fix: abort pipeline on deadlock detection when recovery is disabled

[nh13]

Summary

• When deadlock detection fires and --deadlock-recover is not enabled, the pipeline now aborts with a clear error instead of logging a warning and hanging indefinitely
• Workers observe has_error() on their next iteration and exit gracefully — no panics, proper output cleanup
• Error uses TimedOut kind with an actionable message suggesting --deadlock-recover
• Both monitor paths fixed: run_monitor_loop (FASTQ pipeline) and the inline BAM monitor thread

Before

Deadlock detected → warning logged → progress timer reset → pipeline continues hanging → repeated warnings every 10s → user must Ctrl-C

After

Deadlock detected → warning logged with diagnostics → set_error() called → all workers exit on next has_error() check → pipeline exits with non-zero status and clear message

Test plan

• All 2347 existing tests pass
• cargo ci-fmt clean
• cargo ci-lint clean
• Manual verification: run with --deadlock-timeout 5 (no --deadlock-recover) on a workload that deadlocks — should exit with error after 5s instead of hanging

[codecov]

Codecov Report

❌ Patch coverage is 0% with 16 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.27%. Comparing base (91c0231) to head (706c295).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/lib/unified_pipeline/bam.rs	0.00%	8 Missing ⚠️
src/lib/unified_pipeline/base.rs	0.00%	8 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #252      +/-   ##
==========================================
- Coverage   89.28%   89.27%   -0.02%     
==========================================
  Files         119      119              
  Lines       57770    57784      +14     
==========================================
+ Hits        51582    51584       +2     
- Misses       6188     6200      +12     

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[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 7e3d3dc7-3f15-4aac-a631-05e5b055923e

📥 Commits

Reviewing files that changed from the base of the PR and between 91c0231 and 706c295.

📒 Files selected for processing (2)

• src/lib/unified_pipeline/bam.rs
• src/lib/unified_pipeline/base.rs

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📝 Walkthrough

Walkthrough

The pull request modifies deadlock detection handling in the unified pipeline's monitor loop across two files. Previously, check_deadlock_and_restore() was invoked without inspecting its return value. The changes now import DeadlockAction, match on the function's return value, and when deadlock is detected, explicitly record a TimedOut error and terminate the monitor loop. This ensures the pipeline stops with an appropriate error when deadlock recovery is disabled.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately captures the main change: aborting the pipeline on deadlock detection when recovery is disabled.
Description check	✅ Passed	The description thoroughly explains the problem, solution, behavior changes, and test plan — all directly related to the changeset.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch nh/abort-on-deadlock

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