[FEATURE,PARAM,TEST,DOC] Added option to annotate protein hits with target/decoy tags in PeptideIndexer.

Also made cosmetic changes in PeptideIndexer documentation/log output and added a test for the protein annotation.
[FEATURE] Added new TOPP tool FidoAdapter (runs the protein inference engine Fido).

Work in progress.
Merge branch 'fix-idpep-mascot' of https://github.com/hendrikweisser/OpenMS into FidoAdapter

Need the fix of the "prob_correct" option in IDPosteriorErrorProbability.
[FIX] fixed clang compiler warnings
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into FidoAdapter
[FEATURE,DOC] completed implementation of Fido adapter, added documentation
[DOC] added FidoAdapter to TOPP docu page (and removed broken links to SILACAnalyzer/FeatureFinderRaw)
Merge branch 'develop' into FidoAdapter

Conflicts:
	src/topp/PeptideIndexer.cpp
[PARAM,DOC] renamed 'protxml' parameter of ProteinQuantifier to 'protein_groups' to signify more general usage
[FIX] corrected listing of relevant parameters in ProteinQuantifier output
[FEATURE] use protein group probabilities as scores in ProteinQuantifier output when available
[FIX] check for presence of target and decoy proteins (Fido requires both)
[TEST] added test files for FidoAdapter
[FEATURE,PARAM,DOC] added option to run Fido without parameter estimation; added saving of parameter estimation results
[DOC] clarified usage of parameters when running Fido instead of FidoChooseParameters
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into FidoAdapter

Conflicts:
	src/tests/topp/CMakeLists.txt
	src/topp/PeptideIndexer.cpp
[FIX] fixed compile error
[BUILD] renamed directory with test data from 'SEARCHENGINES' to 'THIRDPARTY' to reflect more general use
[TEST] added (small) test case for FidoAdapter
[FIX] fixed integration of Fido tests