Improve building AVITI submanifests

[kedhammar]

Detect and implement whether index mismatch thresholds need tweaking for demux to run

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 77.77778% with 8 lines in your changes missing coverage. Please review.

Project coverage is 28.23%. Comparing base (d7b8a92) to head (9fde223).
Report is 11 commits behind head on master.

Files with missing lines	Patch %	Lines
taca/element/Element_Runs.py	77.77%	8 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #462      +/-   ##
==========================================
+ Coverage   27.90%   28.23%   +0.33%     
==========================================
  Files          37       37              
  Lines        5487     5521      +34     
==========================================
+ Hits         1531     1559      +28     
- Misses       3956     3962       +6     

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[ssjunnebo]

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