[FEATURE,PARAM,DOC] added option to treat isoleucine/leucine as equivalent ('-IL_equivalent'), updated doc; resolves #872
[TEST] test for 'PeptideIndexer -IL_equivalent'
fix order of arguments to STL_DEBUG option
capitalization (minor)
Merge pull request #928 from cbielow/AMT

[FIX,BUILD] fixes wrong parameter ordering of cmake option command
Merge pull request #927 from hendrikweisser/PeptideIndexer-isobaric

PeptideIndexer: support for treating isoleucine/leucine as equivalent (resolves #872)
TextFile feature (skip empty lines) and docu fix
Merge pull request #929 from cbielow/feat-TextFile

TextFile feature (skip empty lines) and docu fix
[INTERNAL] check for peak not found in filter 2
[INTERNAL] check for peak not found in filter 3
[FIX] Enable multiple identification runs result, multiple protein hits and FDR/q-value analysed results.
add peptideHit metaValue nextscore in XTandemFile() and remove scan_index
[TEST] add test files.
Merge branch 'develop' into pepXMl
[FIX] Fixed SpectrumIdentificationList_Ref hickup
[FIX] fixed correct number of proteinhits
[INTERNAL] checks for -1 indices and NaN intensities added
[INTERNAL] check for -1 indices and NaN intensities added
[FIX] mzid writing (both stream and dom) fixed technically - not
semantically
[INTERNAL] check for -1 indices and NaN intensities added