title: Sonar-Runner doesn't index any files
body: <p>I'm trying to run a sonar analysis on my playframework jave code. There are no files indexed: </p>
  
  <pre><code>me@fhnw:/home/mycomp/myReporting/sonar-runner/java-sonar-runner-simple$ /home/me/tmp/sonar-runner-2.4/bin/sonar-runner 
  SonarQube Runner 2.4
  Java 1.7.0_55 Oracle Corporation (64-bit)
  Linux 3.5.0-49-generic amd64
  INFO: Runner configuration file: /home/me/tmp/sonar-runner-2.4/conf/sonar-runner.properties
  INFO: Project configuration file: /home/mycomp/myReporting/sonar-runner/java-sonar-runner-simple/sonar-project.properties
  INFO: Default locale: "en_US", source code encoding: "UTF-8"
  INFO: Work directory: /home/mycomp/myReporting/sonar-runner/java-sonar-runner-simple/./.sonar
  INFO: SonarQube Server 4.2
  16:15:45.869 INFO  - Load batch settings
  16:15:46.002 INFO  - User cache: /home/me/.sonar/cache
  16:15:46.009 INFO  - Install plugins
  16:15:46.120 INFO  - Install JDBC driver
  16:15:46.127 WARN  - H2 database should be used for evaluation purpose only
  16:15:46.127 INFO  - Create JDBC datasource for jdbc:h2:tcp://localhost/sonar
  16:15:47.170 INFO  - Initializing Hibernate
  16:15:48.391 WARN  - /!\ The 'tests' property is deprecated and is replaced by 'sonar.tests'. Don't forget to update your files.
  16:15:48.391 WARN  - /!\ The 'binaries' property is deprecated and is replaced by 'sonar.binaries'. Don't forget to update your files.
  16:15:48.954 INFO  - Load project settings
  16:15:49.003 INFO  - Apply project exclusions
  16:15:49.148 INFO  - -------------  Scan My project
  16:15:49.152 INFO  - Load module settings
  16:15:49.719 INFO  - Language is forced to java
  16:15:49.739 INFO  - Loading technical debt model...
  16:15:50.109 INFO  - Loading technical debt model done: 370 ms
  16:15:50.120 INFO  - Configure Maven plugins
  16:15:50.303 INFO  - Compare to previous analysis (2014-05-09)
  16:15:50.328 INFO  - Compare over 30 days (2014-04-09, analysis of 2014-05-07 13:39:57.555)
  16:15:50.480 INFO  - Base dir: /home/mycomp/myReporting/sonar-runner/java-sonar-runner-simple/.
  16:15:50.480 INFO  - Working dir: /home/mycomp/myReporting/sonar-runner/java-sonar-runner-simple/./.sonar
  16:15:50.480 INFO  - Source dirs: /home/mycomp/myReporting/app
  16:15:50.480 INFO  - Test dirs: /home/mycomp/myReporting/test
  16:15:50.480 INFO  - Binary dirs: /home/mycomp/myReporting/target/scala-2.10/classes
  16:15:50.480 INFO  - Source encoding: UTF-8, default locale: en_US
  16:15:50.480 INFO  - Index files
  16:15:50.516 WARN  - File '%s' is ignored. It is not located in module basedir '%s'.
  ...
  16:15:50.539 WARN  - File '%s' is ignored. It is not located in module basedir '%s'.
  16:15:50.539 INFO  - 0 files indexed
  16:15:50.541 INFO  - Quality profile for java: Sonar way
  16:15:50.549 INFO  - Sensor Quality gate loader...
  16:15:50.550 INFO  - Sensor Quality gate loader done: 1 ms
  16:15:50.550 INFO  - Sensor QProfileSensor...
  16:15:50.555 INFO  - Sensor QProfileSensor done: 5 ms
  16:15:50.556 INFO  - Sensor CpdSensor...
  16:15:50.556 INFO  - SonarEngine is used for java
  16:15:50.556 INFO  - Sensor CpdSensor done: 0 ms
  16:15:50.556 INFO  - Sensor InitialOpenIssuesSensor...
  16:15:50.565 INFO  - Sensor InitialOpenIssuesSensor done: 9 ms
  16:15:50.565 INFO  - Sensor ProfileEventsSensor...
  16:15:50.590 INFO  - Sensor ProfileEventsSensor done: 25 ms
  16:15:50.590 INFO  - Sensor ProjectLinksSensor...
  16:15:50.595 INFO  - Sensor ProjectLinksSensor done: 5 ms
  16:15:50.595 INFO  - Sensor VersionEventsSensor...
  16:15:50.605 INFO  - Sensor VersionEventsSensor done: 10 ms
  16:15:50.606 INFO  - Sensor FileHashSensor...
  16:15:50.606 INFO  - Sensor FileHashSensor done: 0 ms
  16:15:51.086 INFO  - Execute decorators...
  16:15:51.272 INFO  - Store results in database
  16:15:51.321 INFO  - ANALYSIS SUCCESSFUL, you can browse http://localhost:9000/dashboard/index/my:project
  16:15:51.376 INFO  - Executing post-job class org.sonar.plugins.core.issue.notification.SendIssueNotificationsPostJob
  16:15:51.377 INFO  - Executing post-job class org.sonar.plugins.core.batch.IndexProjectPostJob
  16:15:51.398 INFO  - Executing post-job class org.sonar.plugins.dbcleaner.ProjectPurgePostJob
  16:15:51.414 INFO  - -&gt; Keep one snapshot per day between 2014-04-11 and 2014-05-08
  16:15:51.415 INFO  - -&gt; Keep one snapshot per week between 2013-05-10 and 2014-04-11
  16:15:51.416 INFO  - -&gt; Keep one snapshot per month between 2009-05-15 and 2013-05-10
  16:15:51.417 INFO  - -&gt; Delete data prior to: 2009-05-15
  16:15:51.424 INFO  - -&gt; Clean My project [id=2]
  16:15:51.428 INFO  - &lt;- Clean snapshot 9
  INFO: ------------------------------------------------------------------------
  INFO: EXECUTION SUCCESS
  INFO: ------------------------------------------------------------------------
  Total time: 6.309s
  Final Memory: 14M/498M
  INFO: ------------------------------------------------------------------------
  </code></pre>
  
  <p>I'm using jacoco for code coverage. My sonar settings look like this: </p>
  
  <pre><code># Required metadata
  sonar.projectKey=my:project
  sonar.projectName=My project
  sonar.projectVersion=1.0
  
  # Language
  sonar.language=java
  
  # Path to the parent source code directory.
  # Path is relative to the sonar-project.properties file. Replace "\" by "/" on Windows.
  # Since SonarQube 4.2, this property is optional. If not set, SonarQube starts looking for source code
  # from the directory containing the sonar-project.properties file.
  sonar.sources=/home/mycomp/myReporting/app/
  tests=/home/mycomp/myReporting/test/
  binaries=/home/mycomp/myReporting/target/scala-2.10/classes
  
  # Encoding of the source code
  sonar.sourceEncoding=UTF-8
  
  # Additional parameters
  sonar.dynamicAnalysis=reuseReports
  sonar.java.coveragePlugin=jacoco
  sonar.jacoco.reportPath=/home/mycomp/myReporting/target/coverage/jacoco.exec
  </code></pre>
  
  <p>Any help is appreciated. Thanks!</p>