Fix some violations

plugins/sonar-clover-plugin/src/main/java/org/sonar/plugins/clover/XmlReportParser.java

@@ -188,8 +188,8 @@ public class XmlReportParser {
   }
 
   private boolean canBeIncludedInFileMetrics(SMInputCursor metricsCursor) throws ParseException, XMLStreamException {
-    // skip class elements on 1.x xml format
     while (metricsCursor.getNext() != null && metricsCursor.getLocalName().equals("class")) {
+      // skip class elements on 1.x xml format
     }
     return ParsingUtils.parseNumber(metricsCursor.getAttrValue("elements")) > 0;
   }

plugins/sonar-surefire-plugin/src/main/java/org/sonar/plugins/surefire/TestSuiteParser.java

@@ -119,8 +119,8 @@ public class TestSuiteParser implements XmlStreamHandler {
         setStackAndMessage(detail, childNode);
       }
     }
-    // make sure we loop till the end of the elements cursor
     while (childNode.getNext() != null) {
+      // make sure we loop till the end of the elements cursor
     }
     detail.setTimeMS(time.intValue());
     detail.setStatus(status);

sonar-channel/src/main/java/org/sonar/channel/CodeReader.java

@@ -125,7 +125,7 @@ public class CodeReader extends CodeBuffer {
   }
 
   /**
-   * @see peekTo(EndMatcher matcher, Appendable appendable)
+   * @deprecated use peekTo(EndMatcher matcher, Appendable appendable)
    */
   @Deprecated
   public final String peekTo(EndMatcher matcher) {
@@ -135,7 +135,7 @@ public class CodeReader extends CodeBuffer {
   }
 
   /**
-   * @see popTo(Matcher matcher, Appendable appendable)
+   * @deprecated use popTo(Matcher matcher, Appendable appendable)
    */
   @Deprecated
   public final void popTo(EndMatcher matcher, Appendable appendable) {

sonar-plugin-api/src/main/java/org/sonar/api/checks/AnnotationCheckFactory.java

@@ -123,16 +123,16 @@ public final class AnnotationCheckFactory extends CheckFactory {
         field.setByte(check, Byte.parseByte(value));
 
       } else if (field.getType().equals(Integer.class)) {
-        field.set(check, new Integer(Integer.parseInt(value)));
+        field.set(check, Integer.parseInt(value));
 
       } else if (field.getType().equals(Long.class)) {
-        field.set(check, new Long(Long.parseLong(value)));
+        field.set(check, Long.parseLong(value));
 
       } else if (field.getType().equals(Double.class)) {
-        field.set(check, new Double(Double.parseDouble(value)));
+        field.set(check, Double.parseDouble(value));
 
       } else if (field.getType().equals(Boolean.class)) {
-        field.set(check, Boolean.valueOf(Boolean.parseBoolean(value)));
+        field.set(check, Boolean.parseBoolean(value));
 
       } else {
         throw new SonarException("The type of the field " + field + " is not supported: " + field.getType());

sonar-plugin-api/src/main/java/org/sonar/api/measures/RangeDistributionBuilder.java

@@ -77,7 +77,7 @@ public class RangeDistributionBuilder implements MeasureBuilder {
     }
     if (onlyInts) {
       for (int i=0 ; i<bottomLimits.length ; i++) {
-        bottomLimits[i] = new Integer(bottomLimits[i].intValue());
+        bottomLimits[i] = bottomLimits[i].intValue();
       }
     }
   }

sonar-plugin-api/src/main/java/org/sonar/api/resources/ProjectFileSystem.java

@@ -64,6 +64,7 @@ public interface ProjectFileSystem extends BatchComponent {
    * @deprecated since 2.6 - ProjectFileSystem should be immutable
    *             See http://jira.codehaus.org/browse/SONAR-2126
    */
+  @Deprecated
   ProjectFileSystem addSourceDir(File dir);
 
   /**
@@ -78,6 +79,7 @@ public interface ProjectFileSystem extends BatchComponent {
    * @deprecated since 2.6 - ProjectFileSystem should be immutable
    *             See http://jira.codehaus.org/browse/SONAR-2126
    */
+  @Deprecated
   ProjectFileSystem addTestDir(File dir);
 
   /**
@@ -100,7 +102,7 @@ public interface ProjectFileSystem extends BatchComponent {
    * Source files, excluding unit tests and files matching project exclusion patterns.
    * 
    * @param langs language filter. Check all files, whatever their language, if null or empty.
-   * @deprecated since 2.6 use {@link #mainFiles(Language...)} instead.
+   * @deprecated since 2.6 use {@link #mainFiles(String...)} instead.
    *             See http://jira.codehaus.org/browse/SONAR-2126
    */
   @Deprecated
@@ -109,7 +111,7 @@ public interface ProjectFileSystem extends BatchComponent {
   /**
    * Java source files, excluding unit tests and files matching project exclusion patterns. Shortcut for getSourceFiles(Java.INSTANCE)
    * 
-   * @deprecated since 2.6 use {@link #mainFiles(Language...)} instead.
+   * @deprecated since 2.6 use {@link #mainFiles(String...)} instead.
    *             See http://jira.codehaus.org/browse/SONAR-2126
    */
   @Deprecated
@@ -126,7 +128,7 @@ public interface ProjectFileSystem extends BatchComponent {
   /**
    * Unit test files, excluding files matching project exclusion patterns.
    * 
-   * @deprecated since 2.6 use {@link #testFiles(Language...)} instead.
+   * @deprecated since 2.6 use {@link #testFiles(String...)} instead.
    *             See http://jira.codehaus.org/browse/SONAR-2126
    */
   @Deprecated
@@ -160,7 +162,7 @@ public interface ProjectFileSystem extends BatchComponent {
   List<InputFile> mainFiles(String... langs);
 
   /**
-   * TODO comment me
+   * Source files of unit tests. Exclusion patterns are not applied.
    * 
    * @param langs language filter. If null or empty, will return empty list
    * @since 2.6

sonar-server/src/main/java/org/sonar/server/ui/JRubyFacade.java

@@ -234,10 +234,6 @@ public final class JRubyFacade implements ServerComponent {
     getAsyncMeasuresService().deleteMeasure(asyncMeasureId);
   }
 
-  private DefaultRulesManager getRulesManager() {
-    return getContainer().getComponent(DefaultRulesManager.class);
-  }
-
   private ProfilesManager getProfilesManager() {
     return getContainer().getComponent(ProfilesManager.class);
   }

sonar-ws-client/src/main/java/org/sonar/wsclient/services/ResourceQuery.java

@@ -141,6 +141,7 @@ public class ResourceQuery extends Query<Resource> {
    * @param ruleCategories values: Maintainability, Usability, Reliability, Efficiency, Portability
    * @deprecated since 2.5 See http://jira.codehaus.org/browse/SONAR-2007
    */
+  @Deprecated
   public ResourceQuery setRuleCategories(String... ruleCategories) {
     return this;
   }
@@ -190,6 +191,7 @@ public class ResourceQuery extends Query<Resource> {
   /**
    * @deprecated since 2.5 not used anymore
    */
+  @Deprecated
   public boolean isExcludeRuleCategories() {
     return false;
   }
@@ -197,6 +199,7 @@ public class ResourceQuery extends Query<Resource> {
   /**
    * @deprecated since 2.5 not used anymore
    */
+  @Deprecated
   public ResourceQuery setExcludeRuleCategories(boolean b) {
     return this;
   }