[BUILD,FIX] adopt Python extension with new Path

- use new path starting with ./src in Python extension checker
[FIX] fix pxd map of Python extension checker
[BUILD,NOP] extract method
[BUILD,DOC] doc improvements to Python checker
[FIX] fix crash
Merge pull request #944 from hroest/fix/pyopenms_parser_fix

[FIX,TOOLS] pyopenms parser fix