[FIX] PeptideIndexer crashes on empty idXML (#653)
[FIX, TEST]
- added tests
- added check for empty FASTA

fixes #653
[FIX, INTERNAL]

on Windows the tests below might fail when OpenMS is configured with a
OPENMS_GET_TEST_DATA_PATH which contains a small device letter, e.g.

//#define OPENMS_GET_TEST_DATA_PATH(filename) (std::string("c:/dev/oms/source/TEST/data/") + filename).c_str()

since getLoadedFilePath() used to call Qt to create absolute paths and
this changes "c" to "C", making the string comparison like

TEST_EQUAL(di2.getLoadedFilePath(), OPENMS_GET_TEST_DATA_PATH("File_test_empty.txt"))

fail. The fix here is to modify/fix the path only if its not absolute,
thus for our tests it will stay untouched since OPENMS_GET_TEST_DATA_PATH
is always absolute.

Alternatively, one could modify each(!) test (e.g. convert to lower case
before comparing),
but this creates invalid paths on unix and is error prone (since the next
developer will surely forget to use it).

Failing tests are

123 - ConsensusXMLFile_test (Failed)
126 - DTA2DFile_test (Failed)
130 - FeatureXMLFile_test (Failed)
142 - MS2File_test (Failed)
143 - MSPFile_test (Failed)
149 - MzDataFile_test (Failed)
153 - MzMLFile_test (Failed)
158 - MzXMLFile_test (Failed)
Merge pull request #657 from cbielow/B_loadedFilePath

[FIX, INTERNAL] make "void DocumentIdentifier::setLoadedFilePath(const String & file_name)" not modify file_name if already absolute
Merge pull request #658 from cbielow/B_PeptideIndexer

[FIX] PeptideIndexer crashes on empty idXML (#653)
[BUILD,INTERNAL] moved openms code including main CMakeLists.txt to subfolder openms
[BUILD] made OpenMS compile again

 * customised variables to point to correct locations
 * removed obsolete qt hack
 * fixed test data path
 * fixed findDoc() w.r.t. to the new layout
[BUILD] proper exposing of include directories and libs for sibling projects
[BUILD] moved some general build system code to top-level project
[BUILD,DOC] moved all doc related code to the doc/CMakeLists.txt file

 * fixed some doc related build issues
[BUILD] moved some more build system config from the openms/CMakeLists.txt to the top-level CMakeLists.txt
[BUILD] moved OpenSWATHAlgo into a separate directory
[NOP] reformatted contrib finding
[BUILD] moved topp/utils to separate directory/project
[BUILD,TEST] moved tests to separate projects
[BUILD] more test restructuring
[BUILD] moved class tests to a separate directory

 * XMassFile_test doesn't compile, fix in follow-up commit
[BUILD,TEST] added test_config.h which manages finding of test files
[TEST] fixed class tests referencing files from the TOPP test data directory
[TEST] fixed XMassFile_test by removing the data include and replacing it with reading of test data on execution