import javax.annotation.Priority;
@@ -137,12 +136,11 @@ public class ScannerMediumTester extends ExternalResource {
   }
 
   public ScannerMediumTester registerPlugin(String pluginKey, Plugin instance) {
-    pluginInstaller.add(pluginKey, instance);
-    return this;
+    return registerPlugin(pluginKey, instance, 1L);
   }
 
-  public ScannerMediumTester registerOptionalPlugin(String pluginKey, Set<String> requiredForLanguages, Plugin instance) {
-    pluginInstaller.addOptional(pluginKey, requiredForLanguages, instance);
+  public ScannerMediumTester registerPlugin(String pluginKey, Plugin instance, long lastUpdatedAt) {
+    pluginInstaller.add(pluginKey, instance, lastUpdatedAt);
     return this;
   }
 
diff --git a/sonar-scanner-engine/src/it/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumIT.java b/sonar-scanner-engine/src/it/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumIT.java
index 66f35f9cfa8..0bfef5a38ad 100644
--- a/sonar-scanner-engine/src/it/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumIT.java
+++ b/sonar-scanner-engine/src/it/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumIT.java
@@ -29,7 +29,6 @@ import java.nio.file.LinkOption;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.Random;
-import java.util.Set;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.lang.SystemUtils;
@@ -40,10 +39,8 @@ import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
 import org.slf4j.event.Level;
 import org.sonar.api.CoreProperties;
-import org.sonar.api.Plugin;
 import org.sonar.api.SonarEdition;
 import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.InputFileFilter;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.testfixtures.log.LogTester;
 import org.sonar.api.utils.MessageException;
@@ -77,7 +74,6 @@ public class FileSystemMediumIT {
   public ScannerMediumTester tester = new ScannerMediumTester()
     .setEdition(SonarEdition.COMMUNITY)
     .registerPlugin("xoo", new XooPlugin())
-    .registerOptionalPlugin("optional-xoo", Set.of("xoo"), new OptionalXooPlugin())
     .addDefaultQProfile("xoo", "Sonar Way")
     .addDefaultQProfile("xoo2", "Sonar Way");
 
@@ -1185,7 +1181,7 @@ public class FileSystemMediumIT {
 
     assertThatThrownBy(result::execute)
       .isExactlyInstanceOf(IllegalStateException.class)
-      .hasMessageEndingWith(format("Failed to preprocess files"));
+      .hasMessageEndingWith(format("Failed to index files"));
   }
 
   @Test
@@ -1256,42 +1252,7 @@ public class FileSystemMediumIT {
 
     assertThatThrownBy(result::execute)
       .isExactlyInstanceOf(IllegalStateException.class)
-      .hasMessageEndingWith(format("Failed to preprocess files"));
-  }
-
-  @Test
-  public void should_load_input_file_filters_for_required_and_optional_plugins() throws IOException {
-    File projectDir = new File("test-resources/mediumtest/xoo/sample-with-input-file-filters");
-    AnalysisResult result = tester
-      .newAnalysis(new File(projectDir, "sonar-project.properties"))
-      .execute();
-
-    assertThat(result.inputFiles()).hasSize(1);
-
-    assertThat(logTester.logs()).contains("'xources/hello/xoo_exclude2.xoo' excluded by org.sonar.scanner.mediumtest.fs" +
-      ".FileSystemMediumIT$OptionalXooPlugin$OptionalXooFileFilter");
-    assertThat(logTester.logs()).contains("'xources/hello/xoo_exclude.xoo' excluded by org.sonar.xoo.extensions.XooExcludeFileFilter");
-    assertThat(logTester.logs()).contains("'xources/hello/HelloJava.xoo' indexed with language 'xoo'");
-
-    assertThat(result.inputFile("xources/hello/xoo_exclude.xoo")).isNull();
-    assertThat(result.inputFile("xources/hello/xoo_exclude2.xoo")).isNull();
-    assertThat(result.inputFile("xources/hello/HelloJava.xoo")).isNotNull();
-  }
-
-  public static class OptionalXooPlugin implements Plugin {
-
-    @Override
-    public void define(Context context) {
-      context.addExtension(OptionalXooFileFilter.class);
-    }
-
-    public static class OptionalXooFileFilter implements InputFileFilter {
-
-      @Override
-      public boolean accept(InputFile f) {
-        return !f.filename().endsWith("_exclude2.xoo");
-      }
-    }
+      .hasMessageEndingWith(format("Failed to index files"));
   }
 
   private static void assertAnalysedFiles(AnalysisResult result, String... files) {
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/PluginInstaller.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/PluginInstaller.java
index de69726669c..eeb35462dab 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/PluginInstaller.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/PluginInstaller.java
@@ -22,7 +22,6 @@ package org.sonar.scanner.bootstrap;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import org.sonar.scanner.mediumtest.LocalPlugin;
 
 public interface PluginInstaller {
 
@@ -46,14 +45,8 @@ public interface PluginInstaller {
   Map<String, ScannerPlugin> installPluginsForLanguages(Set<String> languageKeys);
 
   /**
-   * Used only by medium tests. Installs required plugins (phase 1)
+   * Used only by medium tests.
    * @see org.sonar.scanner.mediumtest.ScannerMediumTester
    */
-  List<LocalPlugin> installLocals();
-
-  /**
-   * Used only by medium tests. Installs optional plugins (phase 2)
-   * @see org.sonar.scanner.mediumtest.ScannerMediumTester
-   */
-  List<LocalPlugin> installOptionalLocals(Set<String> languageKeys);
+  List<Object[]> installLocals();
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/ScannerPluginInstaller.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/ScannerPluginInstaller.java
index e05b7d08471..efed3403147 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/ScannerPluginInstaller.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/ScannerPluginInstaller.java
@@ -36,7 +36,6 @@ import org.sonar.api.utils.log.Loggers;
 import org.sonar.api.utils.log.Profiler;
 import org.sonar.core.platform.PluginInfo;
 import org.sonar.core.plugin.PluginType;
-import org.sonar.scanner.mediumtest.LocalPlugin;
 import org.sonarqube.ws.client.GetRequest;
 
 import static java.lang.String.format;
@@ -138,15 +137,7 @@ public class ScannerPluginInstaller implements PluginInstaller {
    * Returns empty on purpose. This method is used only by medium tests.
    */
   @Override
-  public List<LocalPlugin> installLocals() {
-    return Collections.emptyList();
-  }
-
-  /**
-   * Returns empty on purpose. This method is used only by medium tests.
-   */
-  @Override
-  public List<LocalPlugin> installOptionalLocals(Set<String> languageKeys) {
+  public List<Object[]> installLocals() {
     return Collections.emptyList();
   }
 
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/ScannerPluginRepository.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/ScannerPluginRepository.java
index 074079f974e..3ce0202292b 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/ScannerPluginRepository.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/ScannerPluginRepository.java
@@ -36,7 +36,6 @@ import org.sonar.core.platform.PluginInfo;
 import org.sonar.core.platform.PluginJarExploder;
 import org.sonar.core.platform.PluginRepository;
 import org.sonar.core.plugin.PluginType;
-import org.sonar.scanner.mediumtest.LocalPlugin;
 
 import static java.util.stream.Collectors.toMap;
 import static org.sonar.api.utils.Preconditions.checkState;
@@ -80,11 +79,11 @@ public class ScannerPluginRepository implements PluginRepository, Startable {
     pluginInstancesByKeys = new HashMap<>(loader.load(explodedPluginsByKey));
 
     // this part is only used by medium tests
-    for (LocalPlugin localPlugin : installer.installLocals()) {
-      ScannerPlugin scannerPlugin = localPlugin.toScannerPlugin();
-      String pluginKey = localPlugin.pluginKey();
-      pluginsByKeys.put(pluginKey, scannerPlugin);
-      pluginInstancesByKeys.put(pluginKey, localPlugin.pluginInstance());
+    for (Object[] localPlugin : installer.installLocals()) {
+      String pluginKey = (String) localPlugin[0];
+      PluginInfo pluginInfo = new PluginInfo(pluginKey);
+      pluginsByKeys.put(pluginKey, new ScannerPlugin(pluginInfo.getKey(), (long) localPlugin[2], PluginType.BUNDLED, pluginInfo));
+      pluginInstancesByKeys.put(pluginKey, (Plugin) localPlugin[1]);
     }
 
     keysByClassLoader = new HashMap<>();
@@ -108,15 +107,6 @@ public class ScannerPluginRepository implements PluginRepository, Startable {
       .collect(toMap(Map.Entry::getKey, e -> pluginJarExploder.explode(e.getValue().getInfo())));
     pluginInstancesByKeys.putAll(new HashMap<>(loader.load(explodedPluginsByKey)));
 
-    // this part is only used by medium tests
-    for (LocalPlugin localPlugin : installer.installOptionalLocals(languageKeys)) {
-      ScannerPlugin scannerPlugin = localPlugin.toScannerPlugin();
-      String pluginKey = localPlugin.pluginKey();
-      languagePluginsByKeys.put(pluginKey, scannerPlugin);
-      pluginsByKeys.put(pluginKey, scannerPlugin);
-      pluginInstancesByKeys.put(pluginKey, localPlugin.pluginInstance());
-    }
-
     keysByClassLoader = new HashMap<>();
     for (Map.Entry<String, Plugin> e : pluginInstancesByKeys.entrySet()) {
       keysByClassLoader.put(e.getValue().getClass().getClassLoader(), e.getKey());
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/SpringScannerContainer.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/SpringScannerContainer.java
index 38972c95071..eedc07f9924 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/SpringScannerContainer.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/SpringScannerContainer.java
@@ -112,14 +112,13 @@ import org.sonar.scanner.scan.branch.BranchConfigurationProvider;
 import org.sonar.scanner.scan.branch.BranchType;
 import org.sonar.scanner.scan.branch.ProjectBranchesProvider;
 import org.sonar.scanner.scan.filesystem.DefaultProjectFileSystem;
-import org.sonar.scanner.scan.filesystem.FilePreprocessor;
+import org.sonar.scanner.scan.filesystem.FileIndexer;
 import org.sonar.scanner.scan.filesystem.InputComponentStore;
 import org.sonar.scanner.scan.filesystem.LanguageDetection;
 import org.sonar.scanner.scan.filesystem.MetadataGenerator;
-import org.sonar.scanner.scan.filesystem.ModuleRelativePathWarner;
 import org.sonar.scanner.scan.filesystem.ProjectCoverageAndDuplicationExclusions;
 import org.sonar.scanner.scan.filesystem.ProjectExclusionFilters;
-import org.sonar.scanner.scan.filesystem.ProjectFilePreprocessor;
+import org.sonar.scanner.scan.filesystem.ProjectFileIndexer;
 import org.sonar.scanner.scan.filesystem.ScannerComponentIdGenerator;
 import org.sonar.scanner.scan.filesystem.StatusDetection;
 import org.sonar.scanner.scan.measure.DefaultMetricFinder;
@@ -194,9 +193,8 @@ public class SpringScannerContainer extends SpringComponentContainer {
       LanguageDetection.class,
       MetadataGenerator.class,
       FileMetadata.class,
-      ModuleRelativePathWarner.class,
-      FilePreprocessor.class,
-      ProjectFilePreprocessor.class,
+      FileIndexer.class,
+      ProjectFileIndexer.class,
       ProjectExclusionFilters.class,
 
       // rules
@@ -337,7 +335,7 @@ public class SpringScannerContainer extends SpringComponentContainer {
 
     getComponentByType(DeprecatedPropertiesWarningGenerator.class).execute();
 
-    getComponentByType(ProjectFilePreprocessor.class).execute();
+    getComponentByType(ProjectFileIndexer.class).index();
     new SpringProjectScanContainer(this).execute();
   }
 
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/mediumtest/FakePluginInstaller.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/mediumtest/FakePluginInstaller.java
index 5aaabab3980..fb48e11b424 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/mediumtest/FakePluginInstaller.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/mediumtest/FakePluginInstaller.java
@@ -36,21 +36,15 @@ import org.sonar.scanner.bootstrap.ScannerPlugin;
 public class FakePluginInstaller implements PluginInstaller {
 
   private final Map<String, ScannerPlugin> pluginsByKeys = new HashMap<>();
-  private final List<LocalPlugin> mediumTestPlugins = new ArrayList<>();
-  private final List<LocalPlugin> optionalMediumTestPlugins = new ArrayList<>();
+  private final List<Object[]> mediumTestPlugins = new ArrayList<>();
 
   public FakePluginInstaller add(String pluginKey, File jarFile, long lastUpdatedAt) {
     pluginsByKeys.put(pluginKey, new ScannerPlugin(pluginKey, lastUpdatedAt, PluginType.BUNDLED, PluginInfo.create(jarFile)));
     return this;
   }
 
-  public FakePluginInstaller add(String pluginKey, Plugin instance) {
-    mediumTestPlugins.add(new LocalPlugin(pluginKey, instance, Set.of()));
-    return this;
-  }
-
-  public FakePluginInstaller addOptional(String pluginKey, Set<String> requiredForLanguages, Plugin instance) {
-    optionalMediumTestPlugins.add(new LocalPlugin(pluginKey, instance, requiredForLanguages));
+  public FakePluginInstaller add(String pluginKey, Plugin instance, long lastUpdatedAt) {
+    mediumTestPlugins.add(new Object[] {pluginKey, instance, lastUpdatedAt});
     return this;
   }
 
@@ -70,14 +64,7 @@ public class FakePluginInstaller implements PluginInstaller {
   }
 
   @Override
-  public List<LocalPlugin> installLocals() {
+  public List<Object[]> installLocals() {
     return mediumTestPlugins;
   }
-
-  @Override
-  public List<LocalPlugin> installOptionalLocals(Set<String> languageKeys) {
-    return optionalMediumTestPlugins.stream()
-      .filter(plugin -> languageKeys.stream().anyMatch(lang -> plugin.requiredForLanguages().contains(lang)))
-      .toList();
-  }
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/mediumtest/LocalPlugin.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/mediumtest/LocalPlugin.java
deleted file mode 100644
index 20bd4895973..00000000000
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/mediumtest/LocalPlugin.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2023 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.mediumtest;
-
-import java.util.Set;
-import org.sonar.api.Plugin;
-import org.sonar.core.platform.PluginInfo;
-import org.sonar.core.plugin.PluginType;
-import org.sonar.scanner.bootstrap.ScannerPlugin;
-
-public record LocalPlugin(String pluginKey, Plugin pluginInstance, Set<String> requiredForLanguages) {
-
-  public ScannerPlugin toScannerPlugin() {
-    return new ScannerPlugin(pluginKey, 1L, PluginType.BUNDLED, new PluginInfo(pluginKey));
-  }
-}
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/SpringProjectScanContainer.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/SpringProjectScanContainer.java
index b70fde51660..351593e9404 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/SpringProjectScanContainer.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/SpringProjectScanContainer.java
@@ -49,10 +49,7 @@ import org.sonar.scanner.qualitygate.QualityGateCheck;
 import org.sonar.scanner.report.ContextPropertiesPublisher;
 import org.sonar.scanner.report.ReportPublisher;
 import org.sonar.scanner.rule.QProfileVerifier;
-import org.sonar.scanner.scan.filesystem.FileIndexer;
-import org.sonar.scanner.scan.filesystem.InputFileFilterRepository;
-import org.sonar.scanner.scan.filesystem.LanguageDetection;
-import org.sonar.scanner.scan.filesystem.ProjectFileIndexer;
+import org.sonar.scanner.scan.filesystem.InputComponentStore;
 import org.sonar.scanner.scm.ScmPublisher;
 import org.sonar.scanner.sensor.ProjectSensorExtensionDictionary;
 import org.sonar.scanner.sensor.ProjectSensorsExecutor;
@@ -72,7 +69,7 @@ public class SpringProjectScanContainer extends SpringComponentContainer {
 
   @Override
   protected void doBeforeStart() {
-    Set<String> languages = getParentComponentByType(LanguageDetection.class).getDetectedLanguages();
+    Set<String> languages = getParentComponentByType(InputComponentStore.class).languages();
     installPluginsForLanguages(languages);
     addScannerComponents();
   }
@@ -117,12 +114,7 @@ public class SpringProjectScanContainer extends SpringComponentContainer {
       ProjectSensorExtensionDictionary.class,
       ProjectSensorsExecutor.class,
 
-      AnalysisObservers.class,
-
-      // file system
-      InputFileFilterRepository.class,
-      FileIndexer.class,
-      ProjectFileIndexer.class);
+      AnalysisObservers.class);
   }
 
   static ExtensionMatcher getScannerProjectExtensionsFilter() {
@@ -138,7 +130,6 @@ public class SpringProjectScanContainer extends SpringComponentContainer {
   protected void doAfterStart() {
     getParentComponentByType(ScannerMetrics.class).addPluginMetrics(getComponentsByType(Metrics.class));
     getComponentByType(ProjectLock.class).tryLock();
-    getComponentByType(ProjectFileIndexer.class).index();
     GlobalAnalysisMode analysisMode = getComponentByType(GlobalAnalysisMode.class);
     InputModuleHierarchy tree = getComponentByType(InputModuleHierarchy.class);
     ScanProperties properties = getComponentByType(ScanProperties.class);
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/DirectoryFileVisitor.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/DirectoryFileVisitor.java
deleted file mode 100644
index eec0ed9c8d0..00000000000
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/DirectoryFileVisitor.java
+++ /dev/null
@@ -1,152 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2023 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.filesystem;
-
-import java.io.IOException;
-import java.nio.file.AccessDeniedException;
-import java.nio.file.FileSystemLoopException;
-import java.nio.file.FileVisitResult;
-import java.nio.file.FileVisitor;
-import java.nio.file.Files;
-import java.nio.file.LinkOption;
-import java.nio.file.Path;
-import java.nio.file.attribute.BasicFileAttributes;
-import java.nio.file.attribute.DosFileAttributes;
-import org.apache.commons.lang.SystemUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.internal.DefaultInputModule;
-import org.sonar.scanner.fs.InputModuleHierarchy;
-
-public class DirectoryFileVisitor implements FileVisitor<Path> {
-
-  private static final Logger LOG = LoggerFactory.getLogger(DirectoryFileVisitor.class);
-
-  private final FileVisitAction fileVisitAction;
-  private final DefaultInputModule module;
-  private final ModuleExclusionFilters moduleExclusionFilters;
-
-  private final InputModuleHierarchy inputModuleHierarchy;
-  private final InputFile.Type type;
-
-  DirectoryFileVisitor(FileVisitAction fileVisitAction, DefaultInputModule module, ModuleExclusionFilters moduleExclusionFilters, InputModuleHierarchy inputModuleHierarchy, InputFile.Type type) {
-    this.fileVisitAction = fileVisitAction;
-    this.module = module;
-    this.moduleExclusionFilters = moduleExclusionFilters;
-    this.inputModuleHierarchy = inputModuleHierarchy;
-    this.type = type;
-  }
-
-  @Override
-  public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) throws IOException {
-    return isHidden(dir) ? FileVisitResult.SKIP_SUBTREE : FileVisitResult.CONTINUE;
-  }
-
-  @Override
-  public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
-    if (!Files.isHidden(file)) {
-      fileVisitAction.execute(file);
-    }
-    return FileVisitResult.CONTINUE;
-  }
-
-  /**
-   * <p>Overridden method to handle exceptions while visiting files in the analysis.</p>
-   *
-   * <p>
-   *   <ul>
-   *     <li>FileSystemLoopException - We show a warning that a symlink loop exists and we skip the file.</li>
-   *     <li>AccessDeniedException for excluded files/directories - We skip the file, as files excluded from the analysis, shouldn't throw access exceptions.</li>
-   *   </ul>
-   * </p>
-   *
-   * @param file a reference to the file
-   * @param exc  the I/O exception that prevented the file from being visited
-   * @throws IOException
-   */
-  @Override
-  public FileVisitResult visitFileFailed(Path file, IOException exc) throws IOException {
-    if (exc instanceof FileSystemLoopException) {
-      LOG.warn("Not indexing due to symlink loop: {}", file.toFile());
-      return FileVisitResult.CONTINUE;
-    } else if (exc instanceof AccessDeniedException && isExcluded(file)) {
-      return FileVisitResult.CONTINUE;
-    }
-    throw exc;
-  }
-
-  /**
-   * <p>Checks if the directory is excluded in the analysis or not. Only the exclusions are checked.</p>
-   *
-   * <p>The inclusions cannot be checked for directories, since the current implementation of pattern matching is intended only for files.</p>
-   *
-   * @param path The file or directory.
-   * @return True if file/directory is excluded from the analysis, false otherwise.
-   */
-  private boolean isExcluded(Path path) throws IOException {
-    Path realAbsoluteFile = path.toRealPath(LinkOption.NOFOLLOW_LINKS).toAbsolutePath().normalize();
-    return isExcludedDirectory(moduleExclusionFilters, realAbsoluteFile, inputModuleHierarchy.root().getBaseDir(), module.getBaseDir(), type);
-  }
-
-  /**
-   * <p>Checks if the path is a directory that is excluded.</p>
-   *
-   * <p>Exclusions patterns are checked both at project and module level.</p>
-   *
-   * @param moduleExclusionFilters The exclusion filters.
-   * @param realAbsoluteFile       The path to be checked.
-   * @param projectBaseDir         The project base directory.
-   * @param moduleBaseDir          The module base directory.
-   * @param type                   The input file type.
-   * @return True if path is an excluded directory, false otherwise.
-   */
-  private static boolean isExcludedDirectory(ModuleExclusionFilters moduleExclusionFilters, Path realAbsoluteFile, Path projectBaseDir, Path moduleBaseDir,
-    InputFile.Type type) {
-    Path projectRelativePath = projectBaseDir.relativize(realAbsoluteFile);
-    Path moduleRelativePath = moduleBaseDir.relativize(realAbsoluteFile);
-    return moduleExclusionFilters.isExcludedAsParentDirectoryOfExcludedChildren(realAbsoluteFile, projectRelativePath, projectBaseDir, type)
-      || moduleExclusionFilters.isExcludedAsParentDirectoryOfExcludedChildren(realAbsoluteFile, moduleRelativePath, moduleBaseDir, type);
-  }
-
-  @Override
-  public FileVisitResult postVisitDirectory(Path dir, IOException exc) {
-    return FileVisitResult.CONTINUE;
-  }
-
-  private static boolean isHidden(Path path) throws IOException {
-    if (SystemUtils.IS_OS_WINDOWS) {
-      try {
-        DosFileAttributes dosFileAttributes = Files.readAttributes(path, DosFileAttributes.class, LinkOption.NOFOLLOW_LINKS);
-        return dosFileAttributes.isHidden();
-      } catch (UnsupportedOperationException e) {
-        return path.toFile().isHidden();
-      }
-    } else {
-      return Files.isHidden(path);
-    }
-  }
-
-  @FunctionalInterface
-  interface FileVisitAction {
-    void execute(Path file) throws IOException;
-  }
-}
-
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/FileIndexer.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/FileIndexer.java
index 4d264590716..4d9b8c2a377 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/FileIndexer.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/FileIndexer.java
@@ -19,10 +19,14 @@
  */
 package org.sonar.scanner.scan.filesystem;
 
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.LinkOption;
 import java.nio.file.Path;
 import java.util.Arrays;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import java.util.function.BooleanSupplier;
+import javax.annotation.Nullable;
+import org.apache.commons.io.FilenameUtils;
 import org.sonar.api.CoreProperties;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.InputFile.Type;
@@ -32,7 +36,11 @@ 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.SensorStrategy;
+import org.sonar.api.batch.scm.IgnoreCommand;
+import org.sonar.api.notifications.AnalysisWarnings;
 import org.sonar.api.utils.MessageException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.sonar.scanner.issue.ignore.scanner.IssueExclusionsLoader;
 import org.sonar.scanner.repository.language.Language;
 import org.sonar.scanner.scan.ScanProperties;
@@ -48,7 +56,10 @@ public class FileIndexer {
 
   private static final Logger LOG = LoggerFactory.getLogger(FileIndexer.class);
 
+  private final AnalysisWarnings analysisWarnings;
   private final ScanProperties properties;
+  private final InputFileFilter[] filters;
+  private final ProjectExclusionFilters projectExclusionFilters;
   private final ProjectCoverageAndDuplicationExclusions projectCoverageAndDuplicationExclusions;
   private final IssueExclusionsLoader issueExclusionsLoader;
   private final MetadataGenerator metadataGenerator;
@@ -60,13 +71,15 @@ public class FileIndexer {
   private final StatusDetection statusDetection;
   private final ScmChangedFiles scmChangedFiles;
 
-  private final ModuleRelativePathWarner moduleRelativePathWarner;
-  private final InputFileFilterRepository inputFileFilterRepository;
+  private boolean warnInclusionsAlreadyLogged;
+  private boolean warnExclusionsAlreadyLogged;
+  private boolean warnCoverageExclusionsAlreadyLogged;
+  private boolean warnDuplicationExclusionsAlreadyLogged;
 
   public FileIndexer(DefaultInputProject project, ScannerComponentIdGenerator scannerComponentIdGenerator, InputComponentStore componentStore,
-    ProjectCoverageAndDuplicationExclusions projectCoverageAndDuplicationExclusions, IssueExclusionsLoader issueExclusionsLoader,
-    MetadataGenerator metadataGenerator, SensorStrategy sensorStrategy, LanguageDetection languageDetection, ScanProperties properties,
-    ScmChangedFiles scmChangedFiles, StatusDetection statusDetection, ModuleRelativePathWarner moduleRelativePathWarner, InputFileFilterRepository inputFileFilterRepository) {
+    ProjectExclusionFilters projectExclusionFilters, ProjectCoverageAndDuplicationExclusions projectCoverageAndDuplicationExclusions, IssueExclusionsLoader issueExclusionsLoader,
+    MetadataGenerator metadataGenerator, SensorStrategy sensorStrategy, LanguageDetection languageDetection, AnalysisWarnings analysisWarnings, ScanProperties properties,
+    InputFileFilter[] filters, ScmChangedFiles scmChangedFiles, StatusDetection statusDetection) {
     this.project = project;
     this.scannerComponentIdGenerator = scannerComponentIdGenerator;
     this.componentStore = componentStore;
@@ -75,23 +88,55 @@ public class FileIndexer {
     this.metadataGenerator = metadataGenerator;
     this.sensorStrategy = sensorStrategy;
     this.langDetection = languageDetection;
+    this.analysisWarnings = analysisWarnings;
     this.properties = properties;
+    this.filters = filters;
+    this.projectExclusionFilters = projectExclusionFilters;
     this.scmChangedFiles = scmChangedFiles;
     this.statusDetection = statusDetection;
-    this.moduleRelativePathWarner = moduleRelativePathWarner;
-    this.inputFileFilterRepository = inputFileFilterRepository;
   }
 
-  void indexFile(DefaultInputModule module, ModuleCoverageAndDuplicationExclusions moduleCoverageAndDuplicationExclusions, Path sourceFile,
-    Type type, ProgressReport progressReport) {
-    Path projectRelativePath = project.getBaseDir().relativize(sourceFile);
-    Path moduleRelativePath = module.getBaseDir().relativize(sourceFile);
+  void indexFile(DefaultInputModule module, ModuleExclusionFilters moduleExclusionFilters, ModuleCoverageAndDuplicationExclusions moduleCoverageAndDuplicationExclusions,
+    Path sourceFile, Type type, ProgressReport progressReport, ProjectFileIndexer.ExclusionCounter exclusionCounter, @Nullable IgnoreCommand ignoreCommand)
+    throws IOException {
+    // get case of real file without resolving link
+    Path realAbsoluteFile = sourceFile.toRealPath(LinkOption.NOFOLLOW_LINKS).toAbsolutePath().normalize();
+    Path projectRelativePath = project.getBaseDir().relativize(realAbsoluteFile);
+    Path moduleRelativePath = module.getBaseDir().relativize(realAbsoluteFile);
+    boolean included = evaluateInclusionsFilters(moduleExclusionFilters, realAbsoluteFile, projectRelativePath, moduleRelativePath, type);
+    if (!included) {
+      exclusionCounter.increaseByPatternsCount();
+      return;
+    }
+    boolean excluded = evaluateExclusionsFilters(moduleExclusionFilters, realAbsoluteFile, projectRelativePath, moduleRelativePath, type);
+    if (excluded) {
+      exclusionCounter.increaseByPatternsCount();
+      return;
+    }
+    if (!realAbsoluteFile.startsWith(project.getBaseDir())) {
+      LOG.warn("File '{}' is ignored. It is not located in project basedir '{}'.", realAbsoluteFile.toAbsolutePath(), project.getBaseDir());
+      return;
+    }
+    if (!realAbsoluteFile.startsWith(module.getBaseDir())) {
+      LOG.warn("File '{}' is ignored. It is not located in module basedir '{}'.", realAbsoluteFile.toAbsolutePath(), module.getBaseDir());
+      return;
+    }
+
+    if (Files.exists(realAbsoluteFile) && isFileSizeBiggerThanLimit(realAbsoluteFile)) {
+      LOG.warn("File '{}' is bigger than {}MB and as consequence is removed from the analysis scope.", realAbsoluteFile.toAbsolutePath(), properties.fileSizeLimit());
+      return;
+    }
+
+    Language language = langDetection.language(realAbsoluteFile, projectRelativePath);
 
-    // This should be fast; language should be cached from preprocessing step
-    Language language = langDetection.language(sourceFile, projectRelativePath);
+    if (ignoreCommand != null && ignoreCommand.isIgnored(realAbsoluteFile)) {
+      LOG.debug("File '{}' is excluded by the scm ignore settings.", realAbsoluteFile);
+      exclusionCounter.increaseByScmCount();
+      return;
+    }
 
     DefaultIndexedFile indexedFile = new DefaultIndexedFile(
-      sourceFile,
+      realAbsoluteFile,
       project.key(),
       projectRelativePath.toString(),
       moduleRelativePath.toString(),
@@ -99,7 +144,7 @@ public class FileIndexer {
       language != null ? language.key() : null,
       scannerComponentIdGenerator.getAsInt(),
       sensorStrategy,
-      scmChangedFiles.getOldRelativeFilePath(sourceFile)
+      scmChangedFiles.getOldRelativeFilePath(realAbsoluteFile)
     );
 
     DefaultInputFile inputFile = new DefaultInputFile(indexedFile, f -> metadataGenerator.setMetadata(module.key(), f, module.getEncoding()),
@@ -114,9 +159,7 @@ public class FileIndexer {
     componentStore.put(module.key(), inputFile);
     issueExclusionsLoader.addMulticriteriaPatterns(inputFile);
     String langStr = inputFile.language() != null ? format("with language '%s'", inputFile.language()) : "with no language";
-    if (LOG.isDebugEnabled()) {
-      LOG.debug("'{}' indexed {}{}", projectRelativePath, type == Type.TEST ? "as test " : "", langStr);
-    }
+    LOG.debug("'{}' indexed {}{}", projectRelativePath, type == Type.TEST ? "as test " : "", langStr);
     evaluateCoverageExclusions(moduleCoverageAndDuplicationExclusions, inputFile);
     evaluateDuplicationExclusions(moduleCoverageAndDuplicationExclusions, inputFile);
     if (properties.preloadFileMetadata()) {
@@ -126,6 +169,42 @@ public class FileIndexer {
     progressReport.message(count + " " + pluralizeFiles(count) + " indexed...  (last one was " + inputFile.getProjectRelativePath() + ")");
   }
 
+  private boolean evaluateInclusionsFilters(ModuleExclusionFilters moduleExclusionFilters, Path realAbsoluteFile, Path projectRelativePath, Path moduleRelativePath,
+    InputFile.Type type) {
+    if (!Arrays.equals(moduleExclusionFilters.getInclusionsConfig(type), projectExclusionFilters.getInclusionsConfig(type))) {
+      // Module specific configuration
+      return moduleExclusionFilters.isIncluded(realAbsoluteFile, moduleRelativePath, type);
+    }
+    boolean includedByProjectConfiguration = projectExclusionFilters.isIncluded(realAbsoluteFile, projectRelativePath, type);
+    if (includedByProjectConfiguration) {
+      return true;
+    } else if (moduleExclusionFilters.isIncluded(realAbsoluteFile, moduleRelativePath, type)) {
+      warnOnce(
+        type == Type.MAIN ? CoreProperties.PROJECT_INCLUSIONS_PROPERTY : CoreProperties.PROJECT_TEST_INCLUSIONS_PROPERTY,
+        FilenameUtils.normalize(projectRelativePath.toString(), true), () -> warnInclusionsAlreadyLogged, () -> warnInclusionsAlreadyLogged = true);
+      return true;
+    }
+    return false;
+  }
+
+  private boolean evaluateExclusionsFilters(ModuleExclusionFilters moduleExclusionFilters, Path realAbsoluteFile, Path projectRelativePath, Path moduleRelativePath,
+    InputFile.Type type) {
+    if (!Arrays.equals(moduleExclusionFilters.getExclusionsConfig(type), projectExclusionFilters.getExclusionsConfig(type))) {
+      // Module specific configuration
+      return moduleExclusionFilters.isExcluded(realAbsoluteFile, moduleRelativePath, type);
+    }
+    boolean includedByProjectConfiguration = projectExclusionFilters.isExcluded(realAbsoluteFile, projectRelativePath, type);
+    if (includedByProjectConfiguration) {
+      return true;
+    } else if (moduleExclusionFilters.isExcluded(realAbsoluteFile, moduleRelativePath, type)) {
+      warnOnce(
+        type == Type.MAIN ? CoreProperties.PROJECT_EXCLUSIONS_PROPERTY : CoreProperties.PROJECT_TEST_EXCLUSIONS_PROPERTY,
+        FilenameUtils.normalize(projectRelativePath.toString(), true), () -> warnExclusionsAlreadyLogged, () -> warnExclusionsAlreadyLogged = true);
+      return true;
+    }
+    return false;
+  }
+
   private void checkIfAlreadyIndexed(DefaultInputFile inputFile) {
     if (componentStore.inputFile(inputFile.getProjectRelativePath()) != null) {
       throw MessageException.of("File " + inputFile + " can't be indexed twice. Please check that inclusion/exclusion patterns produce "
@@ -150,7 +229,8 @@ public class FileIndexer {
     if (excludedByProjectConfiguration) {
       return true;
     } else if (moduleCoverageAndDuplicationExclusions.isExcludedForCoverage(inputFile)) {
-      moduleRelativePathWarner.warnOnce(CoreProperties.PROJECT_COVERAGE_EXCLUSIONS_PROPERTY, inputFile.getProjectRelativePath());
+      warnOnce(CoreProperties.PROJECT_COVERAGE_EXCLUSIONS_PROPERTY, inputFile.getProjectRelativePath(), () -> warnCoverageExclusionsAlreadyLogged,
+        () -> warnCoverageExclusionsAlreadyLogged = true);
       return true;
     }
     return false;
@@ -173,15 +253,26 @@ public class FileIndexer {
     if (excludedByProjectConfiguration) {
       return true;
     } else if (moduleCoverageAndDuplicationExclusions.isExcludedForDuplication(inputFile)) {
-      moduleRelativePathWarner.warnOnce(CoreProperties.CPD_EXCLUSIONS, inputFile.getProjectRelativePath());
+      warnOnce(CoreProperties.CPD_EXCLUSIONS, inputFile.getProjectRelativePath(), () -> warnDuplicationExclusionsAlreadyLogged,
+        () -> warnDuplicationExclusionsAlreadyLogged = true);
       return true;
     }
     return false;
   }
 
+  private void warnOnce(String propKey, String filePath, BooleanSupplier alreadyLoggedGetter, Runnable markAsLogged) {
+    if (!alreadyLoggedGetter.getAsBoolean()) {
+      String msg = "Specifying module-relative paths at project level in the property '" + propKey + "' is deprecated. " +
+        "To continue matching files like '" + filePath + "', update this property so that patterns refer to project-relative paths.";
+      LOG.warn(msg);
+      analysisWarnings.addUnique(msg);
+      markAsLogged.run();
+    }
+  }
+
   private boolean accept(InputFile indexedFile) {
     // InputFileFilter extensions. Might trigger generation of metadata
-    for (InputFileFilter filter : inputFileFilterRepository.getInputFileFilters()) {
+    for (InputFileFilter filter : filters) {
       if (!filter.accept(indexedFile)) {
         LOG.debug("'{}' excluded by {}", indexedFile, filter.getClass().getName());
         return false;
@@ -194,5 +285,7 @@ public class FileIndexer {
     return count == 1 ? "file" : "files";
   }
 
-
+  private boolean isFileSizeBiggerThanLimit(Path filePath) throws IOException {
+    return Files.size(filePath) > properties.fileSizeLimit() * 1024L * 1024L;
+  }
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/FilePreprocessor.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/FilePreprocessor.java
deleted file mode 100644
index 6faa87cc42a..00000000000
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/FilePreprocessor.java
+++ /dev/null
@@ -1,139 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2023 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.filesystem;
-
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.LinkOption;
-import java.nio.file.Path;
-import java.util.Arrays;
-import java.util.Optional;
-import javax.annotation.CheckForNull;
-import org.apache.commons.io.FilenameUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.sonar.api.CoreProperties;
-import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.internal.DefaultInputModule;
-import org.sonar.api.batch.fs.internal.DefaultInputProject;
-import org.sonar.api.batch.scm.IgnoreCommand;
-import org.sonar.scanner.scan.ScanProperties;
-
-public class FilePreprocessor {
-
-  private static final Logger LOG = LoggerFactory.getLogger(FilePreprocessor.class);
-
-  private final ModuleRelativePathWarner moduleRelativePathWarner;
-  private final DefaultInputProject project;
-  private final LanguageDetection languageDetection;
-  private final ProjectExclusionFilters projectExclusionFilters;
-  private final ScanProperties properties;
-
-  public FilePreprocessor(ModuleRelativePathWarner moduleRelativePathWarner, DefaultInputProject project,
-    LanguageDetection languageDetection, ProjectExclusionFilters projectExclusionFilters, ScanProperties properties) {
-    this.moduleRelativePathWarner = moduleRelativePathWarner;
-    this.project = project;
-    this.languageDetection = languageDetection;
-    this.projectExclusionFilters = projectExclusionFilters;
-    this.properties = properties;
-  }
-
-  public Optional<Path> processFile(DefaultInputModule module, ModuleExclusionFilters moduleExclusionFilters, Path sourceFile,
-    InputFile.Type type, ProjectFilePreprocessor.ExclusionCounter exclusionCounter, @CheckForNull IgnoreCommand ignoreCommand) throws IOException {
-    // get case of real file without resolving link
-    Path realAbsoluteFile = sourceFile.toRealPath(LinkOption.NOFOLLOW_LINKS).toAbsolutePath().normalize();
-    Path projectRelativePath = project.getBaseDir().relativize(realAbsoluteFile);
-    Path moduleRelativePath = module.getBaseDir().relativize(realAbsoluteFile);
-    boolean included = isFileIncluded(moduleExclusionFilters, realAbsoluteFile, projectRelativePath, moduleRelativePath, type);
-    if (!included) {
-      exclusionCounter.increaseByPatternsCount();
-      return Optional.empty();
-    }
-    boolean excluded = isFileExcluded(moduleExclusionFilters, realAbsoluteFile, projectRelativePath, moduleRelativePath, type);
-    if (excluded) {
-      exclusionCounter.increaseByPatternsCount();
-      return Optional.empty();
-    }
-
-    if (!realAbsoluteFile.startsWith(project.getBaseDir())) {
-      LOG.warn("File '{}' is ignored. It is not located in project basedir '{}'.", realAbsoluteFile.toAbsolutePath(), project.getBaseDir());
-      return Optional.empty();
-    }
-    if (!realAbsoluteFile.startsWith(module.getBaseDir())) {
-      LOG.warn("File '{}' is ignored. It is not located in module basedir '{}'.", realAbsoluteFile.toAbsolutePath(), module.getBaseDir());
-      return Optional.empty();
-    }
-
-    if (ignoreCommand != null && ignoreCommand.isIgnored(realAbsoluteFile)) {
-      LOG.debug("File '{}' is excluded by the scm ignore settings.", realAbsoluteFile);
-      exclusionCounter.increaseByScmCount();
-      return Optional.empty();
-    }
-
-    if (Files.exists(realAbsoluteFile) && isFileSizeBiggerThanLimit(realAbsoluteFile)) {
-      LOG.warn("File '{}' is bigger than {}MB and as consequence is removed from the analysis scope.", realAbsoluteFile.toAbsolutePath(), properties.fileSizeLimit());
-      return Optional.empty();
-    }
-
-    languageDetection.language(realAbsoluteFile, projectRelativePath);
-
-    return Optional.of(realAbsoluteFile);
-  }
-
-  private boolean isFileIncluded(ModuleExclusionFilters moduleExclusionFilters, Path realAbsoluteFile, Path projectRelativePath,
-    Path moduleRelativePath, InputFile.Type type) {
-    if (!Arrays.equals(moduleExclusionFilters.getInclusionsConfig(type), projectExclusionFilters.getInclusionsConfig(type))) {
-      return moduleExclusionFilters.isIncluded(realAbsoluteFile, moduleRelativePath, type);
-    }
-    boolean includedByProjectConfiguration = projectExclusionFilters.isIncluded(realAbsoluteFile, projectRelativePath, type);
-    if (includedByProjectConfiguration) {
-      return true;
-    }
-    if (moduleExclusionFilters.isIncluded(realAbsoluteFile, moduleRelativePath, type)) {
-      moduleRelativePathWarner.warnOnce(
-        type == InputFile.Type.MAIN ? CoreProperties.PROJECT_INCLUSIONS_PROPERTY : CoreProperties.PROJECT_TEST_INCLUSIONS_PROPERTY,
-        FilenameUtils.normalize(projectRelativePath.toString(), true));
-      return true;
-    }
-    return false;
-  }
-
-  private boolean isFileExcluded(ModuleExclusionFilters moduleExclusionFilters, Path realAbsoluteFile, Path projectRelativePath,
-    Path moduleRelativePath, InputFile.Type type) {
-    if (!Arrays.equals(moduleExclusionFilters.getExclusionsConfig(type), projectExclusionFilters.getExclusionsConfig(type))) {
-      return moduleExclusionFilters.isExcluded(realAbsoluteFile, moduleRelativePath, type);
-    }
-    boolean includedByProjectConfiguration = projectExclusionFilters.isExcluded(realAbsoluteFile, projectRelativePath, type);
-    if (includedByProjectConfiguration) {
-      return true;
-    }
-    if (moduleExclusionFilters.isExcluded(realAbsoluteFile, moduleRelativePath, type)) {
-      moduleRelativePathWarner.warnOnce(
-        type == InputFile.Type.MAIN ? CoreProperties.PROJECT_EXCLUSIONS_PROPERTY : CoreProperties.PROJECT_TEST_EXCLUSIONS_PROPERTY,
-        FilenameUtils.normalize(projectRelativePath.toString(), true));
-      return true;
-    }
-    return false;
-  }
-
-  private boolean isFileSizeBiggerThanLimit(Path filePath) throws IOException {
-    return Files.size(filePath) > properties.fileSizeLimit() * 1024L * 1024L;
-  }
-}
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/InputFileFilterRepository.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/InputFileFilterRepository.java
deleted file mode 100644
index b6e14af85eb..00000000000
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/InputFileFilterRepository.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2023 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.filesystem;
-
-import org.sonar.api.batch.fs.InputFileFilter;
-
-public class InputFileFilterRepository {
-  private final InputFileFilter[] inputFileFilters;
-
-  public InputFileFilterRepository(InputFileFilter... inputFileFilters) {
-    this.inputFileFilters = inputFileFilters;
-  }
-
-  public InputFileFilter[] getInputFileFilters() {
-    return inputFileFilters;
-  }
-}
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/LanguageDetection.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/LanguageDetection.java
index 24128133824..5ede0250c08 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/LanguageDetection.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/LanguageDetection.java
@@ -25,7 +25,6 @@ import java.util.Arrays;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 import javax.annotation.CheckForNull;
@@ -54,9 +53,8 @@ public class LanguageDetection {
    */
   private final Map<Language, PathPattern[]> patternsByLanguage;
   private final List<Language> languagesToConsider;
-  private final Map<String, Language> languageCacheByPath;
 
-  public LanguageDetection(Configuration settings, LanguagesRepository languages, Map<String, Language> languageCache) {
+  public LanguageDetection(Configuration settings, LanguagesRepository languages) {
     Map<Language, PathPattern[]> patternsByLanguageBuilder = new LinkedHashMap<>();
     for (Language language : languages.all()) {
       String[] filePatterns = settings.getStringArray(getFileLangPatternPropKey(language.key()));
@@ -71,7 +69,6 @@ public class LanguageDetection {
 
     languagesToConsider = List.copyOf(patternsByLanguageBuilder.keySet());
     patternsByLanguage = unmodifiableMap(patternsByLanguageBuilder);
-    languageCacheByPath = languageCache;
   }
 
   private static PathPattern[] getLanguagePatterns(Language language) {
@@ -92,16 +89,11 @@ public class LanguageDetection {
 
   @CheckForNull
   Language language(Path absolutePath, Path relativePath) {
-    Language detectedLanguage = languageCacheByPath.get(absolutePath.toString());
-    if (detectedLanguage != null) {
-      return detectedLanguage;
-    }
-
+    Language detectedLanguage = null;
     for (Language language : languagesToConsider) {
       if (isCandidateForLanguage(absolutePath, relativePath, language)) {
         if (detectedLanguage == null) {
           detectedLanguage = language;
-          languageCacheByPath.put(absolutePath.toString(), language);
         } else {
           // Language was already forced by another pattern
           throw MessageException.of(MessageFormat.format("Language of file ''{0}'' can not be decided as the file matches patterns of both {1} and {2}",
@@ -113,10 +105,6 @@ public class LanguageDetection {
     return detectedLanguage;
   }
 
-  public Set<String> getDetectedLanguages() {
-    return languageCacheByPath.values().stream().map(Language::key).collect(Collectors.toSet());
-  }
-
   private boolean isCandidateForLanguage(Path absolutePath, Path relativePath, Language language) {
     PathPattern[] patterns = patternsByLanguage.get(language);
     return patterns != null && Arrays.stream(patterns).anyMatch(pattern -> pattern.match(absolutePath, relativePath, false));
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleRelativePathWarner.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleRelativePathWarner.java
deleted file mode 100644
index 766955e438c..00000000000
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleRelativePathWarner.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2023 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.filesystem;
-
-import java.util.HashSet;
-import java.util.Set;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.sonar.api.notifications.AnalysisWarnings;
-
-public class ModuleRelativePathWarner {
-
-  private static final Logger LOG = LoggerFactory.getLogger(ModuleRelativePathWarner.class);
-  private final AnalysisWarnings analysisWarnings;
-  private final Set<String> previouslyWarnedProps = new HashSet<>();
-
-  public ModuleRelativePathWarner(AnalysisWarnings analysisWarnings) {
-    this.analysisWarnings = analysisWarnings;
-  }
-
-  public void warnOnce(String propKey, String filePath) {
-    if (!previouslyWarnedProps.contains(propKey)) {
-      previouslyWarnedProps.add(propKey);
-      String msg = "Specifying module-relative paths at project level in the property '" + propKey + "' is deprecated. " +
-        "To continue matching files like '" + filePath + "', update this property so that patterns refer to project-relative paths.";
-      LOG.warn(msg);
-      analysisWarnings.addUnique(msg);
-    }
-  }
-}
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ProjectFileIndexer.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ProjectFileIndexer.java
index 5ff7ca1ef17..35d5bf3fdb4 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ProjectFileIndexer.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ProjectFileIndexer.java
@@ -20,22 +20,33 @@
 package org.sonar.scanner.scan.filesystem;
 
 import java.io.IOException;
+import java.nio.file.AccessDeniedException;
+import java.nio.file.FileSystemLoopException;
 import java.nio.file.FileVisitOption;
+import java.nio.file.FileVisitResult;
+import java.nio.file.FileVisitor;
 import java.nio.file.Files;
+import java.nio.file.LinkOption;
 import java.nio.file.Path;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.nio.file.attribute.DosFileAttributes;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Optional;
 import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicInteger;
 import org.apache.commons.lang.StringUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import org.apache.commons.lang.SystemUtils;
+import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.InputFile.Type;
 import org.sonar.api.batch.fs.internal.DefaultInputModule;
+import org.sonar.api.batch.scm.IgnoreCommand;
 import org.sonar.api.notifications.AnalysisWarnings;
 import org.sonar.api.scan.filesystem.PathResolver;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.sonar.scanner.bootstrap.GlobalConfiguration;
 import org.sonar.scanner.bootstrap.GlobalServerSettings;
 import org.sonar.scanner.fs.InputModuleHierarchy;
@@ -43,8 +54,12 @@ import org.sonar.scanner.scan.ModuleConfiguration;
 import org.sonar.scanner.scan.ModuleConfigurationProvider;
 import org.sonar.scanner.scan.ProjectServerSettings;
 import org.sonar.scanner.scan.SonarGlobalPropertiesFilter;
+import org.sonar.scanner.scm.ScmConfiguration;
 import org.sonar.scanner.util.ProgressReport;
 
+import static java.util.Collections.emptyList;
+import static java.util.Collections.singletonList;
+
 /**
  * Index project input files into {@link InputComponentStore}.
  */
@@ -54,13 +69,15 @@ public class ProjectFileIndexer {
   private final ProjectExclusionFilters projectExclusionFilters;
   private final SonarGlobalPropertiesFilter sonarGlobalPropertiesFilter;
   private final ProjectCoverageAndDuplicationExclusions projectCoverageAndDuplicationExclusions;
+  private final ScmConfiguration scmConfiguration;
   private final InputComponentStore componentStore;
   private final InputModuleHierarchy inputModuleHierarchy;
   private final GlobalConfiguration globalConfig;
   private final GlobalServerSettings globalServerSettings;
   private final ProjectServerSettings projectServerSettings;
   private final FileIndexer fileIndexer;
-  private final ProjectFilePreprocessor projectFilePreprocessor;
+  private final IgnoreCommand ignoreCommand;
+  private final boolean useScmExclusion;
   private final AnalysisWarnings analysisWarnings;
 
   private ProgressReport progressReport;
@@ -68,8 +85,8 @@ public class ProjectFileIndexer {
   public ProjectFileIndexer(InputComponentStore componentStore, ProjectExclusionFilters exclusionFilters,
     SonarGlobalPropertiesFilter sonarGlobalPropertiesFilter, InputModuleHierarchy inputModuleHierarchy,
     GlobalConfiguration globalConfig, GlobalServerSettings globalServerSettings, ProjectServerSettings projectServerSettings,
-    FileIndexer fileIndexer, ProjectCoverageAndDuplicationExclusions projectCoverageAndDuplicationExclusions,
-    ProjectFilePreprocessor projectFilePreprocessor, AnalysisWarnings analysisWarnings) {
+    FileIndexer fileIndexer, ProjectCoverageAndDuplicationExclusions projectCoverageAndDuplicationExclusions, ScmConfiguration scmConfiguration,
+    AnalysisWarnings analysisWarnings) {
     this.componentStore = componentStore;
     this.sonarGlobalPropertiesFilter = sonarGlobalPropertiesFilter;
     this.inputModuleHierarchy = inputModuleHierarchy;
@@ -79,8 +96,10 @@ public class ProjectFileIndexer {
     this.fileIndexer = fileIndexer;
     this.projectExclusionFilters = exclusionFilters;
     this.projectCoverageAndDuplicationExclusions = projectCoverageAndDuplicationExclusions;
-    this.projectFilePreprocessor = projectFilePreprocessor;
+    this.scmConfiguration = scmConfiguration;
     this.analysisWarnings = analysisWarnings;
+    this.ignoreCommand = loadIgnoreCommand();
+    this.useScmExclusion = ignoreCommand != null;
   }
 
   public void index() {
@@ -89,22 +108,47 @@ public class ProjectFileIndexer {
     LOG.info("Project configuration:");
     projectExclusionFilters.log("  ");
     projectCoverageAndDuplicationExclusions.log("  ");
+    ExclusionCounter exclusionCounter = new ExclusionCounter();
 
-    indexModulesRecursively(inputModuleHierarchy.root());
+    if (useScmExclusion) {
+      ignoreCommand.init(inputModuleHierarchy.root().getBaseDir().toAbsolutePath());
+      indexModulesRecursively(inputModuleHierarchy.root(), exclusionCounter);
+      ignoreCommand.clean();
+    } else {
+      indexModulesRecursively(inputModuleHierarchy.root(), exclusionCounter);
+    }
 
     int totalIndexed = componentStore.inputFiles().size();
     progressReport.stop(totalIndexed + " " + pluralizeFiles(totalIndexed) + " indexed");
 
+    int excludedFileByPatternCount = exclusionCounter.getByPatternsCount();
+    if (projectExclusionFilters.hasPattern() || excludedFileByPatternCount > 0) {
+      LOG.info("{} {} ignored because of inclusion/exclusion patterns", excludedFileByPatternCount, pluralizeFiles(excludedFileByPatternCount));
+    }
+    int excludedFileByScmCount = exclusionCounter.getByScmCount();
+    if (useScmExclusion) {
+      LOG.info("{} {} ignored because of scm ignore settings", excludedFileByScmCount, pluralizeFiles(excludedFileByScmCount));
+    }
   }
 
-  private void indexModulesRecursively(DefaultInputModule module) {
-    inputModuleHierarchy.children(module).stream()
-      .sorted(Comparator.comparing(DefaultInputModule::key))
-      .forEach(this::indexModulesRecursively);
-    index(module);
+  private IgnoreCommand loadIgnoreCommand() {
+    try {
+      if (!scmConfiguration.isExclusionDisabled() && scmConfiguration.provider() != null) {
+        return scmConfiguration.provider().ignoreCommand();
+      }
+    } catch (UnsupportedOperationException e) {
+      LOG.debug("File exclusion based on SCM ignore information is not available with this plugin.");
+    }
+
+    return null;
   }
 
-  private void index(DefaultInputModule module) {
+  private void indexModulesRecursively(DefaultInputModule module, ExclusionCounter exclusionCounter) {
+    inputModuleHierarchy.children(module).stream().sorted(Comparator.comparing(DefaultInputModule::key)).forEach(m -> indexModulesRecursively(m, exclusionCounter));
+    index(module, exclusionCounter);
+  }
+
+  private void index(DefaultInputModule module, ExclusionCounter exclusionCounter) {
     // Emulate creation of module level settings
     ModuleConfiguration moduleConfig = new ModuleConfigurationProvider(sonarGlobalPropertiesFilter).provide(globalConfig, module, globalServerSettings, projectServerSettings);
     ModuleExclusionFilters moduleExclusionFilters = new ModuleExclusionFilters(moduleConfig, analysisWarnings);
@@ -117,10 +161,13 @@ public class ProjectFileIndexer {
       moduleExclusionFilters.log("  ");
       moduleCoverageAndDuplicationExclusions.log("  ");
     }
-    List<Path> mainSourceDirsOrFiles = projectFilePreprocessor.getMainSourcesByModule(module);
-    indexFiles(module, moduleExclusionFilters, moduleCoverageAndDuplicationExclusions, mainSourceDirsOrFiles, Type.MAIN);
-    projectFilePreprocessor.getTestSourcesByModule(module)
-      .ifPresent(tests -> indexFiles(module, moduleExclusionFilters, moduleCoverageAndDuplicationExclusions, tests, Type.TEST));
+    boolean hasChildModules = !module.definition().getSubProjects().isEmpty();
+    boolean hasTests = module.getTestDirsOrFiles().isPresent();
+    // Default to index basedir when no sources provided
+    List<Path> mainSourceDirsOrFiles = module.getSourceDirsOrFiles()
+      .orElseGet(() -> hasChildModules || hasTests ? emptyList() : singletonList(module.getBaseDir().toAbsolutePath()));
+    indexFiles(module, moduleExclusionFilters, moduleCoverageAndDuplicationExclusions, mainSourceDirsOrFiles, Type.MAIN, exclusionCounter);
+    module.getTestDirsOrFiles().ifPresent(tests -> indexFiles(module, moduleExclusionFilters, moduleCoverageAndDuplicationExclusions, tests, Type.TEST, exclusionCounter));
   }
 
   private static void logPaths(String label, Path baseDir, List<Path> paths) {
@@ -129,7 +176,7 @@ public class ProjectFileIndexer {
       for (Iterator<Path> it = paths.iterator(); it.hasNext(); ) {
         Path file = it.next();
         Optional<String> relativePathToBaseDir = PathResolver.relativize(baseDir, file);
-        if (relativePathToBaseDir.isEmpty()) {
+        if (!relativePathToBaseDir.isPresent()) {
           sb.append(file);
         } else if (StringUtils.isBlank(relativePathToBaseDir.get())) {
           sb.append(".");
@@ -148,14 +195,19 @@ public class ProjectFileIndexer {
     }
   }
 
-  private void indexFiles(DefaultInputModule module, ModuleExclusionFilters moduleExclusionFilters, ModuleCoverageAndDuplicationExclusions moduleCoverageAndDuplicationExclusions,
-    List<Path> sources, Type type) {
+  private static String pluralizeFiles(int count) {
+    return count == 1 ? "file" : "files";
+  }
+
+  private void indexFiles(DefaultInputModule module, ModuleExclusionFilters moduleExclusionFilters,
+    ModuleCoverageAndDuplicationExclusions moduleCoverageAndDuplicationExclusions, List<Path> sources, Type type, ExclusionCounter exclusionCounter) {
     try {
       for (Path dirOrFile : sources) {
         if (dirOrFile.toFile().isDirectory()) {
-          indexDirectory(module, moduleExclusionFilters, moduleCoverageAndDuplicationExclusions, dirOrFile, type);
+          indexDirectory(module, moduleExclusionFilters, moduleCoverageAndDuplicationExclusions, dirOrFile, type, exclusionCounter);
         } else {
-          fileIndexer.indexFile(module, moduleCoverageAndDuplicationExclusions, dirOrFile, type, progressReport);
+          fileIndexer.indexFile(module, moduleExclusionFilters, moduleCoverageAndDuplicationExclusions, dirOrFile, type, progressReport, exclusionCounter,
+            ignoreCommand);
         }
       }
     } catch (IOException e) {
@@ -164,17 +216,141 @@ public class ProjectFileIndexer {
   }
 
   private void indexDirectory(DefaultInputModule module, ModuleExclusionFilters moduleExclusionFilters,
-    ModuleCoverageAndDuplicationExclusions moduleCoverageAndDuplicationExclusions,
-    Path dirToIndex, Type type) throws IOException {
+    ModuleCoverageAndDuplicationExclusions moduleCoverageAndDuplicationExclusions, Path dirToIndex, Type type, ExclusionCounter exclusionCounter)
+    throws IOException {
     Files.walkFileTree(dirToIndex.normalize(), Collections.singleton(FileVisitOption.FOLLOW_LINKS), Integer.MAX_VALUE,
-      new DirectoryFileVisitor(file -> fileIndexer.indexFile(module, moduleCoverageAndDuplicationExclusions, file, type, progressReport),
-        module, moduleExclusionFilters, inputModuleHierarchy, type));
+      new IndexFileVisitor(module, moduleExclusionFilters, moduleCoverageAndDuplicationExclusions, type, exclusionCounter));
   }
 
-  private static String pluralizeFiles(int count) {
-    return count == 1 ? "file" : "files";
+
+  /**
+   * <p>Checks if the path is a directory that is excluded.</p>
+   *
+   * <p>Exclusions patterns are checked both at project and module level.</p>
+   *
+   * @param moduleExclusionFilters The exclusion filters.
+   * @param realAbsoluteFile       The path to be checked.
+   * @param projectBaseDir         The project base directory.
+   * @param moduleBaseDir          The module base directory.
+   * @param type                   The input file type.
+   * @return True if path is an excluded directory, false otherwise.
+   */
+  private static boolean isExcludedDirectory(ModuleExclusionFilters moduleExclusionFilters, Path realAbsoluteFile, Path projectBaseDir, Path moduleBaseDir,
+    InputFile.Type type) {
+    Path projectRelativePath = projectBaseDir.relativize(realAbsoluteFile);
+    Path moduleRelativePath = moduleBaseDir.relativize(realAbsoluteFile);
+    return moduleExclusionFilters.isExcludedAsParentDirectoryOfExcludedChildren(realAbsoluteFile, projectRelativePath, projectBaseDir, type)
+      || moduleExclusionFilters.isExcludedAsParentDirectoryOfExcludedChildren(realAbsoluteFile, moduleRelativePath, moduleBaseDir, type);
+  }
+
+  private class IndexFileVisitor implements FileVisitor<Path> {
+    private final DefaultInputModule module;
+    private final ModuleExclusionFilters moduleExclusionFilters;
+    private final ModuleCoverageAndDuplicationExclusions moduleCoverageAndDuplicationExclusions;
+    private final Type type;
+    private final ExclusionCounter exclusionCounter;
+
+    IndexFileVisitor(DefaultInputModule module, ModuleExclusionFilters moduleExclusionFilters, ModuleCoverageAndDuplicationExclusions moduleCoverageAndDuplicationExclusions,
+      Type type,
+      ExclusionCounter exclusionCounter) {
+      this.module = module;
+      this.moduleExclusionFilters = moduleExclusionFilters;
+      this.moduleCoverageAndDuplicationExclusions = moduleCoverageAndDuplicationExclusions;
+      this.type = type;
+      this.exclusionCounter = exclusionCounter;
+    }
+
+    @Override
+    public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) throws IOException {
+      if (isHidden(dir)) {
+        return FileVisitResult.SKIP_SUBTREE;
+      }
+      return FileVisitResult.CONTINUE;
+    }
+
+    @Override
+    public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
+      if (!Files.isHidden(file)) {
+        fileIndexer.indexFile(module, moduleExclusionFilters, moduleCoverageAndDuplicationExclusions, file, type, progressReport, exclusionCounter, ignoreCommand);
+      }
+      return FileVisitResult.CONTINUE;
+    }
+
+    /**
+     * <p>Overridden method to handle exceptions while visiting files in the analysis.</p>
+     *
+     * <p>
+     *   <ul>
+     *     <li>FileSystemLoopException - We show a warning that a symlink loop exists and we skip the file.</li>
+     *     <li>AccessDeniedException for excluded files/directories - We skip the file, as files excluded from the analysis, shouldn't throw access exceptions.</li>
+     *   </ul>
+     * </p>
+     *
+     * @param file a reference to the file
+     * @param exc  the I/O exception that prevented the file from being visited
+     * @throws IOException
+     */
+    @Override
+    public FileVisitResult visitFileFailed(Path file, IOException exc) throws IOException {
+      if (exc instanceof FileSystemLoopException) {
+        LOG.warn("Not indexing due to symlink loop: {}", file.toFile());
+        return FileVisitResult.CONTINUE;
+      } else if (exc instanceof AccessDeniedException && isExcluded(file)) {
+        return FileVisitResult.CONTINUE;
+      }
+      throw exc;
+    }
+
+    /**
+     * <p>Checks if the directory is excluded in the analysis or not. Only the exclusions are checked.</p>
+     *
+     * <p>The inclusions cannot be checked for directories, since the current implementation of pattern matching is intended only for files.</p>
+     *
+     * @param path The file or directory.
+     * @return True if file/directory is excluded from the analysis, false otherwise.
+     */
+    private boolean isExcluded(Path path) throws IOException {
+      Path realAbsoluteFile = path.toRealPath(LinkOption.NOFOLLOW_LINKS).toAbsolutePath().normalize();
+      return isExcludedDirectory(moduleExclusionFilters, realAbsoluteFile, inputModuleHierarchy.root().getBaseDir(), module.getBaseDir(), type);
+    }
+
+    @Override
+    public FileVisitResult postVisitDirectory(Path dir, IOException exc) {
+      return FileVisitResult.CONTINUE;
+    }
+
+    private boolean isHidden(Path path) throws IOException {
+      if (SystemUtils.IS_OS_WINDOWS) {
+        try {
+          DosFileAttributes dosFileAttributes = Files.readAttributes(path, DosFileAttributes.class, LinkOption.NOFOLLOW_LINKS);
+          return dosFileAttributes.isHidden();
+        } catch (UnsupportedOperationException e) {
+          return path.toFile().isHidden();
+        }
+      } else {
+        return Files.isHidden(path);
+      }
+    }
   }
 
+  static class ExclusionCounter {
+    private final AtomicInteger excludedByPatternsCount = new AtomicInteger(0);
+    private final AtomicInteger excludedByScmCount = new AtomicInteger(0);
+
+    public void increaseByPatternsCount() {
+      excludedByPatternsCount.incrementAndGet();
+    }
+
+    public int getByPatternsCount() {
+      return excludedByPatternsCount.get();
+    }
 
+    public void increaseByScmCount() {
+      excludedByScmCount.incrementAndGet();
+    }
 
+    public int getByScmCount() {
+      return excludedByScmCount.get();
+    }
+  }
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ProjectFilePreprocessor.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ProjectFilePreprocessor.java
deleted file mode 100644
index 54d4f2b8d6c..00000000000
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ProjectFilePreprocessor.java
+++ /dev/null
@@ -1,230 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2023 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.filesystem;
-
-import java.io.IOException;
-import java.nio.file.FileVisitOption;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Optional;
-import java.util.concurrent.TimeUnit;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.internal.DefaultInputModule;
-import org.sonar.api.batch.scm.IgnoreCommand;
-import org.sonar.api.batch.scm.ScmProvider;
-import org.sonar.api.notifications.AnalysisWarnings;
-import org.sonar.scanner.bootstrap.GlobalConfiguration;
-import org.sonar.scanner.bootstrap.GlobalServerSettings;
-import org.sonar.scanner.fs.InputModuleHierarchy;
-import org.sonar.scanner.scan.ModuleConfiguration;
-import org.sonar.scanner.scan.ModuleConfigurationProvider;
-import org.sonar.scanner.scan.ProjectServerSettings;
-import org.sonar.scanner.scan.SonarGlobalPropertiesFilter;
-import org.sonar.scanner.scm.ScmConfiguration;
-import org.sonar.scanner.util.ProgressReport;
-
-import static java.util.Collections.emptyList;
-import static java.util.Collections.singletonList;
-
-public class ProjectFilePreprocessor {
-
-  private static final Logger LOG = LoggerFactory.getLogger(ProjectFilePreprocessor.class);
-  private static final String TELEMETRY_STEP_NAME = "file.preprocessing";
-
-  private final AnalysisWarnings analysisWarnings;
-  private final IgnoreCommand ignoreCommand;
-  private final boolean useScmExclusion;
-  private final ScmConfiguration scmConfiguration;
-  private final InputModuleHierarchy inputModuleHierarchy;
-  private final GlobalConfiguration globalConfig;
-  private final GlobalServerSettings globalServerSettings;
-  private final ProjectServerSettings projectServerSettings;
-  private final LanguageDetection languageDetection;
-  private final FilePreprocessor filePreprocessor;
-  private final ProjectExclusionFilters projectExclusionFilters;
-
-  private final SonarGlobalPropertiesFilter sonarGlobalPropertiesFilter;
-
-  private final Map<DefaultInputModule, List<Path>> mainSourcesByModule = new HashMap<>();
-  private final Map<DefaultInputModule, List<Path>> testSourcesByModule = new HashMap<>();
-
-  private int totalFilesPreprocessed = 0;
-
-  public ProjectFilePreprocessor(AnalysisWarnings analysisWarnings, ScmConfiguration scmConfiguration, InputModuleHierarchy inputModuleHierarchy,
-    GlobalConfiguration globalConfig, GlobalServerSettings globalServerSettings, ProjectServerSettings projectServerSettings,
-    LanguageDetection languageDetection, FilePreprocessor filePreprocessor,
-    ProjectExclusionFilters projectExclusionFilters, SonarGlobalPropertiesFilter sonarGlobalPropertiesFilter) {
-    this.analysisWarnings = analysisWarnings;
-    this.scmConfiguration = scmConfiguration;
-    this.inputModuleHierarchy = inputModuleHierarchy;
-    this.globalConfig = globalConfig;
-    this.globalServerSettings = globalServerSettings;
-    this.projectServerSettings = projectServerSettings;
-    this.languageDetection = languageDetection;
-    this.filePreprocessor = filePreprocessor;
-    this.projectExclusionFilters = projectExclusionFilters;
-    this.sonarGlobalPropertiesFilter = sonarGlobalPropertiesFilter;
-    this.ignoreCommand = loadIgnoreCommand();
-    this.useScmExclusion = ignoreCommand != null;
-  }
-
-  public void execute() {
-    ProgressReport progressReport = new ProgressReport("Report about progress of file preprocessing",
-      TimeUnit.SECONDS.toMillis(10));
-    progressReport.start("Preprocessing files...");
-    ExclusionCounter exclusionCounter = new ExclusionCounter();
-
-    if (useScmExclusion) {
-      ignoreCommand.init(inputModuleHierarchy.root().getBaseDir().toAbsolutePath());
-      processModulesRecursively(inputModuleHierarchy.root(), exclusionCounter);
-      ignoreCommand.clean();
-    } else {
-      processModulesRecursively(inputModuleHierarchy.root(), exclusionCounter);
-    }
-
-    int totalLanguagesDetected = languageDetection.getDetectedLanguages().size();
-
-    progressReport.stop(String.format("%s detected in %s", pluralizeWithCount("language", totalLanguagesDetected),
-      pluralizeWithCount("preprocessed file", totalFilesPreprocessed)));
-
-    int excludedFileByPatternCount = exclusionCounter.getByPatternsCount();
-    if (projectExclusionFilters.hasPattern() || excludedFileByPatternCount > 0) {
-      if (LOG.isInfoEnabled()) {
-        LOG.info("{} ignored because of inclusion/exclusion patterns", pluralizeWithCount("file", excludedFileByPatternCount));
-      }
-    }
-
-    int excludedFileByScmCount = exclusionCounter.getByScmCount();
-    if (useScmExclusion) {
-      if (LOG.isInfoEnabled()) {
-        LOG.info("{} ignored because of scm ignore settings", pluralizeWithCount("file", excludedFileByScmCount));
-      }
-    }
-  }
-
-  private void processModulesRecursively(DefaultInputModule module, ExclusionCounter exclusionCounter) {
-    inputModuleHierarchy.children(module).stream().sorted(Comparator.comparing(DefaultInputModule::key)).forEach(
-      m -> processModulesRecursively(m, exclusionCounter));
-    processModule(module, exclusionCounter);
-  }
-
-  private void processModule(DefaultInputModule module, ExclusionCounter exclusionCounter) {
-    // Emulate creation of module level settings
-    ModuleConfiguration moduleConfig = new ModuleConfigurationProvider(sonarGlobalPropertiesFilter).provide(globalConfig, module, globalServerSettings, projectServerSettings);
-    ModuleExclusionFilters moduleExclusionFilters = new ModuleExclusionFilters(moduleConfig, analysisWarnings);
-    boolean hasChildModules = !module.definition().getSubProjects().isEmpty();
-    boolean hasTests = module.getTestDirsOrFiles().isPresent();
-    // Default to index basedir when no sources provided
-    List<Path> mainSourceDirsOrFiles = module.getSourceDirsOrFiles()
-      .orElseGet(() -> hasChildModules || hasTests ? emptyList() : singletonList(module.getBaseDir().toAbsolutePath()));
-    List<Path> processedSources = processModuleSources(module, moduleExclusionFilters, mainSourceDirsOrFiles, InputFile.Type.MAIN,
-      exclusionCounter);
-    mainSourcesByModule.put(module, processedSources);
-    totalFilesPreprocessed += processedSources.size();
-    module.getTestDirsOrFiles().ifPresent(tests -> {
-      List<Path> processedTestSources = processModuleSources(module, moduleExclusionFilters, tests, InputFile.Type.TEST, exclusionCounter);
-      testSourcesByModule.put(module, processedTestSources);
-      totalFilesPreprocessed += processedTestSources.size();
-    });
-  }
-
-  private List<Path> processModuleSources(DefaultInputModule module, ModuleExclusionFilters moduleExclusionFilters, List<Path> sources,
-    InputFile.Type type, ExclusionCounter exclusionCounter) {
-    List<Path> processedFiles = new ArrayList<>();
-    try {
-      for (Path dirOrFile : sources) {
-        if (dirOrFile.toFile().isDirectory()) {
-          processedFiles.addAll(processDirectory(module, moduleExclusionFilters, dirOrFile, type, exclusionCounter));
-        } else {
-          filePreprocessor.processFile(module, moduleExclusionFilters, dirOrFile, type, exclusionCounter, ignoreCommand)
-            .ifPresent(processedFiles::add);
-        }
-      }
-    } catch (IOException e) {
-      throw new IllegalStateException("Failed to preprocess files", e);
-    }
-    return processedFiles;
-  }
-
-  private List<Path> processDirectory(DefaultInputModule module, ModuleExclusionFilters moduleExclusionFilters, Path path,
-    InputFile.Type type, ExclusionCounter exclusionCounter) throws IOException {
-    List<Path> processedFiles = new ArrayList<>();
-    Files.walkFileTree(path.normalize(), Collections.singleton(FileVisitOption.FOLLOW_LINKS), Integer.MAX_VALUE,
-      new DirectoryFileVisitor(file -> filePreprocessor.processFile(module, moduleExclusionFilters, file, type, exclusionCounter,
-        ignoreCommand).ifPresent(processedFiles::add), module, moduleExclusionFilters, inputModuleHierarchy, type)
-    );
-    return processedFiles;
-  }
-
-  public List<Path> getMainSourcesByModule(DefaultInputModule module) {
-    return Collections.unmodifiableList(mainSourcesByModule.get(module));
-  }
-
-  public Optional<List<Path>> getTestSourcesByModule(DefaultInputModule module) {
-    return Optional.ofNullable(testSourcesByModule.get(module)).map(Collections::unmodifiableList);
-  }
-
-  private IgnoreCommand loadIgnoreCommand() {
-    try {
-      ScmProvider provider = scmConfiguration.provider();
-      if (!scmConfiguration.isExclusionDisabled() && provider != null) {
-        return provider.ignoreCommand();
-      }
-    } catch (UnsupportedOperationException e) {
-      LOG.debug("File exclusion based on SCM ignore information is not available with this plugin.");
-    }
-
-    return null;
-  }
-
-  private static String pluralizeWithCount(String str, int count) {
-    String pluralized = count == 1 ? str : (str + "s");
-    return count + " " + pluralized;
-  }
-
-  public static class ExclusionCounter {
-    private int excludedByPatternsCount = 0;
-    private int excludedByScmCount = 0;
-
-    public void increaseByPatternsCount() {
-      excludedByPatternsCount++;
-    }
-
-    public int getByPatternsCount() {
-      return excludedByPatternsCount;
-    }
-
-    public void increaseByScmCount() {
-      excludedByScmCount++;
-    }
-
-    public int getByScmCount() {
-      return excludedByScmCount;
-    }
-  }
-}
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/DirectoryFileVisitorTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/DirectoryFileVisitorTest.java
deleted file mode 100644
index fd79238f65d..00000000000
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/DirectoryFileVisitorTest.java
+++ /dev/null
@@ -1,93 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2023 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.filesystem;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.FileSystemLoopException;
-import java.nio.file.FileVisitResult;
-import java.nio.file.Files;
-import java.nio.file.LinkOption;
-import java.nio.file.Path;
-import java.nio.file.attribute.BasicFileAttributes;
-import org.apache.commons.lang.SystemUtils;
-import org.junit.ClassRule;
-import org.junit.Test;
-import org.junit.rules.TemporaryFolder;
-import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.fs.internal.DefaultInputModule;
-import org.sonar.scanner.fs.InputModuleHierarchy;
-
-import static org.assertj.core.api.Assertions.assertThat;
-import static org.junit.Assert.assertThrows;
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.never;
-import static org.mockito.Mockito.verify;
-
-public class DirectoryFileVisitorTest {
-
-  @ClassRule
-  public static TemporaryFolder temp = new TemporaryFolder();
-
-  private final DefaultInputModule module = mock();
-  private final ModuleExclusionFilters moduleExclusionFilters = mock();
-  private final InputModuleHierarchy inputModuleHierarchy = mock();
-  private final InputFile.Type type = mock();
-
-  @Test
-  public void visit_hidden_file() throws IOException {
-    DirectoryFileVisitor.FileVisitAction action = mock(DirectoryFileVisitor.FileVisitAction.class);
-
-    File hidden = temp.newFile(".hidden");
-    if (SystemUtils.IS_OS_WINDOWS) {
-      Files.setAttribute(hidden.toPath(), "dos:hidden", true, LinkOption.NOFOLLOW_LINKS);
-    }
-
-
-    DirectoryFileVisitor underTest = new DirectoryFileVisitor(action, module, moduleExclusionFilters, inputModuleHierarchy, type);
-    underTest.visitFile(hidden.toPath(), Files.readAttributes(hidden.toPath(), BasicFileAttributes.class));
-
-    verify(action, never()).execute(any(Path.class));
-  }
-
-  @Test
-  public void test_visit_file_failed_generic_io_exception() throws IOException {
-    DirectoryFileVisitor.FileVisitAction action = mock(DirectoryFileVisitor.FileVisitAction.class);
-
-    File file = temp.newFile("failed");
-
-    DirectoryFileVisitor underTest = new DirectoryFileVisitor(action, module, moduleExclusionFilters, inputModuleHierarchy, type);
-    assertThrows(IOException.class, () -> underTest.visitFileFailed(file.toPath(), new IOException()));
-  }
-
-  @Test
-  public void test_visit_file_failed_file_system_loop_exception() throws IOException {
-    DirectoryFileVisitor.FileVisitAction action = mock(DirectoryFileVisitor.FileVisitAction.class);
-
-    File file = temp.newFile("symlink");
-
-    DirectoryFileVisitor underTest = new DirectoryFileVisitor(action, module, moduleExclusionFilters, inputModuleHierarchy, type);
-    FileVisitResult result = underTest.visitFileFailed(file.toPath(), new FileSystemLoopException(file.getPath()));
-
-    assertThat(result).isEqualTo(FileVisitResult.CONTINUE);
-  }
-
-}
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputFileFilterRepositoryTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputFileFilterRepositoryTest.java
deleted file mode 100644
index 12f1cb0c63a..00000000000
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputFileFilterRepositoryTest.java
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2023 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.filesystem;
-
-import org.junit.Test;
-
-import static org.assertj.core.api.Assertions.assertThat;
-
-public class InputFileFilterRepositoryTest {
-
-  @Test
-  public void should_not_return_null_if_initialized_with_no_filters() {
-    InputFileFilterRepository underTest = new InputFileFilterRepository();
-    assertThat(underTest.getInputFileFilters()).isNotNull();
-  }
-
-  @Test
-  public void should_return_filters_from_initialization() {
-    InputFileFilterRepository underTest = new InputFileFilterRepository(f -> true);
-    assertThat(underTest.getInputFileFilters()).isNotNull();
-    assertThat(underTest.getInputFileFilters()).hasSize(1);
-  }
-
-}
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/LanguageDetectionTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/LanguageDetectionTest.java
index 18408451557..e5810baba5a 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/LanguageDetectionTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/LanguageDetectionTest.java
@@ -24,8 +24,6 @@ import com.tngtech.java.junit.dataprovider.DataProviderRunner;
 import com.tngtech.java.junit.dataprovider.UseDataProvider;
 import java.io.File;
 import java.nio.file.Paths;
-import java.util.HashMap;
-import java.util.Map;
 import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
@@ -40,11 +38,7 @@ import org.sonar.scanner.repository.language.LanguagesRepository;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.assertj.core.api.Assertions.assertThatThrownBy;
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.ArgumentMatchers.endsWith;
 import static org.mockito.Mockito.spy;
-import static org.mockito.Mockito.times;
-import static org.mockito.Mockito.verify;
 
 @RunWith(DataProviderRunner.class)
 public class LanguageDetectionTest {
@@ -78,7 +72,7 @@ public class LanguageDetectionTest {
   @Test
   public void detectLanguageKey_shouldDetectByFileExtension() {
     LanguagesRepository languages = new FakeLanguagesRepository(new Languages(new MockLanguage("java", "java", "jav"), new MockLanguage("cobol", "cbl", "cob")));
-    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages, new HashMap<>());
+    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages);
 
     assertThat(detectLanguageKey(detection, "Foo.java")).isEqualTo("java");
     assertThat(detectLanguageKey(detection, "src/Foo.java")).isEqualTo("java");
@@ -100,7 +94,7 @@ public class LanguageDetectionTest {
       new MockLanguage("docker", new String[0], new String[] {"*.dockerfile", "*.Dockerfile", "Dockerfile", "Dockerfile.*"}),
       new MockLanguage("terraform", new String[] {"tf"}, new String[] {".tf"}),
       new MockLanguage("java", new String[0], new String[] {"**/*Test.java"})));
-    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages, new HashMap<>());
+    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages);
     assertThat(detectLanguageKey(detection, fileName)).isEqualTo(expectedLanguageKey);
   }
 
@@ -123,7 +117,7 @@ public class LanguageDetectionTest {
 
   @Test
   public void detectLanguageKey_shouldNotFailIfNoLanguage() {
-    LanguageDetection detection = spy(new LanguageDetection(settings.asConfig(), new FakeLanguagesRepository(new Languages()), new HashMap<>()));
+    LanguageDetection detection = spy(new LanguageDetection(settings.asConfig(), new FakeLanguagesRepository(new Languages())));
     assertThat(detectLanguageKey(detection, "Foo.java")).isNull();
   }
 
@@ -131,14 +125,14 @@ public class LanguageDetectionTest {
   public void detectLanguageKey_shouldAllowPluginsToDeclareFileExtensionTwiceForCaseSensitivity() {
     LanguagesRepository languages = new FakeLanguagesRepository(new Languages(new MockLanguage("abap", "abap", "ABAP")));
 
-    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages, new HashMap<>());
+    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages);
     assertThat(detectLanguageKey(detection, "abc.abap")).isEqualTo("abap");
   }
 
   @Test
   public void detectLanguageKey_shouldFailIfConflictingLanguageSuffix() {
     LanguagesRepository languages = new FakeLanguagesRepository(new Languages(new MockLanguage("xml", "xhtml"), new MockLanguage("web", "xhtml")));
-    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages, new HashMap<>());
+    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages);
     assertThatThrownBy(() -> detectLanguageKey(detection, "abc.xhtml"))
       .isInstanceOf(MessageException.class)
       .hasMessageContaining("Language of file 'abc.xhtml' can not be decided as the file matches patterns of both ")
@@ -152,7 +146,7 @@ public class LanguageDetectionTest {
 
     settings.setProperty("sonar.lang.patterns.xml", "xml/**");
     settings.setProperty("sonar.lang.patterns.web", "web/**");
-    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages, new HashMap<>());
+    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages);
     assertThat(detectLanguageKey(detection, "xml/abc.xhtml")).isEqualTo("xml");
     assertThat(detectLanguageKey(detection, "web/abc.xhtml")).isEqualTo("web");
   }
@@ -163,7 +157,7 @@ public class LanguageDetectionTest {
     settings.setProperty("sonar.lang.patterns.abap", "*.abap,*.txt");
     settings.setProperty("sonar.lang.patterns.cobol", "*.cobol,*.txt");
 
-    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages, new HashMap<>());
+    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages);
 
     assertThat(detectLanguageKey(detection, "abc.abap")).isEqualTo("abap");
     assertThat(detectLanguageKey(detection, "abc.cobol")).isEqualTo("cobol");
@@ -174,19 +168,6 @@ public class LanguageDetectionTest {
       .hasMessageContaining("sonar.lang.patterns.cobol : *.cobol,*.txt");
   }
 
-  @Test
-  public void should_cache_detected_language_by_file_path() {
-    Map<String, org.sonar.scanner.repository.language.Language> languageCacheSpy = spy(new HashMap<>());
-    LanguagesRepository languages = new FakeLanguagesRepository(new Languages(
-      new MockLanguage("java", "java", "jav"), new MockLanguage("cobol", "cbl", "cob")));
-    LanguageDetection detection = new LanguageDetection(settings.asConfig(), languages, languageCacheSpy);
-
-    assertThat(detectLanguageKey(detection, "Foo.java")).isEqualTo("java");
-    assertThat(detectLanguageKey(detection, "Foo.java")).isEqualTo("java");
-    verify(languageCacheSpy, times(1)).put(endsWith("/Foo.java"), any(org.sonar.scanner.repository.language.Language.class));
-    verify(languageCacheSpy, times(2)).get(endsWith("/Foo.java"));
-  }
-
   private String detectLanguageKey(LanguageDetection detection, String path) {
     org.sonar.scanner.repository.language.Language language = detection.language(new File(temp.getRoot(), path).toPath(), Paths.get(path));
     return language != null ? language.key() : null;
diff --git a/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/sonar-project.properties b/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/sonar-project.properties
deleted file mode 100644
index 57c2c062b0e..00000000000
--- a/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/sonar-project.properties
+++ /dev/null
@@ -1,5 +0,0 @@
-sonar.organization=org1
-sonar.projectKey=sample-with-empty-file
-sonar.projectName=Sample With Empty
-sonar.projectVersion=0.1-SNAPSHOT
-sonar.sources=xources
diff --git a/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/xources/hello/HelloJava.xoo b/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/xources/hello/HelloJava.xoo
deleted file mode 100644
index ee9bf789a53..00000000000
--- a/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/xources/hello/HelloJava.xoo
+++ /dev/null
@@ -1,8 +0,0 @@
-package hello;
-
-public class HelloJava {
-
-  public static void main(String[] args) {
-    System.out.println("Hello");
-  }
-}
diff --git a/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/xources/hello/xoo_exclude.xoo b/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/xources/hello/xoo_exclude.xoo
deleted file mode 100644
index 35965a8484c..00000000000
--- a/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/xources/hello/xoo_exclude.xoo
+++ /dev/null
@@ -1 +0,0 @@
-this file should be excluded from indexing.
diff --git a/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/xources/hello/xoo_exclude2.xoo b/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/xources/hello/xoo_exclude2.xoo
deleted file mode 100644
index d04e465a561..00000000000
--- a/sonar-scanner-engine/test-resources/mediumtest/xoo/sample-with-input-file-filters/xources/hello/xoo_exclude2.xoo
+++ /dev/null
@@ -1 +0,0 @@
-this file should ALSO be excluded from indexing.