SONAR-11480 SONAR-11508 Consider server side settings when evaluating module level exclusions

24 files changed, 187 insertions, 133 deletions

diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalConfiguration.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalConfiguration.java
index a9fa6e899b7..0bbc32c5a3b 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalConfiguration.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalConfiguration.java
@@ -28,10 +28,8 @@ import org.sonar.scanner.config.DefaultConfiguration;
 @Immutable
 public class GlobalConfiguration extends DefaultConfiguration {
 
-  public GlobalConfiguration(PropertyDefinitions propertyDefinitions, Encryption encryption, GlobalAnalysisMode mode,
-                             Map<String, String> settings) {
-    super(propertyDefinitions, encryption, mode, settings);
+  public GlobalConfiguration(PropertyDefinitions propertyDefinitions, Encryption encryption, Map<String, String> settings) {
+    super(propertyDefinitions, encryption, settings);
   }
 
-
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalConfigurationProvider.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalConfigurationProvider.java
index 255700fd0a0..be54e94b258 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalConfigurationProvider.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalConfigurationProvider.java
@@ -28,13 +28,13 @@ public class GlobalConfigurationProvider extends ProviderAdapter {
 
   private GlobalConfiguration globalConfig;
 
-  public GlobalConfiguration provide(GlobalServerSettings globalServerSettings, ScannerProperties scannerProps, PropertyDefinitions propertyDefinitions, GlobalAnalysisMode mode) {
+  public GlobalConfiguration provide(GlobalServerSettings globalServerSettings, ScannerProperties scannerProps, PropertyDefinitions propertyDefinitions) {
     if (globalConfig == null) {
       Map<String, String> mergedSettings = new LinkedHashMap<>();
       mergedSettings.putAll(globalServerSettings.properties());
       mergedSettings.putAll(scannerProps.properties());
 
-      globalConfig = new GlobalConfiguration(propertyDefinitions, scannerProps.getEncryption(), mode, mergedSettings);
+      globalConfig = new GlobalConfiguration(propertyDefinitions, scannerProps.getEncryption(), mergedSettings);
     }
     return globalConfig;
   }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalServerSettingsProvider.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalServerSettingsProvider.java
index 53cb91e5d9b..9f2ff35d9d0 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalServerSettingsProvider.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/bootstrap/GlobalServerSettingsProvider.java
@@ -35,7 +35,7 @@ public class GlobalServerSettingsProvider extends ProviderAdapter {
 
   public GlobalServerSettings provide(SettingsLoader loader) {
     if (singleton == null) {
-      Map<String, String> serverSideSettings = loader.load(null);
+      Map<String, String> serverSideSettings = loader.loadGlobalSettings();
       singleton = new GlobalServerSettings(serverSideSettings);
       Optional.ofNullable(serverSideSettings.get(CoreProperties.SERVER_ID)).ifPresent(v -> LOG.info("Server id: {}", v));
     }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/config/DefaultConfiguration.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/config/DefaultConfiguration.java
index f79c496b962..d57b46c7994 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/config/DefaultConfiguration.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/config/DefaultConfiguration.java
@@ -29,10 +29,8 @@ import org.sonar.api.config.Configuration;
 import org.sonar.api.config.Encryption;
 import org.sonar.api.config.PropertyDefinition;
 import org.sonar.api.config.PropertyDefinitions;
-import org.sonar.api.utils.MessageException;
 import org.sonar.api.utils.log.Logger;
 import org.sonar.api.utils.log.Loggers;
-import org.sonar.scanner.bootstrap.GlobalAnalysisMode;
 
 import static java.util.Objects.requireNonNull;
 import static org.apache.commons.lang.StringUtils.trim;
@@ -45,14 +43,12 @@ public abstract class DefaultConfiguration implements Configuration {
 
   private final PropertyDefinitions definitions;
   private final Encryption encryption;
-  private final GlobalAnalysisMode mode;
   private final Map<String, String> properties;
   private final Map<String, String> originalProperties;
 
-  public DefaultConfiguration(PropertyDefinitions propertyDefinitions, Encryption encryption, GlobalAnalysisMode mode, Map<String, String> props) {
+  public DefaultConfiguration(PropertyDefinitions propertyDefinitions, Encryption encryption, Map<String, String> props) {
     this.definitions = requireNonNull(propertyDefinitions);
     this.encryption = encryption;
-    this.mode = mode;
     this.properties = unmodifiableMapWithTrimmedValues(definitions, props);
     this.originalProperties = Collections.unmodifiableMap(props);
   }
@@ -66,10 +62,6 @@ public abstract class DefaultConfiguration implements Configuration {
     return Collections.unmodifiableMap(map);
   }
 
-  public GlobalAnalysisMode getMode() {
-    return mode;
-  }
-
   public Encryption getEncryption() {
     return encryption;
   }
@@ -119,10 +111,6 @@ public abstract class DefaultConfiguration implements Configuration {
   }
 
   private Optional<String> getInternal(String key) {
-    if (mode.isIssues() && key.endsWith(".secured") && !key.contains(".license")) {
-      throw MessageException.of("Access to the secured property '" + key
-        + "' is not possible in issues mode. The SonarQube plugin which requires this property must be deactivated in issues mode.");
-    }
     Optional<String> value = Optional.ofNullable(properties.get(key));
     if (!value.isPresent()) {
       // default values cannot be encrypted, so return value as-is.
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/repository/settings/DefaultSettingsLoader.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/repository/settings/DefaultSettingsLoader.java
index 47ffbe18cf1..e3f820b0cbb 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/repository/settings/DefaultSettingsLoader.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/repository/settings/DefaultSettingsLoader.java
@@ -34,6 +34,7 @@ import org.apache.commons.lang.StringEscapeUtils;
 import org.sonar.api.utils.log.Logger;
 import org.sonar.api.utils.log.Loggers;
 import org.sonar.api.utils.log.Profiler;
+import org.sonar.scanner.bootstrap.ScannerProperties;
 import org.sonar.scanner.bootstrap.ScannerWsClient;
 import org.sonar.scanner.util.ScannerUtils;
 import org.sonarqube.ws.Settings.FieldValues.Value;
@@ -45,14 +46,25 @@ import org.sonarqube.ws.client.HttpException;
 public class DefaultSettingsLoader implements SettingsLoader {
 
   private ScannerWsClient wsClient;
+  private final ScannerProperties scannerProperties;
   private static final Logger LOG = Loggers.get(DefaultSettingsLoader.class);
 
-  public DefaultSettingsLoader(ScannerWsClient wsClient) {
+  public DefaultSettingsLoader(ScannerWsClient wsClient, ScannerProperties scannerProperties) {
     this.wsClient = wsClient;
+    this.scannerProperties = scannerProperties;
   }
 
   @Override
-  public Map<String, String> load(@Nullable String componentKey) {
+  public Map<String, String> loadGlobalSettings() {
+    return load(null);
+  }
+
+  @Override
+  public Map<String, String> loadProjectSettings() {
+    return load(scannerProperties.getKeyWithBranch());
+  }
+
+  private Map<String, String> load(@Nullable String componentKey) {
     String url = "api/settings/values.protobuf";
     Profiler profiler = Profiler.create(LOG);
     if (componentKey != null) {
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/repository/settings/SettingsLoader.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/repository/settings/SettingsLoader.java
index adcd48e6003..b7942a6cf8d 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/repository/settings/SettingsLoader.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/repository/settings/SettingsLoader.java
@@ -20,9 +20,9 @@
 package org.sonar.scanner.repository.settings;
 
 import java.util.Map;
-import javax.annotation.Nullable;
 
-@FunctionalInterface
 public interface SettingsLoader {
-  Map<String, String> load(@Nullable String componentKey);
+  Map<String, String> loadGlobalSettings();
+
+  Map<String, String> loadProjectSettings();
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ModuleConfiguration.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ModuleConfiguration.java
index 2dbcc577806..89def6f7e23 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ModuleConfiguration.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ModuleConfiguration.java
@@ -22,13 +22,12 @@ package org.sonar.scanner.scan;
 import java.util.Map;
 import org.sonar.api.config.Encryption;
 import org.sonar.api.config.PropertyDefinitions;
-import org.sonar.scanner.bootstrap.GlobalAnalysisMode;
 import org.sonar.scanner.config.DefaultConfiguration;
 
 public class ModuleConfiguration extends DefaultConfiguration {
 
-  public ModuleConfiguration(PropertyDefinitions propertyDefinitions, Encryption encryption, GlobalAnalysisMode mode, Map<String, String> props) {
-    super(propertyDefinitions, encryption, mode, props);
+  public ModuleConfiguration(PropertyDefinitions propertyDefinitions, Encryption encryption, Map<String, String> props) {
+    super(propertyDefinitions, encryption, props);
   }
 
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ModuleConfigurationProvider.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ModuleConfigurationProvider.java
index a60556dee6c..7e19c53af74 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ModuleConfigurationProvider.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ModuleConfigurationProvider.java
@@ -26,20 +26,19 @@ import java.util.Map;
 import org.picocontainer.injectors.ProviderAdapter;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.fs.internal.DefaultInputModule;
-import org.sonar.scanner.bootstrap.GlobalAnalysisMode;
 import org.sonar.scanner.bootstrap.GlobalConfiguration;
 
 public class ModuleConfigurationProvider extends ProviderAdapter {
 
   private ModuleConfiguration moduleConfiguration;
 
-  public ModuleConfiguration provide(GlobalConfiguration globalConfig, DefaultInputModule module, ProjectServerSettings projectServerSettings, GlobalAnalysisMode analysisMode) {
+  public ModuleConfiguration provide(GlobalConfiguration globalConfig, DefaultInputModule module, ProjectServerSettings projectServerSettings) {
     if (moduleConfiguration == null) {
 
       Map<String, String> settings = new LinkedHashMap<>(projectServerSettings.properties());
       addScannerSideProperties(settings, module.definition());
 
-      moduleConfiguration = new ModuleConfiguration(globalConfig.getDefinitions(), globalConfig.getEncryption(), analysisMode, settings);
+      moduleConfiguration = new ModuleConfiguration(globalConfig.getDefinitions(), globalConfig.getEncryption(), settings);
     }
     return moduleConfiguration;
   }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectConfiguration.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectConfiguration.java
index 53a727b50e4..c4f1c002d1d 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectConfiguration.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectConfiguration.java
@@ -22,13 +22,12 @@ package org.sonar.scanner.scan;
 import java.util.Map;
 import org.sonar.api.config.Encryption;
 import org.sonar.api.config.PropertyDefinitions;
-import org.sonar.scanner.bootstrap.GlobalAnalysisMode;
 import org.sonar.scanner.config.DefaultConfiguration;
 
 public class ProjectConfiguration extends DefaultConfiguration {
 
-  public ProjectConfiguration(PropertyDefinitions propertyDefinitions, Encryption encryption, GlobalAnalysisMode mode, Map<String, String> props) {
-    super(propertyDefinitions, encryption, mode, props);
+  public ProjectConfiguration(PropertyDefinitions propertyDefinitions, Encryption encryption, Map<String, String> props) {
+    super(propertyDefinitions, encryption, props);
   }
 
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectConfigurationProvider.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectConfigurationProvider.java
index 8f5752d6a36..b3e127a80cd 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectConfigurationProvider.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectConfigurationProvider.java
@@ -23,7 +23,6 @@ import java.util.LinkedHashMap;
 import java.util.Map;
 import org.picocontainer.injectors.ProviderAdapter;
 import org.sonar.api.batch.fs.internal.DefaultInputProject;
-import org.sonar.scanner.bootstrap.GlobalAnalysisMode;
 import org.sonar.scanner.bootstrap.GlobalConfiguration;
 import org.sonar.scanner.bootstrap.GlobalServerSettings;
 
@@ -32,7 +31,7 @@ public class ProjectConfigurationProvider extends ProviderAdapter {
   private ProjectConfiguration projectConfig;
 
   public ProjectConfiguration provide(DefaultInputProject project, GlobalConfiguration globalConfig, GlobalServerSettings globalServerSettings,
-    ProjectServerSettings projectServerSettings, GlobalAnalysisMode mode, MutableProjectSettings projectSettings) {
+    ProjectServerSettings projectServerSettings, MutableProjectSettings projectSettings) {
     if (projectConfig == null) {
 
       Map<String, String> settings = new LinkedHashMap<>();
@@ -40,7 +39,7 @@ public class ProjectConfigurationProvider extends ProviderAdapter {
       settings.putAll(projectServerSettings.properties());
       settings.putAll(project.properties());
 
-      projectConfig = new ProjectConfiguration(globalConfig.getDefinitions(), globalConfig.getEncryption(), mode, settings);
+      projectConfig = new ProjectConfiguration(globalConfig.getDefinitions(), globalConfig.getEncryption(), settings);
       projectSettings.complete(projectConfig);
     }
     return projectConfig;
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectServerSettingsProvider.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectServerSettingsProvider.java
index a0545e1dd5b..6635faf14e9 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectServerSettingsProvider.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectServerSettingsProvider.java
@@ -26,7 +26,6 @@ import org.sonar.api.CoreProperties;
 import org.sonar.api.notifications.AnalysisWarnings;
 import org.sonar.api.utils.log.Logger;
 import org.sonar.api.utils.log.Loggers;
-import org.sonar.scanner.bootstrap.ScannerProperties;
 import org.sonar.scanner.repository.settings.SettingsLoader;
 
 public class ProjectServerSettingsProvider extends ProviderAdapter {
@@ -40,9 +39,9 @@ public class ProjectServerSettingsProvider extends ProviderAdapter {
 
   private ProjectServerSettings singleton = null;
 
-  public ProjectServerSettings provide(SettingsLoader loader, ScannerProperties scannerProperties, AnalysisWarnings analysisWarnings) {
+  public ProjectServerSettings provide(SettingsLoader loader, AnalysisWarnings analysisWarnings) {
     if (singleton == null) {
-      Map<String, String> serverSideSettings = loader.load(scannerProperties.getKeyWithBranch());
+      Map<String, String> serverSideSettings = loader.loadProjectSettings();
       if (StringUtils.isNotBlank(serverSideSettings.get(CoreProperties.MODULE_LEVEL_ARCHIVED_SETTINGS))) {
         LOG.warn(MODULE_LEVEL_ARCHIVED_SETTINGS_WARNING);
         analysisWarnings.addUnique(MODULE_LEVEL_ARCHIVED_SETTINGS_WARNING);
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 c2ad796935f..cd9767328a2 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
@@ -110,7 +110,7 @@ public class FileIndexer {
       if (projectExclusionFilters.equals(moduleExclusionFilters)) {
         warnOnceDeprecatedExclusion(
           "Specifying module-relative paths at project level in the files exclusions/inclusions properties is deprecated. " +
-            "To continue including/excluding files like '" + projectRelativePath + "' from the analysis, " +
+            "To continue matching files like '" + projectRelativePath + "', " +
             "update these properties so that patterns refer to project-relative paths.");
       }
       excludedByPatternsCount.incrementAndGet();
@@ -163,7 +163,7 @@ public class FileIndexer {
       if (Arrays.equals(moduleCoverageExclusions.getCoverageExclusionConfig(), projectCoverageExclusions.getCoverageExclusionConfig())) {
         warnOnceDeprecatedCoverageExclusion(
           "Specifying module-relative paths at project level in the property '" + CoreProperties.PROJECT_COVERAGE_EXCLUSIONS_PROPERTY + "' is deprecated. " +
-            "To continue excluding files like '" + inputFile + "' from coverage, update this property so that patterns refer to project-relative paths.");
+            "To continue matching files like '" + inputFile + "', update this property so that patterns refer to project-relative paths.");
       }
       LOG.debug("File {} excluded for coverage", inputFile);
     }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleCoverageExclusions.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleCoverageExclusions.java
index ba870bc2a17..d49f5aff482 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleCoverageExclusions.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleCoverageExclusions.java
@@ -21,17 +21,12 @@ package org.sonar.scanner.scan.filesystem;
 
 import javax.annotation.concurrent.Immutable;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
-import org.sonar.api.batch.fs.internal.DefaultInputModule;
-
-import static org.sonar.api.config.internal.MultivalueProperty.parseAsCsv;
+import org.sonar.scanner.scan.ModuleConfiguration;
 
 @Immutable
 public class ModuleCoverageExclusions extends AbstractCoverageExclusions {
 
-  public ModuleCoverageExclusions(DefaultInputModule module) {
-    super(k -> {
-      String value = module.properties().get(k);
-      return value != null ? parseAsCsv(k, value) : new String[0];
-    }, DefaultInputFile::getModuleRelativePath);
+  public ModuleCoverageExclusions(ModuleConfiguration moduleConfiguration) {
+    super(moduleConfiguration::getStringArray, DefaultInputFile::getModuleRelativePath);
   }
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleExclusionFilters.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleExclusionFilters.java
index fe673788fb5..aaad3dc3511 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleExclusionFilters.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/ModuleExclusionFilters.java
@@ -19,17 +19,12 @@
  */
 package org.sonar.scanner.scan.filesystem;
 
-import org.sonar.api.batch.fs.internal.DefaultInputModule;
-
-import static org.sonar.api.config.internal.MultivalueProperty.parseAsCsv;
+import org.sonar.scanner.scan.ModuleConfiguration;
 
 public class ModuleExclusionFilters extends AbstractExclusionFilters {
 
-  public ModuleExclusionFilters(DefaultInputModule module) {
-    super(k -> {
-      String value = module.properties().get(k);
-      return value != null ? parseAsCsv(k, value) : new String[0];
-    });
+  public ModuleExclusionFilters(ModuleConfiguration moduleConfiguration) {
+    super(moduleConfiguration::getStringArray);
   }
 
 }
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 6663c08ec88..ece4b46784b 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
@@ -41,6 +41,10 @@ import org.sonar.api.batch.fs.InputFile.Type;
 import org.sonar.api.batch.fs.internal.DefaultInputModule;
 import org.sonar.api.batch.fs.internal.InputModuleHierarchy;
 import org.sonar.api.scan.filesystem.PathResolver;
+import org.sonar.scanner.bootstrap.GlobalConfiguration;
+import org.sonar.scanner.scan.ModuleConfiguration;
+import org.sonar.scanner.scan.ModuleConfigurationProvider;
+import org.sonar.scanner.scan.ProjectServerSettings;
 import org.sonar.scanner.util.ProgressReport;
 
 /**
@@ -52,15 +56,19 @@ public class ProjectFileIndexer {
   private final AbstractExclusionFilters projectExclusionFilters;
   private final InputComponentStore componentStore;
   private final InputModuleHierarchy inputModuleHierarchy;
+  private final GlobalConfiguration globalConfig;
+  private final ProjectServerSettings projectServerSettings;
   private final FileIndexer fileIndexer;
 
   private ProgressReport progressReport;
 
   public ProjectFileIndexer(InputComponentStore componentStore, AbstractExclusionFilters exclusionFilters,
-    InputModuleHierarchy inputModuleHierarchy,
+    InputModuleHierarchy inputModuleHierarchy, GlobalConfiguration globalConfig, ProjectServerSettings projectServerSettings,
     FileIndexer fileIndexer) {
     this.componentStore = componentStore;
     this.inputModuleHierarchy = inputModuleHierarchy;
+    this.globalConfig = globalConfig;
+    this.projectServerSettings = projectServerSettings;
     this.fileIndexer = fileIndexer;
     this.projectExclusionFilters = exclusionFilters;
   }
@@ -94,8 +102,10 @@ public class ProjectFileIndexer {
       logPaths("    Source paths: ", module.getBaseDir(), module.getSourceDirsOrFiles());
       logPaths("    Test paths: ", module.getBaseDir(), module.getTestDirsOrFiles());
     }
-    ModuleExclusionFilters moduleExclusionFilters = new ModuleExclusionFilters(module);
-    ModuleCoverageExclusions moduleCoverageExclusions = new ModuleCoverageExclusions(module);
+    // Emulate creation of module level settings
+    ModuleConfiguration moduleConfig = new ModuleConfigurationProvider().provide(globalConfig, module, projectServerSettings);
+    ModuleExclusionFilters moduleExclusionFilters = new ModuleExclusionFilters(moduleConfig);
+    ModuleCoverageExclusions moduleCoverageExclusions = new ModuleCoverageExclusions(moduleConfig);
     indexFiles(module, moduleExclusionFilters, moduleCoverageExclusions, module.getSourceDirsOrFiles(), Type.MAIN, excludedByPatternsCount);
     indexFiles(module, moduleExclusionFilters, moduleCoverageExclusions, module.getTestDirsOrFiles(), Type.TEST, excludedByPatternsCount);
   }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/bootstrap/GlobalConfigurationProviderTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/bootstrap/GlobalConfigurationProviderTest.java
index 0799d8b049e..f81093cc676 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/bootstrap/GlobalConfigurationProviderTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/bootstrap/GlobalConfigurationProviderTest.java
@@ -43,20 +43,18 @@ public class GlobalConfigurationProviderTest {
   GlobalServerSettings globalServerSettings;
   ScannerProperties scannerProps;
 
-  private GlobalAnalysisMode mode;
 
   @Before
   public void prepare() {
     globalServerSettings = mock(GlobalServerSettings.class);
     scannerProps = new ScannerProperties(Collections.<String, String>emptyMap());
-    mode = mock(GlobalAnalysisMode.class);
   }
 
   @Test
   public void should_load_global_settings() {
     when(globalServerSettings.properties()).thenReturn(ImmutableMap.of("sonar.cpd.cross", "true"));
 
-    GlobalConfiguration globalConfig = new GlobalConfigurationProvider().provide(globalServerSettings, scannerProps, new PropertyDefinitions(), mode);
+    GlobalConfiguration globalConfig = new GlobalConfigurationProvider().provide(globalServerSettings, scannerProps, new PropertyDefinitions());
 
     assertThat(globalConfig.get("sonar.cpd.cross")).hasValue("true");
   }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/config/DefaultConfigurationTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/config/DefaultConfigurationTest.java
index 443c0638185..a39ed539b92 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/config/DefaultConfigurationTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/config/DefaultConfigurationTest.java
@@ -30,11 +30,9 @@ import org.sonar.api.config.PropertyDefinitions;
 import org.sonar.api.config.PropertyFieldDefinition;
 import org.sonar.api.utils.log.LogTester;
 import org.sonar.api.utils.log.LoggerLevel;
-import org.sonar.scanner.bootstrap.GlobalAnalysisMode;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.assertj.core.api.Assertions.fail;
-import static org.mockito.Mockito.mock;
 
 public class DefaultConfigurationTest {
 
@@ -46,7 +44,6 @@ public class DefaultConfigurationTest {
     Configuration config = new DefaultConfiguration(new PropertyDefinitions(Arrays.asList(
       PropertyDefinition.builder("single").multiValues(false).build(),
       PropertyDefinition.builder("multiA").multiValues(true).build())), new Encryption(null),
-      mock(GlobalAnalysisMode.class),
       ImmutableMap.of("single", "foo", "multiA", "a,b", "notDeclared", "c,d")) {
     };
 
@@ -74,7 +71,6 @@ public class DefaultConfigurationTest {
     Configuration config = new DefaultConfiguration(new PropertyDefinitions(Arrays.asList(
       PropertyDefinition.builder("props").fields(PropertyFieldDefinition.build("foo1").name("Foo1").build(), PropertyFieldDefinition.build("foo2").name("Foo2").build()).build())),
       new Encryption(null),
-      mock(GlobalAnalysisMode.class),
       ImmutableMap.of("props", "1,2", "props.1.foo1", "a", "props.1.foo2", "b")) {
     };
 
@@ -94,7 +90,6 @@ public class DefaultConfigurationTest {
     Configuration config = new DefaultConfiguration(new PropertyDefinitions(Arrays.asList(
       PropertyDefinition.builder("single").multiValues(false).defaultValue("default").build(),
       PropertyDefinition.builder("multiA").multiValues(true).defaultValue("foo,bar").build())), new Encryption(null),
-      mock(GlobalAnalysisMode.class),
       ImmutableMap.of()) {
     };
 
@@ -134,7 +129,6 @@ public class DefaultConfigurationTest {
   private String[] getStringArray(String value) {
     return new DefaultConfiguration(new PropertyDefinitions(Arrays.asList(
       PropertyDefinition.builder("multi").multiValues(true).build())), new Encryption(null),
-      mock(GlobalAnalysisMode.class),
       ImmutableMap.of("multi", value)) {
     }.getStringArray("multi");
   }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/genericcoverage/GenericCoverageSensorTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/genericcoverage/GenericCoverageSensorTest.java
index 4baae856d69..6dc3de2ae2b 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/genericcoverage/GenericCoverageSensorTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/genericcoverage/GenericCoverageSensorTest.java
@@ -28,12 +28,10 @@ import org.sonar.api.config.Encryption;
 import org.sonar.api.config.PropertyDefinitions;
 import org.sonar.api.utils.log.LogTester;
 import org.sonar.api.utils.log.LoggerLevel;
-import org.sonar.scanner.bootstrap.GlobalAnalysisMode;
 import org.sonar.scanner.config.DefaultConfiguration;
 import org.sonar.scanner.scan.ProjectConfiguration;
 
 import static org.assertj.core.api.Assertions.assertThat;
-import static org.mockito.Mockito.mock;
 
 public class GenericCoverageSensorTest {
 
@@ -49,7 +47,7 @@ public class GenericCoverageSensorTest {
     settings.put(GenericCoverageSensor.OLD_OVERALL_COVERAGE_REPORT_PATHS_PROPERTY_KEY, "old5.xml,old6.xml");
 
     PropertyDefinitions defs = new PropertyDefinitions(GenericCoverageSensor.properties());
-    DefaultConfiguration config = new ProjectConfiguration(defs, new Encryption(null), mock(GlobalAnalysisMode.class), settings);
+    DefaultConfiguration config = new ProjectConfiguration(defs, new Encryption(null), settings);
 
     Set<String> reportPaths = new GenericCoverageSensor(config).loadReportPaths();
 
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/genericcoverage/GenericTestExecutionSensorTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/genericcoverage/GenericTestExecutionSensorTest.java
index 739532a9d2c..eb479cc0bce 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/genericcoverage/GenericTestExecutionSensorTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/genericcoverage/GenericTestExecutionSensorTest.java
@@ -33,7 +33,6 @@ import org.sonar.api.config.Encryption;
 import org.sonar.api.config.PropertyDefinitions;
 import org.sonar.api.utils.log.LogTester;
 import org.sonar.api.utils.log.LoggerLevel;
-import org.sonar.scanner.bootstrap.GlobalAnalysisMode;
 import org.sonar.scanner.config.DefaultConfiguration;
 import org.sonar.scanner.deprecated.test.TestPlanBuilder;
 import org.sonar.scanner.scan.ProjectConfiguration;
@@ -59,7 +58,7 @@ public class GenericTestExecutionSensorTest {
     Map<String, String> settings = new HashMap<>();
     settings.put(GenericTestExecutionSensor.OLD_UNIT_TEST_REPORT_PATHS_PROPERTY_KEY, "report.xml");
     PropertyDefinitions defs = new PropertyDefinitions(GenericTestExecutionSensor.properties());
-    DefaultConfiguration config = new ProjectConfiguration(defs, new Encryption(null), mock(GlobalAnalysisMode.class), settings);
+    DefaultConfiguration config = new ProjectConfiguration(defs, new Encryption(null), settings);
 
     new GenericTestExecutionSensor(mock(TestPlanBuilder.class), config).execute(context);
     assertThat(logTester.logs(LoggerLevel.WARN)).contains(
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/ScannerMediumTester.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/ScannerMediumTester.java
index 75111308e82..46f6e6ef7c0 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/ScannerMediumTester.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/ScannerMediumTester.java
@@ -19,9 +19,7 @@
  */
 package org.sonar.scanner.mediumtest;
 
-import com.google.common.collect.HashBasedTable;
 import com.google.common.collect.Maps;
-import com.google.common.collect.Table;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
@@ -91,6 +89,7 @@ public class ScannerMediumTester extends ExternalResource {
   private final FakeProjectRepositoriesLoader projectRefProvider = new FakeProjectRepositoriesLoader();
   private final FakePluginInstaller pluginInstaller = new FakePluginInstaller();
   private final FakeServerIssuesLoader serverIssues = new FakeServerIssuesLoader();
+  private final FakeSettingsLoader settingsLoader = new FakeSettingsLoader();
   private final FakeServerLineHashesLoader serverLineHashes = new FakeServerLineHashesLoader();
   private final FakeRulesLoader rulesLoader = new FakeRulesLoader();
   private final FakeQualityProfileLoader qualityProfiles = new FakeQualityProfileLoader();
@@ -230,6 +229,16 @@ public class ScannerMediumTester extends ExternalResource {
     return this;
   }
 
+  public ScannerMediumTester addGlobalServerSettings(String key, String value) {
+    settingsLoader.getGlobalSettings().put(key, value);
+    return this;
+  }
+
+  public ScannerMediumTester addProjectServerSettings(String key, String value) {
+    settingsLoader.getProjectSettings().put(key, value);
+    return this;
+  }
+
   public ScannerMediumTester mockLineHashes(String fileKey, String[] lineHashes) {
     serverLineHashes.byKey.put(fileKey, lineHashes);
     return this;
@@ -302,7 +311,7 @@ public class ScannerMediumTester extends ExternalResource {
           tester.projectRefProvider,
           tester.activeRules,
           tester.serverIssues,
-          new FakeSettingsLoader(),
+          tester.settingsLoader,
           result)
         .setLogOutput(tester.logOutput)
         .build().execute();
@@ -495,9 +504,25 @@ public class ScannerMediumTester extends ExternalResource {
 
   private static class FakeSettingsLoader implements SettingsLoader {
 
+    private Map<String, String> globalSettings = new HashMap<>();
+    private Map<String, String> projectSettings = new HashMap<>();
+
+    public Map<String, String> getGlobalSettings() {
+      return globalSettings;
+    }
+
+    public Map<String, String> getProjectSettings() {
+      return projectSettings;
+    }
+
+    @Override
+    public Map<String, String> loadGlobalSettings() {
+      return Collections.unmodifiableMap(globalSettings);
+    }
+
     @Override
-    public Map<String, String> load(String componentKey) {
-      return Collections.emptyMap();
+    public Map<String, String> loadProjectSettings() {
+      return Collections.unmodifiableMap(projectSettings);
     }
   }
 
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/coverage/CoverageMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/coverage/CoverageMediumTest.java
index 93fa2a44fbb..9226bf38199 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/coverage/CoverageMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/coverage/CoverageMediumTest.java
@@ -159,7 +159,7 @@ public class CoverageMediumTest {
   }
 
   @Test
-  public void warn_user_for_outdated_inherited_exclusions_for_multi_module_project() throws IOException {
+  public void warn_user_for_outdated_inherited_scanner_side_exclusions_for_multi_module_project() throws IOException {
 
     File baseDir = temp.getRoot();
     File baseDirModuleA = new File(baseDir, "moduleA");
@@ -197,7 +197,50 @@ public class CoverageMediumTest {
     assertThat(result.coverageFor(fileB, 2)).isNull();
 
     assertThat(logTester.logs(LoggerLevel.WARN)).contains("Specifying module-relative paths at project level in the property 'sonar.coverage.exclusions' is deprecated. " +
-      "To continue excluding files like 'moduleA/src/sample.xoo' from coverage, update this property so that patterns refer to project-relative paths.");
+      "To continue matching files like 'moduleA/src/sample.xoo', update this property so that patterns refer to project-relative paths.");
+  }
+
+  @Test
+  public void warn_user_for_outdated_server_side_exclusions_for_multi_module_project() throws IOException {
+
+    File baseDir = temp.getRoot();
+    File baseDirModuleA = new File(baseDir, "moduleA");
+    File baseDirModuleB = new File(baseDir, "moduleB");
+    File srcDirA = new File(baseDirModuleA, "src");
+    srcDirA.mkdirs();
+    File srcDirB = new File(baseDirModuleB, "src");
+    srcDirB.mkdirs();
+
+    File xooFileA = new File(srcDirA, "sample.xoo");
+    File xooUtCoverageFileA = new File(srcDirA, "sample.xoo.coverage");
+    FileUtils.write(xooFileA, "function foo() {\n  if (a && b) {\nalert('hello');\n}\n}", StandardCharsets.UTF_8);
+    FileUtils.write(xooUtCoverageFileA, "2:2:2:1\n3:1", StandardCharsets.UTF_8);
+
+    File xooFileB = new File(srcDirB, "sample.xoo");
+    File xooUtCoverageFileB = new File(srcDirB, "sample.xoo.coverage");
+    FileUtils.write(xooFileB, "function foo() {\n  if (a && b) {\nalert('hello');\n}\n}", StandardCharsets.UTF_8);
+    FileUtils.write(xooUtCoverageFileB, "2:2:2:1\n3:1", StandardCharsets.UTF_8);
+
+    tester.addProjectServerSettings("sonar.coverage.exclusions", "src/sample.xoo");
+
+    AnalysisResult result = tester.newAnalysis()
+      .properties(ImmutableMap.<String, String>builder()
+        .put("sonar.task", "scan")
+        .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
+        .put("sonar.projectKey", "com.foo.project")
+        .put("sonar.sources", "src")
+        .put("sonar.modules", "moduleA,moduleB")
+        .build())
+      .execute();
+
+    InputFile fileA = result.inputFile("moduleA/src/sample.xoo");
+    assertThat(result.coverageFor(fileA, 2)).isNull();
+
+    InputFile fileB = result.inputFile("moduleB/src/sample.xoo");
+    assertThat(result.coverageFor(fileB, 2)).isNull();
+
+    assertThat(logTester.logs(LoggerLevel.WARN)).contains("Specifying module-relative paths at project level in the property 'sonar.coverage.exclusions' is deprecated. " +
+      "To continue matching files like 'moduleA/src/sample.xoo', update this property so that patterns refer to project-relative paths.");
   }
 
   @Test
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java
index b93776906e4..e2103e18828 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java
@@ -71,32 +71,16 @@ public class FileSystemMediumTest {
   private ImmutableMap.Builder<String, String> builder;
 
   @Before
-  public void prepare() throws IOException {
+  public void prepare() {
     baseDir = temp.getRoot();
 
     builder = ImmutableMap.<String, String>builder()
-      .put("sonar.task", "scan")
       .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
-      .put("sonar.projectKey", "com.foo.project")
-      .put("sonar.projectName", "Foo Project")
-      .put("sonar.projectVersion", "1.0-SNAPSHOT")
-      .put("sonar.projectDescription", "Description of Foo Project");
-  }
-
-  private ImmutableMap.Builder<String, String> createBuilder() {
-    return ImmutableMap.<String, String>builder()
-      .put("sonar.task", "scan")
-      .put("sonar.verbose", "true")
-      .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
-      .put("sonar.projectKey", "com.foo.project")
-      .put("sonar.projectVersion", "1.0-SNAPSHOT")
-      .put("sonar.projectDescription", "Description of Foo Project");
+      .put("sonar.projectKey", "com.foo.project");
   }
 
   @Test
   public void scanProjectWithoutProjectName() throws IOException {
-    builder = createBuilder();
-
     File srcDir = new File(baseDir, "src");
     srcDir.mkdir();
 
@@ -125,7 +109,6 @@ public class FileSystemMediumTest {
 
   @Test
   public void logProjectKeyAndOrganizationKey() throws IOException {
-    builder = createBuilder();
     builder.put("sonar.organization", "my org");
     builder.put("sonar.branch", "");
     File srcDir = new File(baseDir, "src");
@@ -147,7 +130,6 @@ public class FileSystemMediumTest {
 
   @Test
   public void logBranchKey() throws IOException {
-    builder = createBuilder();
     builder.put("sonar.branch", "my-branch");
     File srcDir = new File(baseDir, "src");
     assertThat(srcDir.mkdir()).isTrue();
@@ -163,20 +145,18 @@ public class FileSystemMediumTest {
 
     assertThat(logTester.logs()).contains("Project key: com.foo.project");
     assertThat(logTester.logs()).contains("Branch key: my-branch");
-    assertThat(logTester.logs()).contains("The use of \"sonar.branch\" is deprecated and replaced by \"sonar.branch.name\". See https://redirect.sonarsource.com/doc/branches.html.");
+    assertThat(logTester.logs())
+      .contains("The use of \"sonar.branch\" is deprecated and replaced by \"sonar.branch.name\". See https://redirect.sonarsource.com/doc/branches.html.");
   }
 
   @Test
   public void logBranchNameAndType() throws IOException {
-    builder = createBuilder();
     builder.put("sonar.branch.name", "my-branch");
     File srcDir = new File(baseDir, "src");
     assertThat(srcDir.mkdir()).isTrue();
 
     // Using sonar.branch.name when the branch plugin is not installed is an error.
-    // IllegalStateException is expected here, because this test is in a bit artificial,
-    // the fail-fast mechanism in the scanner should have prevented reaching this point.
-    thrown.expect(IllegalStateException.class);
+    thrown.expect(MessageException.class);
 
     tester.newAnalysis()
       .properties(builder
@@ -187,7 +167,6 @@ public class FileSystemMediumTest {
 
   @Test
   public void dontLogInvalidOrganization() throws IOException {
-    builder = createBuilder();
     File srcDir = new File(baseDir, "src");
     srcDir.mkdir();
 
@@ -207,8 +186,6 @@ public class FileSystemMediumTest {
 
   @Test
   public void onlyGenerateMetadataIfNeeded() throws IOException {
-    builder = createBuilder();
-
     File srcDir = new File(baseDir, "src");
     srcDir.mkdir();
 
@@ -234,8 +211,7 @@ public class FileSystemMediumTest {
 
   @Test
   public void preloadFileMetadata() throws IOException {
-    builder = createBuilder()
-      .put("sonar.preloadFileMetadata", "true");
+    builder.put("sonar.preloadFileMetadata", "true");
 
     File srcDir = new File(baseDir, "src");
     srcDir.mkdir();
@@ -261,8 +237,6 @@ public class FileSystemMediumTest {
 
   @Test
   public void dontPublishFilesWithoutDetectedLanguage() throws IOException {
-    builder = createBuilder();
-
     Path mainDir = baseDir.toPath().resolve("src").resolve("main");
     Files.createDirectories(mainDir);
 
@@ -305,8 +279,6 @@ public class FileSystemMediumTest {
       .addRules(new XooRulesDefinition())
       .addActiveRule("xoo", "OneIssuePerUnknownFile", null, "OneIssuePerUnknownFile", "MAJOR", null, "xoo");
 
-    builder = createBuilder();
-
     File srcDir = new File(baseDir, "src");
     srcDir.mkdir();
 
@@ -334,7 +306,6 @@ public class FileSystemMediumTest {
       .addRules(new XooRulesDefinition())
       .addActiveRule("xoo", "OneIssuePerFile", null, "OneIssuePerFile", "MAJOR", null, "xoo");
 
-    builder = createBuilder();
     builder.put("sonar.issue.ignore.allfile", "1")
       .put("sonar.issue.ignore.allfile.1.fileRegexp", "pattern");
     File srcDir = new File(baseDir, "src");
@@ -363,7 +334,6 @@ public class FileSystemMediumTest {
 
   @Test
   public void preloadIssueExclusions() throws IOException {
-    builder = createBuilder();
     builder.put("sonar.issue.ignore.allfile", "1")
       .put("sonar.issue.ignore.allfile.1.fileRegexp", "pattern")
       .put("sonar.preloadFileMetadata", "true");
@@ -394,8 +364,6 @@ public class FileSystemMediumTest {
       .addRules(new XooRulesDefinition())
       .addActiveRule("xoo", "OneIssueOnDirPerFile", null, "OneIssueOnDirPerFile", "MAJOR", null, "xoo");
 
-    builder = createBuilder();
-
     File srcDir = new File(baseDir, "src");
     srcDir.mkdir();
 
@@ -541,8 +509,7 @@ public class FileSystemMediumTest {
   }
 
   @Test
-  public void warn_user_for_outdated_inherited_exclusions_for_multi_module_project() throws IOException {
-
+  public void warn_user_for_outdated_scanner_side_inherited_exclusions_for_multi_module_project() throws IOException {
     File baseDir = temp.getRoot();
     File baseDirModuleA = new File(baseDir, "moduleA");
     File baseDirModuleB = new File(baseDir, "moduleB");
@@ -576,7 +543,46 @@ public class FileSystemMediumTest {
 
     assertThat(logTester.logs(LoggerLevel.WARN))
       .contains("Specifying module-relative paths at project level in the files exclusions/inclusions properties is deprecated. " +
-        "To continue including/excluding files like 'moduleA/src/sample.xoo' from the analysis, update these properties so that patterns refer to project-relative paths.");
+        "To continue matching files like 'moduleA/src/sample.xoo', update these properties so that patterns refer to project-relative paths.");
+  }
+
+  @Test
+  public void warn_user_for_outdated_server_side_inherited_exclusions_for_multi_module_project() throws IOException {
+    File baseDir = temp.getRoot();
+    File baseDirModuleA = new File(baseDir, "moduleA");
+    File baseDirModuleB = new File(baseDir, "moduleB");
+    File srcDirA = new File(baseDirModuleA, "src");
+    srcDirA.mkdirs();
+    File srcDirB = new File(baseDirModuleB, "src");
+    srcDirB.mkdirs();
+
+    File xooFileA = new File(srcDirA, "sample.xoo");
+    FileUtils.write(xooFileA, "Sample xoo\ncontent", StandardCharsets.UTF_8);
+
+    File xooFileB = new File(srcDirB, "sample.xoo");
+    FileUtils.write(xooFileB, "Sample xoo\ncontent", StandardCharsets.UTF_8);
+
+    tester.addProjectServerSettings("sonar.exclusions", "src/sample.xoo");
+
+    AnalysisResult result = tester.newAnalysis()
+      .properties(ImmutableMap.<String, String>builder()
+        .put("sonar.task", "scan")
+        .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
+        .put("sonar.projectKey", "com.foo.project")
+        .put("sonar.sources", "src")
+        .put("sonar.modules", "moduleA,moduleB")
+        .build())
+      .execute();
+
+    InputFile fileA = result.inputFile("moduleA/src/sample.xoo");
+    assertThat(fileA).isNull();
+
+    InputFile fileB = result.inputFile("moduleB/src/sample.xoo");
+    assertThat(fileB).isNull();
+
+    assertThat(logTester.logs(LoggerLevel.WARN))
+      .contains("Specifying module-relative paths at project level in the files exclusions/inclusions properties is deprecated. " +
+        "To continue matching files like 'moduleA/src/sample.xoo', update these properties so that patterns refer to project-relative paths.");
   }
 
   @Test
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/log/ExceptionHandlingMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/log/ExceptionHandlingMediumTest.java
index feae49a1bbe..ce9e0d393ae 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/log/ExceptionHandlingMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/log/ExceptionHandlingMediumTest.java
@@ -102,7 +102,7 @@ public class ExceptionHandlingMediumTest {
     boolean withCause = false;
 
     @Override
-    public Map<String, String> load(String componentKey) {
+    public Map<String, String> loadGlobalSettings() {
       if (withCause) {
         IllegalStateException cause = new IllegalStateException("Code 401");
         throw MessageException.of("Error loading settings", cause);
@@ -110,5 +110,10 @@ public class ExceptionHandlingMediumTest {
         throw MessageException.of("Error loading settings");
       }
     }
+
+    @Override
+    public Map<String, String> loadProjectSettings() {
+      return null;
+    }
   }
 }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/phases/ModuleCoverageExclusionsTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/phases/ModuleCoverageExclusionsTest.java
index 88c746ba89a..7a3287dd882 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/phases/ModuleCoverageExclusionsTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/phases/ModuleCoverageExclusionsTest.java
@@ -20,15 +20,11 @@
 package org.sonar.scanner.phases;
 
 import java.io.File;
-import java.util.Arrays;
-import java.util.stream.Collectors;
 import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
-import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
-import org.sonar.api.batch.fs.internal.DefaultInputModule;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.scanner.scan.ModuleConfiguration;
 import org.sonar.scanner.scan.filesystem.ModuleCoverageExclusions;
@@ -68,12 +64,9 @@ public class ModuleCoverageExclusionsTest {
     assertThat(coverageExclusions.isExcluded(file)).isFalse();
   }
 
-  private DefaultInputModule mockConfig(String... values) {
+  private ModuleConfiguration mockConfig(String... values) {
     ModuleConfiguration config = mock(ModuleConfiguration.class);
     when(config.getStringArray("sonar.coverage.exclusions")).thenReturn(values);
-    return new DefaultInputModule(ProjectDefinition.create()
-      .setBaseDir(baseDir)
-      .setWorkDir(baseDir)
-      .setProperty("sonar.coverage.exclusions", Arrays.asList(values).stream().collect(Collectors.joining(","))));
+    return config;
   }
 }