[FEATURE] added option to keep, ensure or reassign UIDs during conversion

[NOP] removed debug code

[NOP] fixed style
Merge pull request #739 from timosachsenberg/feature/uids_fileconverter

Feature/uids fileconverter
replace recursive connected components in ProteinResolver with Queue to avoid stack overflow which occurs even for medium sized tasks
proper status message, small fix
removed sourceforge and 'svn' references where possible; in addition, we should redirect http://open-ms.sourceforge.net/schemas to github (using Wordpress interface)
more cleanup
minor fix
Merge pull request #742 from cbielow/svn_clean

[DOC] removed svn occurrences from documentation
Merge pull request #741 from cbielow/proteinresolver_mem

[FIX] ProteinResolver switch from recursive to iterative to avoid stack overflow
[FIX] fixed compilation error on vs2013
Merge pull request #743 from timosachsenberg/feature/vs2013_compile_fix

[FIX] fixed compilation error on vs2013
[FIX] fixed MRMDecoy.pxd
[PYOPENMS, FIX] fixed import path in pxds/RichPeak1D.pxd
[PYOPENMS] added conversion streampos -> Python long
[PYOPENMS,FIX] fixed wrapping of IndexedMzMLDecoder

Conflicts:

	pyOpenMS/pxds/IndexedMzMLDecoder.pxd
[PYOPENMS] better error message for MzMLFile.transform
[PYOPENMS,FIX] added missing test_MzMlDecoder.py to pyopenms.cmake

Conflicts:

	pyOpenMS/pyopenms.cmake
[BUILD] use consistent file names for test files
[FIX] missing include
[FIX] fixes for Python 2.6