fix(warehouse): include tracked deleted files in summary + tracked-paths expansion (PER-186)

[Shadowsong27]

Summary

• summarize_changes.py:_expand_pattern and _tracked_paths.py:_expand_pattern filtered glob matches by Path.is_file(), silently excluding tracked-but-deleted files from /contribute-warehouse triage.
• Supplement the glob branch with git ls-files -- <pattern> so tracked deletions are included.
• Applied the fix to BOTH copies (skill + domain) to keep them in sync — consolidation deferred to PER-183.
• 4 new tests in test_summarize_changes.py (glob+explicit deletion, is_dirty for D/D ) and 2 new tests in test_tracked_paths.py (glob+explicit deletion).

Closes PER-186.

Test plan

• pytest test_summarize_changes.py test_tracked_paths.py → 37 passed
• ruff check on touched files → clean
• CI green
• opencode-review bot clean

🤖 Generated by diligent-supervisor / delegate-to-oc (kimi-for-coding/k2p6)

[github-actions]

OpenCode Review

Model: openai/gpt-5.5
Reviewed commit: 93f2b755e00f4bd4cf6fee1692e85935d8887683
Workflow run: https://github.com/Shadowsong27/agentic-beacon/actions/runs/26093266821

I’ll check the repository review context instructions, then evaluate only the attached diff for correctness and project-rule violations.

Findings

• [Medium] Staged deletions matched by globs are still omitted - libs/beacon/src/beacon/data/skills/contribute-warehouse/scripts/summarize_changes.py:56
git ls-files -- <pattern> does not return files that have already been staged for deletion, so a D path matching contexts/*.md will not be summarized. Add staged deleted paths via git diff --cached --name-only --diff-filter=D -- <pattern> in both this script and the mirrored warehouse helper.

• [Medium] Directory patterns still miss deleted tracked files - libs/beacon/src/beacon/domains/warehouse/_tracked_paths.py:64
  The fix only supplements wildcard patterns; beacon.yaml entries that name a directory still expand through filesystem globbing only, so deleted files under that directory disappear from tracked paths. Apply the same git-backed deleted-path supplementation to directory expansion, and mirror it in summarize_changes.py.

Open Questions

• None.

Notes

• PR title and commits were not included in the attached diff, so Conventional Commits could not be assessed.

Token Usage

Input tokens: 16464
Output tokens: 720
Reasoning tokens: 1741
Cache read tokens: 70144
Cache write tokens: 0
Total tokens: 89069

[Shadowsong27]

Supervisor triage — bot round 1

Bot reviewed commit: 93f2b755. CI green.

Findings

• Medium — Staged deletions matched by globs are still omitted (summarize_changes.py:56 + mirror).
  • Decision: fix in round 2. Verified: git ls-files -- <pattern> excludes index-removed paths, so a D (staged-deleted) match is dropped.
• Medium — Directory patterns still miss deleted tracked files (_tracked_paths.py:64 + mirror).
  • Decision: fix in round 2. Verified: _expand_pattern's directory branch (if p.is_dir()) uses glob only — no git supplementation.

Notes / residual risks

• "PR title and commits were not included in the attached diff, so Conventional Commits could not be assessed."
  • Decision: acknowledged, no action — title fix(warehouse): ... follows convention; bot sees diff-only.

Dispatching round 2 fix-up.

🤖 diligent-supervisor

[github-actions]

OpenCode Review

Model: openai/gpt-5.5
Reviewed commit: 0bab6ab7de9648eadf2b7aabb564f5b875fe24b9
Workflow run: https://github.com/Shadowsong27/agentic-beacon/actions/runs/26093694134

I’ll check the repository review context rules, then assess only the attached diff for concrete regressions and test gaps.

Findings

• [High] Deleted explicit paths are still omitted - libs/beacon/src/beacon/domains/warehouse/_tracked_paths.py:154
  The new git-backed expansion only runs for glob and directory patterns. A tracked file listed explicitly in beacon.yaml and then deleted will make p.is_file() false and still return nothing, so the added test_deleted_explicit_path_included should fail. Fix by checking git-tracked/staged-deleted matches for non-glob explicit patterns before returning [].

• [High] Summarizer has the same explicit-deletion gap - libs/beacon/src/beacon/data/skills/contribute-warehouse/scripts/summarize_changes.py:65
summarize() uses the copied _expand_pattern, so explicitly configured deleted files are omitted from the contribution summary despite the new test expecting them. Apply the same explicit-path git lookup there, or share the expansion logic to avoid this duplicate bug.

Open Questions

• None.

Notes

• Review was limited to the attached diff.

Token Usage

Input tokens: 7801
Output tokens: 306
Reasoning tokens: 550
Cache read tokens: 27136
Cache write tokens: 0
Total tokens: 35793

[Shadowsong27]

Supervisor triage — bot round 2

Bot reviewed commit: 0bab6ab7. CI green across all jobs.

Findings

• High — "Deleted explicit paths are still omitted (_tracked_paths.py:154)"

  • Decision: false alarm. The bot missed the final return [pattern] fallthrough on line 99 of _tracked_paths.py (and the same in summarize_changes.py). Explicit-path patterns that don't exist on disk fall through both the glob branch (no *) and the dir branch (no trailing /, not a dir) and return [pattern] as-is. Verified by running the exact tests the bot claimed should fail:

    $ pytest -k deleted_explicit -v
    test_deleted_explicit_path_included PASSED
    test_deleted_explicit_path_appears_with_deletion_status PASSED
    

• High — "Summarizer has the same explicit-deletion gap (summarize_changes.py:65)"

  • Decision: false alarm, same root cause. Same fallthrough applies to summarize_changes.py. Same test confirms.

Notes / residual risks

• "Review was limited to the attached diff." — acknowledged; the fallthrough is in the unchanged tail of _expand_pattern so it wasn't in the diff. That's why the bot missed it.
• "PR title and commits were not included in the attached diff." — same as round 1; title fix(warehouse): ... follows convention.

PR is READY. CI green; bot findings verified-false. No round 3 needed.

🤖 diligent-supervisor