Cls indices fix

[garrettwrong]

Small patch. Mainly to address storing the alignment results someone may need for their project...

• Fixes bug introduced with class source batching that was only saving the most recently aligned batch results (vars were just for potential reference).
• Sets several progress bars to leave=False, less spammy
• Couple minor string/logger updates

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.66%. Comparing base (c92fa17) to head (59cf2be).
⚠️ Report is 4 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1346      +/-   ##
===========================================
+ Coverage    90.65%   90.66%   +0.01%     
===========================================
  Files          134      134              
  Lines        14430    14446      +16     
===========================================
+ Hits         13082    13098      +16     
  Misses        1348     1348              

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[j-c-c]

Looks good!

[garrettwrong]

Checked recon still good. Merging.