Bump version and update changelog

Add in more CV accession numbers that are children of MS:1000767

Add functionality to support carrying over specific additional cvPara…

…ms from mzML to mzid.

Adding upon request from Matt Chambers to support some IMS-specific CV params.

Update documentation

Update documentation

Update documentation

Allow the FASTA file to have extension .faa

Fix a issue with the packaged .jar by removing dependency signature f…

…iles from it.

Remove library reference files and update MSGF-Plus.iml

Update mzml and mzidentml reading dependencies to get their performan…

…ce improvements

On a test file the conversion from mzid to tsv was 4x faster
Also bump the version