[FIX, #645] fix memory access violation in ms-numpress
[FIX] MS Numpress upstream fixes

- update to commit 21259b4a9eba62e8c398c2cfef4e80b875ff91d5 at
  https://github.com/ms-numpress/ms-numpress
[TEST] add test for corrupt numpress mzML file

- the corrupt file should not be read but rather a ConversionError
  should be thrown
[FIX] numpress fix

- wrong description was used for MS:1002313 CV term
[FIX] add CV terms for MS Numpress

- allows OpenMS to also read ms-numpress files (and not complain any
  more about unknown CV values)
Merge pull request #649 from hroest/fix-ms-numpress

Fix ms numpress
[DOC] moved redundary information to the wiki
[NOP] added .gitignore containing the svn:ignore entries
[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