DecoyScrambler now accounts for modifications

[Alexander-Sol]

Now, when creating scrambled decoy proteins, modifications come along for the ride.

Rearranges the OneBasedPossibleLocalizedModifications dictionary to correspond to the new scrambled protein sequenc

[codecov]

Codecov Report

Attention: Patch coverage is 88.09524% with 5 lines in your changes missing coverage. Please review.

Project coverage is 75.47%. Comparing base (a78eea2) to head (838df4f).
Report is 1 commits behind head on master.

Files	Patch %	Lines
mzLib/Proteomics/Protein/Protein.cs	87.17%	4 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #795      +/-   ##
==========================================
+ Coverage   75.46%   75.47%   +0.01%     
==========================================
  Files         201      201              
  Lines       30814    30851      +37     
  Branches     3106     3112       +6     
==========================================
+ Hits        23254    23286      +32     
- Misses       7035     7039       +4     
- Partials      525      526       +1     

Files	Coverage Δ
mzLib/MzLibUtil/ClassExtensions.cs	100.00% <100.00%> (ø)
mzLib/Proteomics/Protein/Protein.cs	95.70% <87.17%> (-0.60%)	⬇️

[nbollis]

What happens with terminal modifications? We have Modifications that are designated as Protein N/C terminal as well as Peptide N/C terminal. How are these cases handled?