SONAR-11587 Rework issue exclusions

17 files changed, 194 insertions, 345 deletions

diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/DefaultFilterableIssue.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/DefaultFilterableIssue.java
index eaf4e0f1edb..bb92a02f31c 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/DefaultFilterableIssue.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/DefaultFilterableIssue.java
@@ -23,6 +23,7 @@ import java.util.Date;
 import javax.annotation.concurrent.ThreadSafe;
 import org.apache.commons.lang.builder.ToStringBuilder;
 import org.apache.commons.lang.builder.ToStringStyle;
+import org.sonar.api.batch.fs.InputComponent;
 import org.sonar.api.batch.fs.TextRange;
 import org.sonar.api.batch.fs.internal.DefaultInputProject;
 import org.sonar.api.batch.fs.internal.DefaultTextPointer;
@@ -35,20 +36,20 @@ import org.sonar.scanner.protocol.output.ScannerReport.Issue;
 @ThreadSafe
 public class DefaultFilterableIssue implements FilterableIssue {
   private final Issue rawIssue;
+  private final InputComponent component;
   private final ProjectAnalysisInfo projectAnalysisInfo;
-  private final String componentKey;
   private DefaultInputProject project;
 
-  public DefaultFilterableIssue(DefaultInputProject project, ProjectAnalysisInfo projectAnalysisInfo, Issue rawIssue, String componentKey) {
+  public DefaultFilterableIssue(DefaultInputProject project, ProjectAnalysisInfo projectAnalysisInfo, Issue rawIssue, InputComponent component) {
     this.project = project;
     this.projectAnalysisInfo = projectAnalysisInfo;
     this.rawIssue = rawIssue;
-    this.componentKey = componentKey;
+    this.component = component;
   }
 
   @Override
   public String componentKey() {
-    return componentKey;
+    return component.key();
   }
 
   @Override
@@ -98,6 +99,10 @@ public class DefaultFilterableIssue implements FilterableIssue {
     return project.key();
   }
 
+  public InputComponent getComponent() {
+    return component;
+  }
+
   @Override
   public String toString() {
     return ToStringBuilder.reflectionToString(this, ToStringStyle.SHORT_PREFIX_STYLE);
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/IssueFilters.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/IssueFilters.java
index 92a8f758249..b4ade123839 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/IssueFilters.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/IssueFilters.java
@@ -19,6 +19,7 @@
  */
 package org.sonar.scanner.issue;
 
+import org.sonar.api.batch.fs.InputComponent;
 import org.sonar.api.batch.fs.internal.DefaultInputProject;
 import org.sonar.api.scan.issue.filter.FilterableIssue;
 import org.sonar.api.scan.issue.filter.IssueFilter;
@@ -45,8 +46,8 @@ public class IssueFilters {
     this(project, projectAnalysisInfo, new IssueFilter[0]);
   }
 
-  public boolean accept(String componentKey, ScannerReport.Issue rawIssue) {
-    FilterableIssue fIssue = new DefaultFilterableIssue(project, projectAnalysisInfo, rawIssue, componentKey);
+  public boolean accept(InputComponent component, ScannerReport.Issue rawIssue) {
+    FilterableIssue fIssue = new DefaultFilterableIssue(project, projectAnalysisInfo, rawIssue, component);
     return filterChain.accept(fIssue);
   }
 
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/IssuePublisher.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/IssuePublisher.java
index ca0a8cc0764..f8a652553ea 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/IssuePublisher.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/IssuePublisher.java
@@ -70,7 +70,7 @@ public class IssuePublisher {
 
     ScannerReport.Issue rawIssue = createReportIssue(issue, inputComponent.scannerId(), activeRule.severity());
 
-    if (filters.accept(inputComponent.key(), rawIssue)) {
+    if (filters.accept(inputComponent, rawIssue)) {
       write(inputComponent.scannerId(), rawIssue);
       return true;
     }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/EnforceIssuesFilter.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/EnforceIssuesFilter.java
index 3f5b74f2390..0cf870ea06b 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/EnforceIssuesFilter.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/EnforceIssuesFilter.java
@@ -22,31 +22,31 @@ package org.sonar.scanner.issue.ignore;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
-
-import javax.annotation.CheckForNull;
 import javax.annotation.concurrent.ThreadSafe;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.sonar.api.batch.fs.InputComponent;
-import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.fs.internal.DefaultInputFile;
+import org.sonar.api.notifications.AnalysisWarnings;
 import org.sonar.api.scan.issue.filter.FilterableIssue;
 import org.sonar.api.scan.issue.filter.IssueFilter;
 import org.sonar.api.scan.issue.filter.IssueFilterChain;
+import org.sonar.api.utils.log.Logger;
+import org.sonar.api.utils.log.Loggers;
+import org.sonar.scanner.issue.DefaultFilterableIssue;
 import org.sonar.scanner.issue.ignore.pattern.IssueInclusionPatternInitializer;
 import org.sonar.scanner.issue.ignore.pattern.IssuePattern;
-import org.sonar.scanner.scan.filesystem.InputComponentStore;
 
 @ThreadSafe
 public class EnforceIssuesFilter implements IssueFilter {
-  private static final Logger LOG = LoggerFactory.getLogger(EnforceIssuesFilter.class);
+  private static final Logger LOG = Loggers.get(EnforceIssuesFilter.class);
 
   private final List<IssuePattern> multicriteriaPatterns;
-  private final InputComponentStore componentStore;
+  private final AnalysisWarnings analysisWarnings;
+
+  private boolean warnDeprecatedIssuePatternAlreadyLogged;
 
-  public EnforceIssuesFilter(IssueInclusionPatternInitializer patternInitializer, InputComponentStore componentStore) {
+  public EnforceIssuesFilter(IssueInclusionPatternInitializer patternInitializer, AnalysisWarnings analysisWarnings) {
     this.multicriteriaPatterns = Collections.unmodifiableList(new ArrayList<>(patternInitializer.getMulticriteriaPatterns()));
-    this.componentStore = componentStore;
+    this.analysisWarnings = analysisWarnings;
   }
 
   @Override
@@ -56,12 +56,22 @@ public class EnforceIssuesFilter implements IssueFilter {
     IssuePattern matchingPattern = null;
 
     for (IssuePattern pattern : multicriteriaPatterns) {
-      if (pattern.getRulePattern().match(issue.ruleKey().toString())) {
+      if (pattern.matchRule(issue.ruleKey())) {
         atLeastOneRuleMatched = true;
-        String relativePath = getRelativePath(issue.componentKey());
-        if (relativePath != null && pattern.getResourcePattern().match(relativePath)) {
-          atLeastOnePatternFullyMatched = true;
-          matchingPattern = pattern;
+        InputComponent component = ((DefaultFilterableIssue) issue).getComponent();
+        if (component.isFile()) {
+          DefaultInputFile file = (DefaultInputFile) component;
+          if (pattern.matchFile(file.getProjectRelativePath())) {
+            atLeastOnePatternFullyMatched = true;
+            matchingPattern = pattern;
+          } else if (pattern.matchFile(file.getModuleRelativePath())) {
+            warnOnceDeprecatedIssuePattern(
+              "Specifying module-relative paths at project level in property '" + IssueInclusionPatternInitializer.CONFIG_KEY + "' is deprecated. " +
+                "To continue matching files like '" + file.getProjectRelativePath() + "', update this property so that patterns refer to project-relative paths.");
+
+            atLeastOnePatternFullyMatched = true;
+            matchingPattern = pattern;
+          }
         }
       }
     }
@@ -76,13 +86,12 @@ public class EnforceIssuesFilter implements IssueFilter {
     }
   }
 
-  @CheckForNull
-  private String getRelativePath(String componentKey) {
-    InputComponent component = componentStore.getByKey(componentKey);
-    if (component == null || !component.isFile()) {
-      return null;
+  private void warnOnceDeprecatedIssuePattern(String msg) {
+    if (!warnDeprecatedIssuePatternAlreadyLogged) {
+      LOG.warn(msg);
+      analysisWarnings.addUnique(msg);
+      warnDeprecatedIssuePatternAlreadyLogged = true;
     }
-    InputFile inputPath = (InputFile) component;
-    return inputPath.relativePath();
   }
+
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/IgnoreIssuesFilter.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/IgnoreIssuesFilter.java
index 723d7eecc4d..666b1732dea 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/IgnoreIssuesFilter.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/IgnoreIssuesFilter.java
@@ -19,42 +19,55 @@
  */
 package org.sonar.scanner.issue.ignore;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import com.google.common.collect.LinkedHashMultimap;
+import com.google.common.collect.Multimap;
+import org.sonar.api.batch.fs.InputComponent;
+import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.scan.issue.filter.FilterableIssue;
 import org.sonar.api.scan.issue.filter.IssueFilter;
 import org.sonar.api.scan.issue.filter.IssueFilterChain;
-import org.sonar.scanner.issue.ignore.pattern.IssuePattern;
-import org.sonar.scanner.issue.ignore.pattern.PatternMatcher;
+import org.sonar.api.utils.WildcardPattern;
+import org.sonar.api.utils.log.Logger;
+import org.sonar.api.utils.log.Loggers;
+import org.sonar.scanner.issue.DefaultFilterableIssue;
 
 public class IgnoreIssuesFilter implements IssueFilter {
 
-  private PatternMatcher patternMatcher;
+  private Multimap<InputComponent, WildcardPattern> rulePatternByComponent = LinkedHashMultimap.create();
 
-  private static final Logger LOG = LoggerFactory.getLogger(IgnoreIssuesFilter.class);
-
-  public IgnoreIssuesFilter(PatternMatcher patternMatcher) {
-    this.patternMatcher = patternMatcher;
-  }
+  private static final Logger LOG = Loggers.get(IgnoreIssuesFilter.class);
 
   @Override
   public boolean accept(FilterableIssue issue, IssueFilterChain chain) {
-    if (hasMatchFor(issue)) {
+    InputComponent component = ((DefaultFilterableIssue) issue).getComponent();
+    if (component.isFile() && ((DefaultInputFile) component).isIgnoreAllIssues()) {
+      return false;
+    }
+    if (component.isFile() && ((DefaultInputFile) component).isIgnoreAllIssuesOnLine(issue.line())) {
+      return false;
+    }
+    if (hasRuleMatchFor(component, issue)) {
       return false;
     }
     return chain.accept(issue);
   }
 
-  private boolean hasMatchFor(FilterableIssue issue) {
-    IssuePattern pattern = patternMatcher.getMatchingPattern(issue.componentKey(), issue.ruleKey(), issue.line());
-    if (pattern != null) {
-      logExclusion(issue, pattern);
-      return true;
+  public void addRuleExclusionPatternForComponent(DefaultInputFile inputFile, WildcardPattern rulePattern) {
+    if ("*".equals(rulePattern.toString())) {
+      inputFile.setIgnoreAllIssues(true);
+    } else {
+      rulePatternByComponent.put(inputFile, rulePattern);
     }
-    return false;
   }
 
-  private static void logExclusion(FilterableIssue issue, IssuePattern pattern) {
-    LOG.debug("Issue {} ignored by exclusion pattern {}", issue, pattern);
+  private boolean hasRuleMatchFor(InputComponent component, FilterableIssue issue) {
+    for (WildcardPattern pattern : rulePatternByComponent.get(component)) {
+      if (pattern.match(issue.ruleKey().toString())) {
+        LOG.debug("Issue {} ignored by exclusion pattern {}", issue, pattern);
+        return true;
+      }
+    }
+    return false;
+
   }
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/AbstractPatternInitializer.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/AbstractPatternInitializer.java
index 51058404811..4b85daf89e4 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/AbstractPatternInitializer.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/AbstractPatternInitializer.java
@@ -22,9 +22,9 @@ package org.sonar.scanner.issue.ignore.pattern;
 import com.google.common.annotations.VisibleForTesting;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Set;
 import org.apache.commons.lang.StringUtils;
 import org.sonar.api.config.Configuration;
+import org.sonar.api.utils.MessageException;
 
 import static com.google.common.base.MoreObjects.firstNonNull;
 
@@ -59,13 +59,15 @@ public abstract class AbstractPatternInitializer {
     multicriteriaPatterns = new ArrayList<>();
     for (String id : settings.getStringArray(getMulticriteriaConfigurationKey())) {
       String propPrefix = getMulticriteriaConfigurationKey() + "." + id + ".";
-      String resourceKeyPattern = settings.get(propPrefix + "resourceKey").orElse(null);
+      String filePathPattern = settings.get(propPrefix + "resourceKey").orElse(null);
+      if (StringUtils.isBlank(filePathPattern)) {
+        throw MessageException.of("Issue exclusions are misconfigured. File pattern is mandatory for each entry of '" + getMulticriteriaConfigurationKey() + "'");
+      }
       String ruleKeyPattern = settings.get(propPrefix + "ruleKey").orElse(null);
-      String lineRange = "*";
-      String[] fields = new String[] {resourceKeyPattern, ruleKeyPattern, lineRange};
-      PatternDecoder.checkRegularLineConstraints(StringUtils.join(fields, ","), fields);
-      Set<LineRange> rangeOfLines = PatternDecoder.decodeRangeOfLines(firstNonNull(lineRange, "*"));
-      IssuePattern pattern = new IssuePattern(firstNonNull(resourceKeyPattern, "*"), firstNonNull(ruleKeyPattern, "*"), rangeOfLines);
+      if (StringUtils.isBlank(ruleKeyPattern)) {
+        throw MessageException.of("Issue exclusions are misconfigured. Rule key pattern is mandatory for each entry of '" + getMulticriteriaConfigurationKey() + "'");
+      }
+      IssuePattern pattern = new IssuePattern(firstNonNull(filePathPattern, "*"), firstNonNull(ruleKeyPattern, "*"));
 
       multicriteriaPatterns.add(pattern);
     }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssueExclusionPatternInitializer.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssueExclusionPatternInitializer.java
index 01e0ab76b06..16c3163cbf7 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssueExclusionPatternInitializer.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssueExclusionPatternInitializer.java
@@ -24,12 +24,14 @@ import java.util.Collections;
 import java.util.List;
 import org.apache.commons.lang.StringUtils;
 import org.sonar.api.config.Configuration;
+import org.sonar.api.utils.MessageException;
 import org.sonar.core.config.IssueExclusionProperties;
 
 import static com.google.common.base.Strings.nullToEmpty;
 
 public class IssueExclusionPatternInitializer extends AbstractPatternInitializer {
 
+  public static final String CONFIG_KEY = IssueExclusionProperties.EXCLUSION_KEY_PREFIX + ".multicriteria";
   private List<BlockIssuePattern> blockPatterns;
   private List<String> allFilePatterns;
 
@@ -40,7 +42,7 @@ public class IssueExclusionPatternInitializer extends AbstractPatternInitializer
 
   @Override
   protected String getMulticriteriaConfigurationKey() {
-    return IssueExclusionProperties.EXCLUSION_KEY_PREFIX + ".multicriteria";
+    return CONFIG_KEY;
   }
 
   @Override
@@ -54,9 +56,11 @@ public class IssueExclusionPatternInitializer extends AbstractPatternInitializer
     for (String id : getSettings().getStringArray(IssueExclusionProperties.PATTERNS_BLOCK_KEY)) {
       String propPrefix = IssueExclusionProperties.PATTERNS_BLOCK_KEY + "." + id + ".";
       String beginBlockRegexp = getSettings().get(propPrefix + IssueExclusionProperties.BEGIN_BLOCK_REGEXP).orElse(null);
+      if (StringUtils.isBlank(beginBlockRegexp)) {
+        throw MessageException.of("Issue exclusions are misconfigured. Start block regexp is mandatory for each entry of '" + IssueExclusionProperties.PATTERNS_BLOCK_KEY + "'");
+      }
       String endBlockRegexp = getSettings().get(propPrefix + IssueExclusionProperties.END_BLOCK_REGEXP).orElse(null);
-      String[] fields = new String[] {beginBlockRegexp, endBlockRegexp};
-      PatternDecoder.checkDoubleRegexpLineConstraints(StringUtils.join(fields, ","), fields);
+      // As per configuration help, missing second field means: from start regexp to EOF
       BlockIssuePattern pattern = new BlockIssuePattern(nullToEmpty(beginBlockRegexp), nullToEmpty(endBlockRegexp));
       blockPatterns.add(pattern);
     }
@@ -67,7 +71,9 @@ public class IssueExclusionPatternInitializer extends AbstractPatternInitializer
     for (String id : getSettings().getStringArray(IssueExclusionProperties.PATTERNS_ALLFILE_KEY)) {
       String propPrefix = IssueExclusionProperties.PATTERNS_ALLFILE_KEY + "." + id + ".";
       String allFileRegexp = getSettings().get(propPrefix + IssueExclusionProperties.FILE_REGEXP).orElse(null);
-      PatternDecoder.checkWholeFileRegexp(allFileRegexp);
+      if (StringUtils.isBlank(allFileRegexp)) {
+        throw MessageException.of("Issue exclusions are misconfigured. Remove blank entries from '" + IssueExclusionProperties.PATTERNS_ALLFILE_KEY + "'");
+      }
       allFilePatterns.add(nullToEmpty(allFileRegexp));
     }
     allFilePatterns = Collections.unmodifiableList(allFilePatterns);
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssueInclusionPatternInitializer.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssueInclusionPatternInitializer.java
index 0fa72da96db..30987808e9d 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssueInclusionPatternInitializer.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssueInclusionPatternInitializer.java
@@ -24,12 +24,14 @@ import org.sonar.core.config.IssueExclusionProperties;
 
 public class IssueInclusionPatternInitializer extends AbstractPatternInitializer {
 
+  public static final String CONFIG_KEY = IssueExclusionProperties.INCLUSION_KEY_PREFIX + ".multicriteria";
+
   public IssueInclusionPatternInitializer(Configuration settings) {
     super(settings);
   }
 
   @Override
   protected String getMulticriteriaConfigurationKey() {
-    return IssueExclusionProperties.INCLUSION_KEY_PREFIX + ".multicriteria";
+    return CONFIG_KEY;
   }
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssuePattern.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssuePattern.java
index 4e76159ab72..9be0fd7c75e 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssuePattern.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/IssuePattern.java
@@ -19,108 +19,32 @@
  */
 package org.sonar.scanner.issue.ignore.pattern;
 
-import java.util.Collections;
-import java.util.LinkedHashSet;
-import java.util.Set;
 import javax.annotation.Nullable;
 import javax.annotation.concurrent.Immutable;
-import org.apache.commons.lang.builder.ToStringBuilder;
-import org.apache.commons.lang.builder.ToStringStyle;
 import org.sonar.api.rule.RuleKey;
 import org.sonar.api.utils.WildcardPattern;
 
 @Immutable
 public class IssuePattern {
 
-  private final WildcardPattern resourcePattern;
+  private final WildcardPattern filePattern;
   private final WildcardPattern rulePattern;
-  private final Set<Integer> lines;
-  private final Set<LineRange> lineRanges;
-  private final boolean checkLines;
 
-  public IssuePattern(String resourcePattern, String rulePattern) {
-    this(resourcePattern, rulePattern, Collections.emptySet());
-  }
-
-  public IssuePattern(String resourcePattern, String rulePattern, Set<LineRange> lineRanges) {
-    this.resourcePattern = WildcardPattern.create(resourcePattern);
+  public IssuePattern(String filePattern, String rulePattern) {
+    this.filePattern = WildcardPattern.create(filePattern);
     this.rulePattern = WildcardPattern.create(rulePattern);
-    this.checkLines = !lineRanges.isEmpty();
-    Set<Integer> modifiableLines = new LinkedHashSet<>();
-    Set<LineRange> modifiableLineRanges = new LinkedHashSet<>();
-
-    for (LineRange range : lineRanges) {
-      if (range.from() == range.to()) {
-        modifiableLines.add(range.from());
-      } else {
-        modifiableLineRanges.add(range);
-      }
-    }
-
-    this.lines = Collections.unmodifiableSet(modifiableLines);
-    this.lineRanges = Collections.unmodifiableSet(modifiableLineRanges);
-  }
-
-  public WildcardPattern getResourcePattern() {
-    return resourcePattern;
   }
 
   public WildcardPattern getRulePattern() {
     return rulePattern;
   }
 
-  boolean isCheckLines() {
-    return checkLines;
-  }
-
-  Set<Integer> getAllLines() {
-    Set<Integer> allLines = new LinkedHashSet<>(lines);
-    for (LineRange lineRange : lineRanges) {
-      allLines.addAll(lineRange.toLines());
-    }
-    return allLines;
+  public boolean matchRule(RuleKey rule) {
+    return rulePattern.match(rule.toString());
   }
 
-  public boolean match(@Nullable String componentKey, RuleKey ruleKey, @Nullable Integer line) {
-    if (checkLines) {
-      if (line == null) {
-        return false;
-      } else {
-        return matchResource(componentKey) && matchRule(ruleKey) && matchLine(line);
-      }
-    }
-    return matchResource(componentKey) && matchRule(ruleKey);
+  public boolean matchFile(@Nullable String filePath) {
+    return filePath != null && filePattern.match(filePath);
   }
 
-  boolean matchLine(int lineId) {
-    if (lines.contains(lineId)) {
-      return true;
-    }
-
-    for (LineRange range : lineRanges) {
-      if (range.in(lineId)) {
-        return true;
-      }
-    }
-
-    return false;
-  }
-
-  boolean matchRule(RuleKey rule) {
-    String key = new StringBuilder().append(rule.repository()).append(':').append(rule.rule()).toString();
-    return rulePattern.match(key);
-  }
-
-  public boolean matchResource(@Nullable String resource) {
-    return resource != null && resourcePattern.match(resource);
-  }
-
-  public IssuePattern forResource(String resource) {
-    return new IssuePattern(resource, rulePattern.toString(), lineRanges);
-  }
-
-  @Override
-  public String toString() {
-    return ToStringBuilder.reflectionToString(this, ToStringStyle.SHORT_PREFIX_STYLE);
-  }
 }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/PatternDecoder.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/PatternDecoder.java
deleted file mode 100644
index bb301e3f57b..00000000000
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/PatternDecoder.java
+++ /dev/null
@@ -1,100 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2019 SonarSource SA
- * mailto:info AT sonarsource DOT com
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
- * version 3 of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
- */
-package org.sonar.scanner.issue.ignore.pattern;
-
-import com.google.common.annotations.VisibleForTesting;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Set;
-import org.apache.commons.lang.StringUtils;
-
-public class PatternDecoder {
-  private static final String LINE_RANGE_REGEXP = "\\[((\\d+|\\d+-\\d+),?)*\\]";
-  private static final String CONFIG_FORMAT_ERROR_PREFIX = "Exclusions > Issues : Invalid format. ";
-
-  private PatternDecoder() {
-    // static only
-  }
-  
-  static void checkRegularLineConstraints(String line, String[] fields) {
-    if (!isResource(fields[0])) {
-      throw new IllegalStateException(CONFIG_FORMAT_ERROR_PREFIX + "The first field does not define a resource pattern: " + line);
-    }
-    if (!isRule(fields[1])) {
-      throw new IllegalStateException(CONFIG_FORMAT_ERROR_PREFIX + "The second field does not define a rule pattern: " + line);
-    }
-    if (!isLinesRange(fields[2])) {
-      throw new IllegalStateException(CONFIG_FORMAT_ERROR_PREFIX + "The third field does not define a range of lines: " + line);
-    }
-  }
-
-  static void checkDoubleRegexpLineConstraints(String line, String[] fields) {
-    if (!isRegexp(fields[0])) {
-      throw new IllegalStateException(CONFIG_FORMAT_ERROR_PREFIX + "The first field does not define a regular expression: " + line);
-    }
-    // As per configuration help, missing second field means: from start regexp to EOF
-  }
-
-  static void checkWholeFileRegexp(String regexp) {
-    if (!isRegexp(regexp)) {
-      throw new IllegalStateException(CONFIG_FORMAT_ERROR_PREFIX + "The field does not define a regular expression: " + regexp);
-    }
-  }
-
-  public static Set<LineRange> decodeRangeOfLines(String field) {
-    if (StringUtils.equals(field, "*")) {
-      return Collections.emptySet();
-    } else {
-      Set<LineRange> lineRanges = new HashSet<>();
-      
-      String s = StringUtils.substringBetween(StringUtils.trim(field), "[", "]");
-      String[] parts = StringUtils.split(s, ',');
-      for (String part : parts) {
-        if (StringUtils.contains(part, '-')) {
-          String[] range = StringUtils.split(part, '-');
-          lineRanges.add(new LineRange(Integer.valueOf(range[0]), Integer.valueOf(range[1])));
-        } else {
-          lineRanges.add(new LineRange(Integer.valueOf(part), Integer.valueOf(part)));
-        }
-      }
-      return lineRanges;
-    }
-  }
-
-  @VisibleForTesting
-  static boolean isLinesRange(String field) {
-    return StringUtils.equals(field, "*") || java.util.regex.Pattern.matches(LINE_RANGE_REGEXP, field);
-  }
-
-  @VisibleForTesting
-  static boolean isResource(String field) {
-    return StringUtils.isNotBlank(field);
-  }
-
-  @VisibleForTesting
-  static boolean isRule(String field) {
-    return StringUtils.isNotBlank(field);
-  }
-
-  @VisibleForTesting
-  static boolean isRegexp(String field) {
-    return StringUtils.isNotBlank(field);
-  }
-}
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/PatternMatcher.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/PatternMatcher.java
deleted file mode 100644
index a9be53e5aa0..00000000000
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/pattern/PatternMatcher.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * SonarQube
- * Copyright (C) 2009-2019 SonarSource SA
- * mailto:info AT sonarsource DOT com
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
- * version 3 of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
- */
-package org.sonar.scanner.issue.ignore.pattern;
-
-import com.google.common.annotations.VisibleForTesting;
-import com.google.common.collect.LinkedHashMultimap;
-import com.google.common.collect.Multimap;
-import java.util.Collection;
-import java.util.Set;
-import javax.annotation.CheckForNull;
-import javax.annotation.Nullable;
-import org.sonar.api.rule.RuleKey;
-
-public class PatternMatcher {
-
-  private Multimap<String, IssuePattern> excludePatternByComponent = LinkedHashMultimap.create();
-
-  @CheckForNull
-  public IssuePattern getMatchingPattern(String componentKey, RuleKey ruleKey, @Nullable Integer line) {
-    for (IssuePattern pattern : getPatternsForComponent(componentKey)) {
-      if (pattern.match(componentKey, ruleKey, line)) {
-        return pattern;
-      }
-    }
-    return null;
-  }
-
-  @VisibleForTesting
-  public Collection<IssuePattern> getPatternsForComponent(String componentKey) {
-    return excludePatternByComponent.get(componentKey);
-  }
-
-  public void addPatternForComponent(String componentKey, IssuePattern pattern) {
-    excludePatternByComponent.put(componentKey, pattern.forResource(componentKey));
-  }
-
-  public void addPatternToExcludeResource(String componentKey) {
-    addPatternForComponent(componentKey, new IssuePattern(componentKey, "*"));
-  }
-
-  public void addPatternToExcludeLines(String componentKey, Set<LineRange> lineRanges) {
-    addPatternForComponent(componentKey, new IssuePattern(componentKey, "*", lineRanges));
-  }
-
-}
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/scanner/IssueExclusionsLoader.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/scanner/IssueExclusionsLoader.java
index 7a3591af10c..6e639385b09 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/scanner/IssueExclusionsLoader.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/scanner/IssueExclusionsLoader.java
@@ -23,22 +23,31 @@ import java.util.ArrayList;
 import java.util.List;
 import javax.annotation.CheckForNull;
 import org.apache.commons.lang.StringUtils;
+import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.charhandler.CharHandler;
+import org.sonar.api.notifications.AnalysisWarnings;
+import org.sonar.api.utils.log.Logger;
+import org.sonar.api.utils.log.Loggers;
+import org.sonar.scanner.issue.ignore.IgnoreIssuesFilter;
 import org.sonar.scanner.issue.ignore.pattern.BlockIssuePattern;
 import org.sonar.scanner.issue.ignore.pattern.IssueExclusionPatternInitializer;
 import org.sonar.scanner.issue.ignore.pattern.IssuePattern;
-import org.sonar.scanner.issue.ignore.pattern.PatternMatcher;
 
 public final class IssueExclusionsLoader {
+  private static final Logger LOG = Loggers.get(IssueExclusionsLoader.class);
+
   private final List<java.util.regex.Pattern> allFilePatterns;
   private final List<DoubleRegexpMatcher> blockMatchers;
-  private final PatternMatcher patternMatcher;
+  private final IgnoreIssuesFilter ignoreIssuesFilter;
+  private final AnalysisWarnings analysisWarnings;
   private final IssueExclusionPatternInitializer patternsInitializer;
   private final boolean enableCharHandler;
+  private boolean warnDeprecatedIssuePatternAlreadyLogged;
 
-  public IssueExclusionsLoader(IssueExclusionPatternInitializer patternsInitializer, PatternMatcher patternMatcher) {
+  public IssueExclusionsLoader(IssueExclusionPatternInitializer patternsInitializer, IgnoreIssuesFilter ignoreIssuesFilter, AnalysisWarnings analysisWarnings) {
     this.patternsInitializer = patternsInitializer;
-    this.patternMatcher = patternMatcher;
+    this.ignoreIssuesFilter = ignoreIssuesFilter;
+    this.analysisWarnings = analysisWarnings;
     this.allFilePatterns = new ArrayList<>();
     this.blockMatchers = new ArrayList<>();
 
@@ -53,22 +62,31 @@ public final class IssueExclusionsLoader {
     enableCharHandler = !allFilePatterns.isEmpty() || !blockMatchers.isEmpty();
   }
 
-  public boolean shouldExecute() {
-    return patternsInitializer.hasMulticriteriaPatterns();
-  }
-
-  public void addMulticriteriaPatterns(String relativePath, String componentKey) {
+  public void addMulticriteriaPatterns(DefaultInputFile inputFile) {
     for (IssuePattern pattern : patternsInitializer.getMulticriteriaPatterns()) {
-      if (pattern.matchResource(relativePath)) {
-        patternMatcher.addPatternForComponent(componentKey, pattern);
+      if (pattern.matchFile(inputFile.getProjectRelativePath())) {
+        ignoreIssuesFilter.addRuleExclusionPatternForComponent(inputFile, pattern.getRulePattern());
+      } else if (pattern.matchFile(inputFile.getModuleRelativePath())) {
+        warnOnceDeprecatedIssuePattern(
+          "Specifying module-relative paths at project level in property '" + IssueExclusionPatternInitializer.CONFIG_KEY + "' is deprecated. " +
+            "To continue matching files like '" + inputFile.getProjectRelativePath() + "', update this property so that patterns refer to project-relative paths.");
+        ignoreIssuesFilter.addRuleExclusionPatternForComponent(inputFile, pattern.getRulePattern());
       }
     }
   }
 
+  private void warnOnceDeprecatedIssuePattern(String msg) {
+    if (!warnDeprecatedIssuePatternAlreadyLogged) {
+      LOG.warn(msg);
+      analysisWarnings.addUnique(msg);
+      warnDeprecatedIssuePatternAlreadyLogged = true;
+    }
+  }
+
   @CheckForNull
-  public CharHandler createCharHandlerFor(String componentKey) {
+  public CharHandler createCharHandlerFor(DefaultInputFile inputFile) {
     if (enableCharHandler) {
-      return new IssueExclusionsRegexpScanner(componentKey, allFilePatterns, blockMatchers, patternMatcher);
+      return new IssueExclusionsRegexpScanner(inputFile, allFilePatterns, blockMatchers);
     }
     return null;
   }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/scanner/IssueExclusionsRegexpScanner.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/scanner/IssueExclusionsRegexpScanner.java
index 5daf24c6075..a08ba55a593 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/scanner/IssueExclusionsRegexpScanner.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/issue/ignore/scanner/IssueExclusionsRegexpScanner.java
@@ -24,12 +24,12 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import java.util.regex.Pattern;
-import org.apache.commons.lang.StringUtils;
+import java.util.stream.Collectors;
+import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.charhandler.CharHandler;
 import org.sonar.api.utils.log.Logger;
 import org.sonar.api.utils.log.Loggers;
 import org.sonar.scanner.issue.ignore.pattern.LineRange;
-import org.sonar.scanner.issue.ignore.pattern.PatternMatcher;
 import org.sonar.scanner.issue.ignore.scanner.IssueExclusionsLoader.DoubleRegexpMatcher;
 
 public class IssueExclusionsRegexpScanner extends CharHandler {
@@ -38,8 +38,7 @@ public class IssueExclusionsRegexpScanner extends CharHandler {
   private final StringBuilder sb = new StringBuilder();
   private final List<Pattern> allFilePatterns;
   private final List<DoubleRegexpMatcher> blockMatchers;
-  private final String componentKey;
-  private final PatternMatcher patternMatcher;
+  private final DefaultInputFile inputFile;
 
   private int lineIndex = 1;
   private List<LineExclusion> lineExclusions = new ArrayList<>();
@@ -47,22 +46,26 @@ public class IssueExclusionsRegexpScanner extends CharHandler {
   private int fileLength = 0;
   private DoubleRegexpMatcher currentMatcher;
 
-  IssueExclusionsRegexpScanner(String componentKey, List<Pattern> allFilePatterns, List<DoubleRegexpMatcher> blockMatchers, PatternMatcher patternMatcher) {
+  IssueExclusionsRegexpScanner(DefaultInputFile inputFile, List<Pattern> allFilePatterns, List<DoubleRegexpMatcher> blockMatchers) {
     this.allFilePatterns = allFilePatterns;
     this.blockMatchers = blockMatchers;
-    this.patternMatcher = patternMatcher;
-    this.componentKey = componentKey;
-    String relativePath = StringUtils.substringAfterLast(componentKey, ":");
-    LOG.info("'{}' generating issue exclusions", relativePath);
+    this.inputFile = inputFile;
+    LOG.debug("Evaluate issue exclusions for '{}'", inputFile.getProjectRelativePath());
   }
 
   @Override
   public void handleIgnoreEoL(char c) {
+    if (inputFile.isIgnoreAllIssues()) {
+      return;
+    }
     sb.append(c);
   }
 
   @Override
   public void newLine() {
+    if (inputFile.isIgnoreAllIssues()) {
+      return;
+    }
     processLine(sb.toString());
     sb.setLength(0);
     lineIndex++;
@@ -70,6 +73,9 @@ public class IssueExclusionsRegexpScanner extends CharHandler {
 
   @Override
   public void eof() {
+    if (inputFile.isIgnoreAllIssues()) {
+      return;
+    }
     processLine(sb.toString());
 
     if (currentMatcher != null && !currentMatcher.hasSecondPattern()) {
@@ -81,8 +87,8 @@ public class IssueExclusionsRegexpScanner extends CharHandler {
     fileLength = lineIndex;
     if (!lineExclusions.isEmpty()) {
       Set<LineRange> lineRanges = convertLineExclusionsToLineRanges();
-      LOG.debug("- Line exclusions found: {}", lineRanges);
-      patternMatcher.addPatternToExcludeLines(componentKey, lineRanges);
+      LOG.debug("  - Line exclusions found: {}", lineRanges.stream().map(LineRange::toString).collect(Collectors.joining(",")));
+      inputFile.addIgnoreIssuesOnLineRanges(lineRanges.stream().map(r -> new int[] {r.from(), r.to()}).collect(Collectors.toList()));
     }
   }
 
@@ -94,9 +100,9 @@ public class IssueExclusionsRegexpScanner extends CharHandler {
     // first check the single regexp patterns that can be used to totally exclude a file
     for (Pattern pattern : allFilePatterns) {
       if (pattern.matcher(line).find()) {
-        patternMatcher.addPatternToExcludeResource(componentKey);
         // nothing more to do on this file
-        LOG.debug("- Exclusion pattern '{}': every issue in this file will be ignored.", pattern);
+        LOG.debug("  - Exclusion pattern '{}': all issues in this file will be ignored.", pattern);
+        inputFile.setIgnoreAllIssues(true);
         return;
       }
     }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectReactorBuilder.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectReactorBuilder.java
index 38d0d60733f..7dceaf350a0 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectReactorBuilder.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectReactorBuilder.java
@@ -20,17 +20,18 @@
 package org.sonar.scanner.scan;
 
 import com.google.common.annotations.VisibleForTesting;
-import com.google.common.collect.Lists;
 import java.io.File;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.text.MessageFormat;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.stream.Stream;
 import javax.annotation.CheckForNull;
 import javax.annotation.Nullable;
 import org.apache.commons.lang.ArrayUtils;
@@ -38,16 +39,21 @@ import org.apache.commons.lang.StringUtils;
 import org.sonar.api.CoreProperties;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.bootstrap.ProjectReactor;
+import org.sonar.api.notifications.AnalysisWarnings;
 import org.sonar.api.utils.MessageException;
 import org.sonar.api.utils.log.Logger;
 import org.sonar.api.utils.log.Loggers;
 import org.sonar.api.utils.log.Profiler;
+import org.sonar.core.config.IssueExclusionProperties;
 import org.sonar.scanner.bootstrap.ScannerProperties;
+import org.sonar.scanner.issue.ignore.pattern.IssueExclusionPatternInitializer;
+import org.sonar.scanner.issue.ignore.pattern.IssueInclusionPatternInitializer;
 import org.sonar.scanner.util.ScannerUtils;
 
+import static java.util.Arrays.asList;
+import static java.util.stream.Collectors.toList;
 import static org.sonar.api.config.internal.MultivalueProperty.parseAsCsv;
 
-
 /**
  * Class that creates a project definition based on a set of properties.
  */
@@ -95,17 +101,23 @@ public class ProjectReactorBuilder {
    */
   private static final String[] MANDATORY_PROPERTIES_FOR_CHILD = {MODULE_KEY_PROPERTY};
 
+  private static final Collection<String> UNSUPPORTED_PROPS_FOR_MODULES = asList(IssueExclusionPatternInitializer.CONFIG_KEY, IssueInclusionPatternInitializer.CONFIG_KEY,
+    IssueExclusionProperties.PATTERNS_BLOCK_KEY, IssueExclusionProperties.PATTERNS_ALLFILE_KEY);
+
   /**
    * Properties that must not be passed from the parent project to its children.
    */
-  private static final List<String> NON_HERITED_PROPERTIES_FOR_CHILD = Lists.newArrayList(PROPERTY_PROJECT_BASEDIR, CoreProperties.WORKING_DIRECTORY, PROPERTY_MODULES,
-    CoreProperties.PROJECT_DESCRIPTION_PROPERTY);
+  private static final List<String> NON_HERITED_PROPERTIES_FOR_CHILD = Stream.concat(Stream.of(PROPERTY_PROJECT_BASEDIR, CoreProperties.WORKING_DIRECTORY, PROPERTY_MODULES,
+    CoreProperties.PROJECT_DESCRIPTION_PROPERTY), UNSUPPORTED_PROPS_FOR_MODULES.stream()).collect(toList());
 
   private final ScannerProperties scannerProps;
+  private final AnalysisWarnings analysisWarnings;
   private File rootProjectWorkDir;
+  private boolean warnExclusionsAlreadyLogged;
 
-  public ProjectReactorBuilder(ScannerProperties props) {
+  public ProjectReactorBuilder(ScannerProperties props, AnalysisWarnings analysisWarnings) {
     this.scannerProps = props;
+    this.analysisWarnings = analysisWarnings;
   }
 
   public ProjectReactor execute() {
@@ -121,7 +133,7 @@ public class ProjectReactorBuilder {
   }
 
   private static void extractPropertiesByModule(Map<String, Map<String, String>> propertiesByModuleIdPath, String currentModuleId, String currentModuleIdPath,
-                                                Map<String, String> parentProperties) {
+    Map<String, String> parentProperties) {
     if (propertiesByModuleIdPath.containsKey(currentModuleIdPath)) {
       throw MessageException.of(String.format("Two modules have the same id: '%s'. Each module must have a unique id.", currentModuleId));
     }
@@ -170,6 +182,7 @@ public class ProjectReactorBuilder {
       workDir = initRootProjectWorkDir(baseDir, moduleProperties);
     } else {
       workDir = initModuleWorkDir(baseDir, moduleProperties);
+      checkUnsupportedIssueExclusions(moduleProperties);
     }
 
     return ProjectDefinition.create().setProperties(moduleProperties)
@@ -178,6 +191,23 @@ public class ProjectReactorBuilder {
       .setBuildDir(initModuleBuildDir(baseDir, moduleProperties));
   }
 
+  private void checkUnsupportedIssueExclusions(Map<String, String> moduleProperties) {
+    UNSUPPORTED_PROPS_FOR_MODULES.stream().forEach(p -> {
+      if (moduleProperties.containsKey(p)) {
+        warnOnceUnsupportedIssueExclusions(
+          "Specifying issue exclusions at module level is not supported anymore. Configure the property '" + p + "' and any other issue exclusions at project level.");
+      }
+    });
+  }
+
+  private void warnOnceUnsupportedIssueExclusions(String msg) {
+    if (!warnExclusionsAlreadyLogged) {
+      LOG.warn(msg);
+      analysisWarnings.addUnique(msg);
+      warnExclusionsAlreadyLogged = true;
+    }
+  }
+
   @VisibleForTesting
   protected File initRootProjectWorkDir(File baseDir, Map<String, String> rootProperties) {
     String workDir = rootProperties.get(CoreProperties.WORKING_DIRECTORY);
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectScanContainer.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectScanContainer.java
index b3d656a55c3..6171c2793de 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectScanContainer.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/ProjectScanContainer.java
@@ -47,7 +47,6 @@ import org.sonar.scanner.bootstrap.MetricProvider;
 import org.sonar.scanner.bootstrap.PostJobExtensionDictionnary;
 import org.sonar.scanner.cpd.CpdExecutor;
 import org.sonar.scanner.cpd.CpdSettings;
-import org.sonar.scanner.cpd.JavaCpdBlockIndexerSensor;
 import org.sonar.scanner.cpd.index.SonarCpdBlockIndex;
 import org.sonar.scanner.deprecated.test.TestPlanBuilder;
 import org.sonar.scanner.deprecated.test.TestableBuilder;
@@ -59,7 +58,6 @@ import org.sonar.scanner.issue.ignore.EnforceIssuesFilter;
 import org.sonar.scanner.issue.ignore.IgnoreIssuesFilter;
 import org.sonar.scanner.issue.ignore.pattern.IssueExclusionPatternInitializer;
 import org.sonar.scanner.issue.ignore.pattern.IssueInclusionPatternInitializer;
-import org.sonar.scanner.issue.ignore.pattern.PatternMatcher;
 import org.sonar.scanner.issue.ignore.scanner.IssueExclusionsLoader;
 import org.sonar.scanner.issue.tracking.DefaultServerLineHashesLoader;
 import org.sonar.scanner.issue.tracking.IssueTransition;
@@ -230,7 +228,6 @@ public class ProjectScanContainer extends ComponentContainer {
       // issue exclusions
       IssueInclusionPatternInitializer.class,
       IssueExclusionPatternInitializer.class,
-      PatternMatcher.class,
       IssueExclusionsLoader.class,
       EnforceIssuesFilter.class,
       IgnoreIssuesFilter.class,
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 cd9767328a2..aba73c172a4 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
@@ -134,9 +134,7 @@ public class FileIndexer {
     }
     checkIfAlreadyIndexed(inputFile);
     componentStore.put(module.key(), inputFile);
-    if (issueExclusionsLoader.shouldExecute()) {
-      issueExclusionsLoader.addMulticriteriaPatterns(inputFile.getProjectRelativePath(), inputFile.key());
-    }
+    issueExclusionsLoader.addMulticriteriaPatterns(inputFile);
     LOG.debug("'{}' indexed {}with language '{}'", projectRelativePath, type == Type.TEST ? "as test " : "", inputFile.language());
     evaluateCoverageExclusions(moduleCoverageExclusions, inputFile);
     if (properties.preloadFileMetadata()) {
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/MetadataGenerator.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/MetadataGenerator.java
index a603edbe6de..cf7833e18fc 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/MetadataGenerator.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/MetadataGenerator.java
@@ -64,7 +64,7 @@ public class MetadataGenerator {
       }
       InputStream is = charsetDetector.inputStream();
       inputFile.setCharset(charset);
-      Metadata metadata = fileMetadata.readMetadata(is, charset, inputFile.absolutePath(), exclusionsScanner.createCharHandlerFor(inputFile.key()));
+      Metadata metadata = fileMetadata.readMetadata(is, charset, inputFile.absolutePath(), exclusionsScanner.createCharHandlerFor(inputFile));
       inputFile.setMetadata(metadata);
       inputFile.setStatus(statusDetection.status(moduleKeyWithBranch, inputFile, metadata.hash()));
       LOG.debug("'{}' generated metadata{} with charset '{}'", inputFile, inputFile.type() == Type.TEST ? " as test " : "", charset);