Pep on peptides first

[trishorts]

We have been training our binary decision tree on psms rather than peptides. PSMs for the same peptide are not independent measurements. Therefore, they are not a good choice for ML training applications. This PR uses peptides instead and then applies that model to the PSMs.

Also, there are some efficiency and orangizational improvements.

[codecov]

Codecov Report

Attention: Patch coverage is 95.16129% with 6 lines in your changes missing coverage. Please review.

Project coverage is 92.85%. Comparing base (a025ca0) to head (a1095fd).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2373      +/-   ##
==========================================
+ Coverage   92.81%   92.85%   +0.04%     
==========================================
  Files         137      137              
  Lines       21188    21242      +54     
  Branches     2929     2931       +2     
==========================================
+ Hits        19666    19725      +59     
+ Misses       1042     1040       -2     
+ Partials      480      477       -3     

Files	Coverage Δ
...pheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs	96.52% <100.00%> (+0.02%)	⬆️
...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs	93.26% <100.00%> (ø)
...EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs	95.71% <93.54%> (-0.39%)	⬇️

... and 2 files with indirect coverage changes