Checker/Test fixes and adds test for CTD writing

Pull request contains .. 

 * added test for CTD writing (PhosphoScoring is ignored see #674); the test also indicates if tool was not added to ToolHandler
 * IDEvaluator_CTD test is ignored in travis build (needs X)
 * fixed some test dependencies
 * and removed svn:keyword test from checker (see #648) and fixed some checker problems