[FIX,BUILD] fix Windows build
[NOP] cleanup
Merge pull request #1100 from OpenMS/fix/windows_fix

Fix/windows fix
[INTERNAL] debug output added
[INTERNAL] knock_out parameter by default false
[API] new user parameter averagine_similarity_scaling added
[INTERNAL] new parameter averagine_similarity_scaling used in algorithm
[API] correct ordering of peak patterns
[DOC] comments added
[API] small changes
Merge pull request #1101 from lars20070/fix/FeatureFinderMultiplex

optimisation for knockout searches in FeatureFinderMultiplex
[FIX] fix compile warning from unused variables
Merge pull request #1104 from timosachsenberg/fix/warning

[FIX] fix compile warning from unused variables