title: Sonar fails with can't be indexed twice. Please check that inclusion/exclusion patterns produce disjoint sets for main and test files
body: <p>I have just upgraded to SonarQube 6.4 and at the same time moved to mysql.  Whenever I try to parse a particular solution I get the message:</p>
  
  <p><strong>can't be indexed twice. Please check that inclusion/exclusion patterns produce disjoint sets for main and test files</strong></p>
  
  <p>I am running the scanner through VSTS using the new SonarQube tasks.  I have also tried to pass the -X flag to SQ but it is not getting through the VSTS task.  I have also upped the mysql max packet to 512M and restarted both mysql and Sonar servers.  I'm at a loss</p>