[FIX] fixed the 'variable' consumption of xslt files for a QcML file. Now expects a valid standalone xslt (i.e. with a xml preamble in the first line, stylesheet starting in the second line).
Merge pull request #936 from mwalzer/feature/QCML

[FIX] fixed the 'variable' consumption of xslt files for a QcML file.
[FIX] add setOptions method for FileHandler
Merge pull request #951 from hroest/fix/FileHandlerSetOptions

[API,PYOPENMS] add setOptions method for FileHandler
Merge remote-tracking branch 'upstream/develop' into feature/FeatureFinderMultiplex