Adapter for Fido (protein inference engine), solves #808

This contains the adapter itself (which can run Fido with/without parameter estimation and now works properly even for inputs with multiple ID runs), adaptations to PeptideIndexer and ProteinQuantifier, and test cases (which may not be properly integrated into the build system yet - see my e-mail to the developers list).
Fido itself is not included, but sources that should work across platforms are available here: https://github.com/hendrikweisser/Fido

Thanks to @liangoaix for her contributions, including the test file.
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