Fix and tests for a bug in reading Mascot XML files

The bug led to the omission of "unassigned peptides" from Mascot results when writing out idXML. The cause was an oversight to set the identifier linking the respective PeptideIdentifications to the ProteinIdentification. "IdXMLFile::store" would skip those cases, but give a warning ("Omitted writing of [N] peptide identifications due to wrong protein mapping.").