JSON and TSV reports for results

* Introduced flag "-f" in `query`, which stands for "format". For now, supported formats are JSON and TSV.
* JSON and TSV representation for outputs, JSON is piped, TSV is written in files. The former appeals programmers and piping, the latter plain users and biologists.
* Updated documentation accordingly.
* Minor robustness fixes on tests.
* Compiler warnings cleanups and coding style issues.

Should fix issue #28 and #4.