Peptide Level PEP-Q Value changes

[Alexander-Sol]

This PR changes the way PSMs are rolled up to peptides for the purpose of PEP-Q Value calculations.

When calculating PEPQ Values at the peptide level, you first have to select the a PSM to represent each full sequence (peptide/proteoform). Previously, PSMs were selected based on their MetaMorpheus score. Now, PSMs will be selected based on PEP (lowest PEP PSM represents the full sequence, MetaMorpheus score is used as a tie-breaker).

The AllPeptides/AllProteoforms outputs will change as a result of this PR. The PSM with the lowest PEP will be used to represent each peptides. The output will still be ordered by MetaMorpheus score. All entries will have a PEP-Q value <= 1.