Added option to quantify ambiguous peptides

[Alexander-Sol]

This PR includes all the commits from nbollis's 539 update PR.

[codecov]

Codecov Report

Merging #2277 (253e808) into master (dedbef8) will decrease coverage by 0.28%.
The diff coverage is 100.00%.

❗ Current head 253e808 differs from pull request most recent head e858611. Consider uploading reports for the commit e858611 to get more accurate results

@@            Coverage Diff             @@
##           master    #2277      +/-   ##
==========================================
- Coverage   92.15%   91.88%   -0.28%     
==========================================
  Files         135      133       -2     
  Lines       20644    20165     -479     
  Branches     2841     2810      -31     
==========================================
- Hits        19025    18528     -497     
- Misses       1134     1156      +22     
+ Partials      485      481       -4     

Files Changed	Coverage Δ
...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs	92.50% <100.00%> (-0.86%)	⬇️
...aMorpheus/TaskLayer/SearchTask/SearchParameters.cs	100.00% <100.00%> (ø)

... and 19 files with indirect coverage changes