analysis: root cause analysis for #59 (worktree teardown deletes branch-committed skills)

[stempeck]

Summary

Root cause analysis for #59, produced by the rootcause-all formula. This PR carries the analysis artifacts only (under .analysis/af-6bc9e66f/) — it is not the code fix, so it does not close the issue.

• 10/10 concerns investigated and VALIDATED by parallel sub-agents, each with code references and (mostly) empirical repro.
• Primary root cause: cleanupMergedSkills (internal/worktree/worktree.go:507-522) decides what to delete by inferring provenance from a name collision with the live factory .claude/skills/, instead of recording what the lifecycle actually merged in — so branch-committed skills whose directory name collides with a factory skill get os.RemoveAll'd on teardown. Identified as the 4th recurrence of the anti-pattern ADR-017 forbids.
• Selected solution (git provenance): gate deletion on git-tracked status — a skill dir tracked in the worktree's index is branch content (preserve); an untracked name-colliding dir is a merge copy (remove). Robust to the byte-identical case, needs no schema/migration, localized to cleanupMergedSkills so all teardown paths inherit the fix. Also resolves the ordering hazard (concern feat: Eliminate Manual File Moves After agent-gen #7) with no separate change.
• Includes Files-to-Modify, implementation code for cleanupMergedSkills + trackedSkillDirs, a regression test, enforcement-level classification (the fix is an Interlock), and verification steps.

See .analysis/af-6bc9e66f/rootcause_analysis.md for the synthesized findings and solution; per-concern investigations are in the sibling rootcause_concern_*.md files.

Next step

Implementation of the selected solution (intended for the ultra-implement pass).

Relates to #59.

🤖 Generated with Claude Code

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[stempeck]

Resolved.