[FIX] pepXML writing format.
[FIX] Distinguish PeptideProphet_pepXMl and raw_pepXMl.

[FIX] RT_index information from XTandem is added to spectrum id and scan_id in stored pepXML file.

[FIX] change parameter name and uncrustify.
[FIX] add test data for PepXMLFile and XTandemAdapter.
[FIX] Fix the spectrum_query in test data for PepXMLFile().store.
[FIX] pepXML: replace spaces by tabs; adapt the raw_data type; edit documentation.
Merge branch 'develop' into pepXMl
[FEATURE] add conversion of tandem.xml output into idXML.
          add test files for tandem.xml conversion.
[FIX] small edit of last commit.
[TEST] CubicSpline2d eval() at input nodes tested
[INTERN] lower bound index fixed
[DOC] comments added
Merge pull request #914 from lars20070/fix/CubicSpline2D

[FIX] fixed index computation in CubicSpline2d::eval and CubicSpline2d::derivatives
fix MSVC warnings (mostly pragma); new IDMapper method for featureMaps; O(n) mapping for IDMapper::annotate (O(n*n) before)
better documentation of IDMapper internals
Merge pull request #916 from cbielow/AMT

[FEATURE,BUILD] IDMapper extension for featureMaps, IDMapper speed improvements, small build system fixes
AccurateMassSearchEngine annotation of input map (not only mzTab output); cleanup of related code (const, duplicated code, inefficient code...); some more documentation
small fix
[NOP] coding style improvements
mzTab-like terms for meta values; consistent use of smooth intensities (crashes otherwise, if switched off); minor fix for FuzzyStringComparator (when testing multiple times, reporting would stop after first call)
gcc fix
Merge pull request #917 from cbielow/AMT

AccurateMassSearchEngine annotation of input map (not only mzTab output)