Switch repeat id assignment from leg to repeat in AFE Protocols

[IAlibay]

This PR changes things so that a single uuid is used for each repeat in a Protocol, rather than each leg. This more strictly adheres to the idea of being a "repeat_id". It is also more intuitive since it allows us to assume that the uuid represents a single DAG execution.

We may have to revisit this formalism if/when we have a case where we have multiple indentical units being executed in a single DAG.

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• Added a news entry, or the changes are not user-facing.
• Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

• GPU integration tests - ran locally
• example notebook testing
• packaging tests: run this for any large feature PRs or PRs that add test data.

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[IAlibay]

pre-commit.ci autofix

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.91%. Comparing base (fc6689e) to head (097595a).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1948      +/-   ##
==========================================
- Coverage   94.28%   89.91%   -4.38%     
==========================================
  Files         214      215       +1     
  Lines       19000    19266     +266     
==========================================
- Hits        17915    17323     -592     
- Misses       1085     1943     +858     

Flag	Coverage Δ
fast-tests	89.91% <100.00%> (?)
slow-tests	?

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[github-actions]

No API break detected ✅