title: Sonar eclipse plugin: Unable to compute position of SonarQube marker
body: <p>Well I am upgrading my sonar instance to 4.5 (4.4 currently), So I copied my config and profile to the new instance, when I run the first analysis from the console its all OK, errors are showing right. after running the first analysis I linked my SonarTest project with the SonarQube eclipse plugin and when I run the analysis it shows the same errors as the server for while, then this message appears in console: </p>
  
  <p>Unable to compute position of SonarQube marker on resource PoolManager.java: Resource is out of sync with the file system: (%HereGoesMyPoolManager.javaPath)</p>
  
  <p>after that message SonarIssues  grow exponentially showing lots of false positives.</p>
  
  <p>Any ideas? </p>
  
  <p>StackTrace:</p>
  
  <pre><code>Retrieve remote issues of project slack-connector...
  Start SonarQube analysis on slack-connector...
  INFO: SonarQube Server 4.5
  12:17:34.615 INFO  - Load global referentials...
  12:17:34.777 INFO  - Load global referentials done: 165 ms
  12:17:34.777 INFO  - Incremental mode
  12:17:34.792 INFO  - User cache: /Users/juandesi/.sonar/cache
  12:17:34.802 INFO  - Install plugins
  12:17:34.823 INFO  - Include plugins: 
  12:17:34.823 INFO  - Exclude plugins: devcockpit, jira, pdfreport, views, report, buildstability, scmactivity, buildbreaker
  12:17:34.955 INFO  - Create JDBC datasource for jdbc:h2:/Users/juandesi/Documents/AnypointStudio/workspace/.metadata/.plugins/org.eclipse.core.resources/.projects/slack-connector/org.sonar.ide.eclipse.core/.sonartmp/preview1412954254863-0
  12:17:36.337 INFO  - Initializing Hibernate
  12:17:37.782 INFO  - Load project referentials...
  12:17:37.975 INFO  - Load project referentials done: 193 ms
  12:17:37.975 INFO  - Load project settings
  12:17:38.255 INFO  - Loading technical debt model...
  12:17:38.291 INFO  - Loading technical debt model done: 35 ms
  12:17:38.293 INFO  - Apply project exclusions
  12:17:38.496 INFO  - -------------  Scan slack-connector
  12:17:38.501 INFO  - Load module settings
  12:17:38.631 INFO  - Loading rules...
  12:17:38.846 INFO  - Loading rules done: 215 ms
  12:17:38.870 INFO  - Configure Maven plugins
  12:17:38.925 INFO  - Compare to previous analysis (2014-10-09)
  12:17:38.927 INFO  - Compare over 30 days (2014-09-10, analysis of 2014-10-09 11:04:35.972)
  12:17:38.929 INFO  - Compare to previous version (2014-10-09)
  12:17:38.930 INFO  - No quality gate is configured.
  12:17:39.196 INFO  - Base dir: /Users/juandesi/Documents/AnypointStudio/workspace/cloned/slack-connector
  12:17:39.196 INFO  - Working dir: /Users/juandesi/Documents/AnypointStudio/workspace/.metadata/.plugins/org.eclipse.core.resources/.projects/slack-connector/org.sonar.ide.eclipse.core
  12:17:39.197 INFO  - Source paths: src/main/java, target/generated-sources/mule, src/main/resources, .apt_generated
  12:17:39.197 INFO  - Test paths: src/test/java, src/test/resources
  12:17:39.197 INFO  - Binary dirs: target/classes
  12:17:39.197 INFO  - Source encoding: UTF-8, default locale: en_US
  12:17:39.197 INFO  - Index files
  12:17:39.373 INFO  - 36 files indexed
  12:17:39.574 INFO  - Quality profile for java: Anypoint Connectors Certification
  12:17:39.593 INFO  - Sensor JavaSquidSensor...
  12:17:39.654 INFO  - Java Main Files AST scan...
  12:17:39.658 INFO  - 36 source files to be analyzed
  12:17:42.432 ERROR - Class not found: org.eclipse.jface.dialogs.IDialogSettings
  12:17:42.433 ERROR - Class not found: org.eclipse.jface.resource.ImageRegistry
  12:17:42.433 ERROR - Class not found: org.eclipse.jface.preference.IPreferenceStore
  12:17:42.433 ERROR - Class not found: org.eclipse.jface.resource.ImageDescriptor
  12:17:42.444 INFO  - 36/36 source files analyzed
  12:17:42.467 INFO  - Java Main Files AST scan done: 2813 ms
  12:17:42.471 INFO  - Java bytecode scan...
  12:17:42.699 INFO  - Java bytecode scan done: 228 ms
  12:17:42.699 INFO  - Java Test Files AST scan...
  12:17:42.699 INFO  - 0 source files to be analyzed
  12:17:42.699 INFO  - Java Test Files AST scan done: 0 ms
  12:17:42.699 INFO  - 0/0 source files analyzed
  12:17:42.710 INFO  - Package design analysis...
  12:17:42.724 INFO  - Package design analysis done: 14 ms
  12:17:43.008 INFO  - Sensor JavaSquidSensor done: 3415 ms
  12:17:43.009 INFO  - Sensor QProfileSensor...
  12:17:43.013 INFO  - Sensor QProfileSensor done: 4 ms
  12:17:43.013 INFO  - Sensor InitialOpenIssuesSensor...
  12:17:43.044 INFO  - Sensor InitialOpenIssuesSensor done: 31 ms
  12:17:43.044 INFO  - Sensor ProjectLinksSensor...
  12:17:43.047 INFO  - Sensor ProjectLinksSensor done: 3 ms
  12:17:43.047 INFO  - Sensor SurefireSensor...
  12:17:43.048 INFO  - parsing /Users/juandesi/Documents/AnypointStudio/workspace/.metadata/.plugins/org.eclipse.core.resources/.projects/slack-connector/org.sonar.ide.eclipse.core/build/surefire-reports
  12:17:43.049 WARN  - Reports path not found: /Users/juandesi/Documents/AnypointStudio/workspace/.metadata/.plugins/org.eclipse.core.resources/.projects/slack-connector/org.sonar.ide.eclipse.core/build/surefire-reports
  12:17:43.049 INFO  - Sensor SurefireSensor done: 2 ms
  12:17:43.049 INFO  - Sensor JaCoCoSensor...
  12:17:43.053 INFO  - Analysing /Users/juandesi/Documents/AnypointStudio/workspace/cloned/slack-connector/target/jacoco.exec
  12:17:43.190 INFO  - No information about coverage per test.
  12:17:43.190 INFO  - Sensor JaCoCoSensor done: 141 ms
  12:17:43.190 INFO  - Sensor CPD Sensor (wrapped)...
  12:17:43.190 INFO  - JavaCpdEngine is used for java
  12:17:43.197 INFO  - Cross-project analysis disabled
  12:17:43.614 INFO  - Sensor CPD Sensor (wrapped) done: 424 ms
  12:17:43.814 INFO  - Execute decorators...
  12:17:45.545 INFO  - Export results to /Users/juandesi/Documents/AnypointStudio/workspace/.metadata/.plugins/org.eclipse.core.resources/.projects/slack-connector/org.sonar.ide.eclipse.core/sonar-report.json
  12:17:45.607 INFO  - Store results in database
  12:17:46.293 INFO  - ANALYSIS SUCCESSFUL
  12:17:46.294 INFO  - Executing post-job class org.sonar.issuesreport.ReportJob
  Unable to compute position of SonarQube marker on resource PoolManager.java: Resource is out of sync with the file system: '/slack-connector/target/generated-sources/mule/org/mule/modules/slackv2/adapter/PoolManager.java'.
  </code></pre>