fix: worktree stale-registration bug + item-pipeline metadata panic

[getappz]

Summary

• create_worktree never pruned stale/broken git worktree registrations before reusing an existing branch — any item whose worktree was removed out-of-band (crash, manual cleanup) got permanently stuck: every dispatch attempt regenerated the identical "already checked out" failure forever. Now prunes before reuse, and execute_work_impl surfaces the real worktree_error instead of a hardcoded generic message.
• persist_run_id panicked (cannot access key "workflow_run_id" in JSON string) whenever an item's metadata field was a non-object JSON value (confirmed live on item feat: migrate artifact storage onto agentflare-store documents+blobs + vent: origin routing, throttle, batched filing, judge-prompt hook #331 — a double-JSON-encoded string). Now coerces to an empty object defensively instead of trusting the caller-supplied value's shape.

Both root-caused and reproduced live against item #331 today, which hit both bugs back-to-back across ~10 dispatch attempts.

Test plan

• cargo test -p flare-git-core — 190 passed
• cargo test --bin agentflare worktree — 17 passed
• cargo test --bin agentflare work_item_pipeline — 53 passed, 2 pre-existing unrelated ignores
• Both new regression tests verified red (reproduce the exact live failure) without their fix, green with it
• cargo fmt --check clean
• cargo clippy --all-targets -- -A unsafe_code -A clippy::pedantic clean
• Live-verified: rebuilt + installed the fixed binary, restarted the daemon, redispatched item feat: migrate artifact storage onto agentflare-store documents+blobs + vent: origin routing, throttle, batched filing, judge-prompt hook #331 — worktree creation now succeeds cleanly (previously failed deterministically every time)

Summary by CodeRabbit

• Bug Fixes

  • Improved worktree recovery when stale Git registrations remain after a directory is removed.
  • Error messages for missing worktrees now include specific failure details when available.
  • Run IDs can now be saved even when existing metadata is not in the expected object format.

• Tests

  • Added coverage for stale worktree recovery and non-object metadata handling.

[coderabbitai]

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📥 Commits

Reviewing files that changed from the base of the PR and between 167a91e and 111c046.

📒 Files selected for processing (1)

• src/cli/work.rs

🚧 Files skipped from review as they are similar to previous changes (1)

• src/cli/work.rs

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📝 Walkthrough

Walkthrough

The PR prunes stale Git worktree registrations before branch checkout, includes detailed worktree errors in failure messages, and normalizes non-object metadata before persisting workflow run IDs. Regression tests cover worktree recreation and metadata persistence.

Changes

Worktree and metadata recovery

Layer / File(s)	Summary
Stale worktree recovery crates/flare-git-core/src/worktree.rs, crates/flare-git-core/src/worktree_tests.rs	create_worktree prunes stale registrations before checkout. The regression test verifies recreation after direct directory deletion.
Workflow metadata normalization src/work_item_pipeline.rs, src/work_item_pipeline/tests.rs	persist_run_id converts non-object metadata to an empty object before storing workflow_run_id. The regression test verifies successful persistence.
Worktree error reporting src/cli/work.rs	Missing-worktree failures now include worktree_error when available. Claim release, reporting, and fatal classification remain unchanged.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Merge Risk: ⚪ Minimal · up to 111c0

The PR fixes two localized failure modes with regression coverage, and no actionable merge-blocking risk remains after normal checks and review.

Possibly related PRs

• getappz/agentflare#414: Both PRs modify create_worktree to improve reuse and recovery of existing Git worktrees.
• getappz/agentflare#471: Both PRs modify create_worktree and its tests around existing worktree reuse.
• getappz/agentflare#486: Both PRs modify worktree failure handling in src/cli/work.rs.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly summarizes both primary fixes: stale Git worktree registrations and item-pipeline metadata panics.
Description check	✅ Passed	The description provides a detailed summary and test results, but it omits the optional Notes for reviewers section.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

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• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/511-worktree-prune-stale-registration

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