[DOC] better error handling in TOPPDocumenter
improved export of ms2 ground truth

 * all hits are exported in idXML scored/sorted by their intensity contribution
[TEST] extended MSSim test
[TEST,INTERNAL] added test access getMS2Identifications before a simulation was performed

 * fixed segfault if getMS2Identifications but no simulation was performed
Merge pull request #967 from aiche/feature/mssim-more-ground-truth-in-idXML

[FEATURE,TEST] mssim more ground truth in id xml