Gptmd approach update

[trishorts]

GPTMD is promiscuous in the addition of potential modifications to the xml database. This PR reduces the number of candidate modifications added to those that produce the highest score for each possible PTM. The high level details of the new algorithm are as follows:

1. Perform notch based search
2. Find modifications that match each notch
3. Find motifs for each modification and create a corresponding peptideWithSetModifications
4. Fragment each peptideWithSetModifications and compute the MetaMorpheus score.
5. Choose a subset of peptideWithSetMods having the highest score and add those localized modifications to the new xml

For bottom up:
six mann A549 files with human fasta.
old method added 200513 mods; new method added 128449 mods
old method 102324 psms; new 103546
old 39283 peptides; new 39277
old 6042 proteins; new 6012

For top down:
14 fractions x 2 techreps jurkate td files from sean dai paper
old method added 19188 mods; new method added 11013 mods
old method 23688 psms; new 24022
old 904 proteoforms; new 899
old 279 proteins; new 273

Additonal updates:

1. Eliminated output of candidate psms in .psmtsv
2. GPTMD database created with parallelization
3. Eliminated PEP from the FDR analysis

[codecov]

Codecov Report

Attention: Patch coverage is 98.06452% with 3 lines in your changes missing coverage. Please review.

Project coverage is 93.81%. Comparing base (14ef43d) to head (f3d1ca3).
Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
MetaMorpheus/TaskLayer/GPTMDTask/GPTMDTask.cs	91.42%	2 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2419      +/-   ##
==========================================
+ Coverage   93.64%   93.81%   +0.16%     
==========================================
  Files         141      141              
  Lines       21920    22020     +100     
  Branches     3004     3015      +11     
==========================================
+ Hits        20528    20659     +131     
+ Misses        935      910      -25     
+ Partials      457      451       -6     

Files with missing lines	Coverage Δ
MetaMorpheus/EngineLayer/Gptmd/GptmdEngine.cs	97.05% <100.00%> (+7.71%)	⬆️
MetaMorpheus/EngineLayer/MetaMorpheusEngine.cs	92.26% <ø> (+3.13%)	⬆️
...ModificationAnalysis/ModificationAnalysisEngine.cs	100.00% <100.00%> (+4.76%)	⬆️
MetaMorpheus/TaskLayer/MetaMorpheusTask.cs	89.13% <100.00%> (ø)
MetaMorpheus/TaskLayer/GPTMDTask/GPTMDTask.cs	92.00% <91.42%> (+10.18%)	⬆️