Adapter for MS-GF+ search engine

This is an extension of pull request #803. It improves some parts of the code and solves the open issues mentioned in the comments (e.g. https://github.com/OpenMS/OpenMS/pull/803#issuecomment-55295789):
- generation of modifications file
- naming of parameters
- check for Java
- arguments of `QProcess::execute`
- test case

#803 can/should be closed.
Maintainer correct?