Baseline degrades to plain diff when the change set deletes a file; action blames a shallow checkout

[niklasp]

Summary

--scope changed degrades to a plain diff (mode: "diff", baselineDegraded: true) whenever the change set contains a deleted source file. The history is complete and the merge-base resolves, yet the GitHub Action comment says the checkout is shallow and asks for fetch-depth: 0, which is already set.

Environment

• react-doctor 0.9.13 (also reproduced with 0.9.11)
• GitHub Action millionco/react-doctor@v2, directory: <subdir>, scope: changed, actions/checkout@v5 with fetch-depth: 0
• Locally: macOS, Node 22.22.0, git 2.52.0, full clone
• Project: TanStack Start app inside a pnpm monorepo (the scanned directory is a subdirectory of the repo)

Repro

PR with four commits; the first one deletes a .tsx component file and edits a handful of other .tsx and locale .json files. <base> is the PR's base commit (merge-base with HEAD is <base> itself, verified with git merge-base).

cd <subdir>
npx react-doctor@0.9.13 . --json --json-compact --scope changed --base <base> --no-cache
# -> "mode":"diff","baselineDegraded":true

Isolating the trigger:

Scenario	mode	baselineDegraded
base = PR base, PR content as committed	diff	true
same with react-doctor 0.9.11	diff	true
base = first PR commit (deletion no longer in the diff)	baseline	–
base = PR base, deleted file staged back (git checkout <base> -- <file>)	baseline	–
base = PR base, every other change of the first commit reverted, deletion kept	diff	true

Reverting the locale JSON edits or the other .tsx edits changes nothing; only the deletion flips the result. Note that restoring the file as an untracked copy is not enough, git diff <base> still reports D for it, which is what the baseline planner reads.

What the action reports

⚠️ Warning: .github/workflows/<workflow>.yml is configured incorrectly.
React Doctor compares against `<base branch>` to report only the issues this pull request introduces.
This run couldn't complete that comparison (usually a shallow CI checkout with no merge base) …
Add `fetch-depth: 0` to the `actions/checkout` step …

In the same run the action's own base step fetched the base SHA and derived the changed files with git diff <base>...HEAD without falling back to the API, so the base is reachable. Earlier PRs on the same repo and workflow (no deletions) got mode: "baseline".

Expected

• A deleted file should not prevent the baseline delta. The file's base diagnostics can simply count as fixed; there is nothing to compare at head.
• If the baseline still has to degrade, the PR comment should say why (e.g. which step returned no delta) instead of attributing it to a shallow checkout. The current text sends people to change a checkout that is already correct (baselineDegraded with rootDir when Action directory is repo root (misattributes to shallow checkout) #1456 fixed the same misattribution for another trigger).

Notes from reading the source

runBaselineComparison returns null in several places without a reason surfacing anywhere (materializeBaselineFiles → null, !snapshot.isComplete, unanalyzed expected head files, base lint failure). parseBaselineDiffPlan puts D entries into baseFiles, so the deleted file is materialised and linted at base; one of the later checks then drops the whole delta. I could not tell which one from the outside, --verbose prints nothing about it. A debug line naming the failing check would make this diagnosable.

[react-doctor-evals]

❌ Triage errored — trace e8eaedcfe280f31a8e3b169f57900186. Check server logs for that trace ID.