[AnalysisSummaryParser] Remove old, unused cgi
[cometresult.cgi] Remove cgi viewer for pre-2012 Comet results
[Pep3D] Remove long unsused cgis (disCidData_xml.cgi and getCidData_xml.cgi); verify that input file exists before running anything else; quell size warnings; clean up comments
[version] Provisional version to help differentiate builds
[Petunia] Fix detection of MSFragger on regis (broken by r9259); create new params files in tmp dir (again) before moving to user dir; capture success code from params file creation by Kojak and Magnum; minor cleanup
[PepXMLViewer] Fix PTMPro filter fields which would display incorrectly when adding/removing any column (bad copy/paste job in original code); also add full list of fields to the undisplayed columns box (formerly all missing); simplified logic; minor code cleanup. ToDo: perhaps missing lability and massdiff fields? Meh. Bug reported by Rob M.
[RefreshParser] New option DISCARD_UNMAPPED removes the parent <spectrum_query> tag and children from the output file whenever a <search_hit> peptide does not map to the specified database (which also means that it cannot be re-map later). Requested for PeptideAtlas. Use with care.
[comet-fasta] properly size message buffer to avoid overruns; remove old code comments; re-tab