Fix switch_ts to reset state & clean up IRC when switching TS guesses

[calvinp0]

When a TS guess fails validation (e.g., NMD check), switch_ts picks the next guess but previously left stale state behind:

1. IRC species from the invalidated guess were never cleaned up. delete_all_species_jobs('TS0') only deletes jobs under the TS0 label, but IRC species like IRC_TS0_1 are separate entries in running_jobs/species_dict/etc. These orphaned species
   continued running in parallel with the new guess, potentially interfering with job processing.
2. job_types flags (freq, sp, opt) were never reset. After guess N's freq completed, job_types['freq'] = True carried over to guess N+1, causing the scheduler to skip re-running freq for the new geometry.
3. convergence was never reset to None.
4. The old line self.output[label]['geo'] = ... wrote to the wrong dict level (top-level keys instead of self.output[label]['paths']), making it dead code.
5. Pending pipe batches from the old guess were never discarded.

[Copilot]

Pull request overview

Fixes Scheduler.switch_ts() to properly reset state when a TS guess is invalidated, preventing stale jobs/flags from affecting the next TS guess.

Changes:

• Clean up IRC species spawned from the invalidated TS guess (remove jobs, output, species entries, labels).
• Reset per-label output[label]['job_types'] flags and convergence so the next guess re-runs the pipeline.
• Discard pending pipe-batch entries for the invalidated TS label/directions.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 4 comments.

File	Description
arc/scheduler.py	Adds TS-switch cleanup for IRC species, resets job state, and clears pending pipe batches.
arc/scheduler_test.py	Adds a unit test intended to validate the cleanup/reset behavior.

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[Copilot]

Pull request overview

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 60.30%. Comparing base (32a8ea1) to head (03fdcba).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #866      +/-   ##
==========================================
+ Coverage   60.11%   60.30%   +0.19%     
==========================================
  Files         102      102              
  Lines       31045    31073      +28     
  Branches     8087     8097      +10     
==========================================
+ Hits        18664    18740      +76     
+ Misses      10067     9994      -73     
- Partials     2314     2339      +25     

Flag	Coverage Δ
functionaltests	60.30% <ø> (+0.19%)	⬆️
unittests	60.30% <ø> (+0.19%)	⬆️

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[alongd]

Looks good, but I think the addition should be inside delete_all_species_jobs()

[calvinp0]

Looks good, but I think the addition should be inside delete_all_species_jobs()
@alongd I made the change, but also in an arc run found another TS bug, so I added it - so please be aware of this:
https://github.com/ReactionMechanismGenerator/ARC/pull/866/changes#diff-556ad66547f14f3f9a3915808a05b59151ee8216b817845d8d716577c0aeb5ebR3557

[alongd]

Thanks, added two comments