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ATR-21589 - infrastructure for chain alignment

Heather Russell requested to merge hrussell/athena:tm_ordering_0615 into master

Adds the necessary infrastructure to align chains.

The ordering is hardcoded at the top of MenuAlignmentTools.py.

The main functions are in MenuAlignmentTools.py, but various changes to other files were also necessary, including a bugfix in TriggerJobOpts/TriggerConfig.py.

The adding of steps itself is done in GenerateMenuMT.py after the chains are loaded but before they are registered. This currently should work for all two-signature chains. Three signature chains should throw an error (in multiple places).

I also added a few chains to LS2_v1.py to test this alignment.

ctests all pass, and the ART tests fail only on counts and the references files are updated (they're probably already out of date, but I'm sure review of this will take long enough that I'll need to remake them anyways)

Note that this will cause conflict with every TMMT merge request that adds chains, because this changes the number of steps in a chain and thus the position of the step counts.

Edited by Heather Russell

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