chore(mcp-4da)(deps): bump better-sqlite3 from 12.11.1 to 13.0.3 in /mcp-4da-server - #446
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… matrix, remove-by wired (#554) Lane D of the 2026-08-31 audit remediation: four known CI holes, each re-verified against live state before touching anything. Two needed changes (shipped here); two turned out to be already closed on the current base — documented below so the audit trail reflects what was actually found, not what the brief assumed. ## Hole 1 — Dependabot NOTICE starvation (FIXED: new `dependabot-notice` job) **The hole.** `Repo guards` requires `node scripts/generate-notice.cjs --check --require` to pass on every PR: third-party attribution must be regenerated in the same change as any dependency move. Dependabot cannot run repo scripts, so every cargo or production-npm bump it opens fails `Third-party attribution is current (NOTICE)` and rots. Verified live at step level before fixing: PRs #457 (cargo `zip`) and #516 (npm `react`) both fail exactly that step, every other repo-guards step green. 27 Dependabot PRs are currently open, several ecosystems pinned at their `open-pull-requests-limit` — the gate had starved automated dependency updates entirely. **The fix.** A `dependabot-notice` job in validate.yml, gated `github.event_name == 'pull_request' && github.actor == 'dependabot[bot]'`, that completes the commit on Dependabot's behalf: - Checks out the **PR branch** (`github.event.pull_request.head.ref`), not the unpushable detached merge ref. Dependabot branches always live in this repo, never a fork, so the job token can push them. - Rebuilds NOTICE with the **exact recipe the gate itself uses** (stable Rust toolchain for `cargo metadata`, `pnpm install --frozen-lockfile --ignore-scripts` for `pnpm licenses list`), so what it generates is byte-for-byte what `--check` will verify. Verified end-to-end locally: that recipe followed by write-mode `generate-notice.cjs` reproduces the committed NOTICE with zero diff on a current tree, and `git diff --quiet -- NOTICE` is the correct changed-detector. - If NOTICE changed: commits it, pushes to the branch, and **re-dispatches Validate** on the healed head. Three GitHub mechanics are load-bearing and documented in the job comment: 1. **Dependabot-triggered runs get a read-only `GITHUB_TOKEN`** regardless of repo defaults. The job-level `permissions:` block (`contents: write`, `actions: write`) elevates this job only; every other job keeps its defaults. 2. **Pushes made with `GITHUB_TOKEN` never trigger workflow runs** (GitHub's recursion guard). Without compensation the healed commit would sit forever with no `Validate Success` on it — and the main ruleset's *sole* required check (verified via `rules/branches/main`: `Validate Success`, strict) reads the PR's head SHA. `workflow_dispatch` is the documented exception to the recursion guard, and validate.yml already runs its full suite on dispatch (the heavy legs' `github.event_name == 'workflow_dispatch'` clauses), so the job dispatches Validate on the healed branch tip. Its check runs attach to the new head SHA, which is what the merge gate reads. Hermetic is deliberately NOT re-dispatched: the healed commit differs from the already-hermetic-tested head by NOTICE text only, `Hermetic Success` is not a required check, and a ~20-min two-OS cacheless matrix would spend metered hosted minutes to learn nothing. 3. **No loop is possible.** The heal push triggers nothing (recursion guard); in the dispatched run the job skips (neither `pull_request` nor the Dependabot actor test holds). If Dependabot force-pushes a rebase, the NOTICE commit is dropped — but that push is a Dependabot-actored `pull_request` event, so the heal simply runs again on the new head. A push race with a Dependabot rebase is rejected non-fast-forward and self-corrects the same way. `validate-success` now includes `dependabot-notice` in `needs`: it skips (== pass) on every non-Dependabot PR, but a heal failure on a Dependabot PR is visible in the aggregate instead of vanishing. Expected behavior on a healed PR: the original run's `Repo guards` still fails against the pre-heal commit (correct — that SHA is stale), and the dispatched run on the healed head goes green and satisfies the ruleset. Bumps that don't move the shipped closure (dev-dep and actions bumps — verified on #517/#518) regenerate to no diff, push nothing, and dispatch nothing. ## Hole 2 — file-size gate skippable on Rust-only PRs (VERIFIED ALREADY CLOSED — no change) The brief said `Check file sizes` runs inside the path-filtered Frontend job. Checked against the current base before acting: it was **moved to `repo-guards` on 2026-08-14** (the job's own comment documents the #423/#430 incident), the Frontend job carries a tombstone comment pointing there, `repo-guards` has no `if:` and no `needs:` so it runs on every PR and dispatch, and live Dependabot runs show `Check file sizes` executing and passing inside `Repo guards`. `node scripts/check-file-sizes.cjs --ci` exits 0 on this tree. Nothing to do; recorded here so the hole is closed with evidence rather than by assumption. ## Hole 3 — Hermetic vacuously green on main (HALF ALREADY CLOSED, other half FIXED: install retry) **Vacuous-green half: already closed.** The `!cancelled()` wrapper on `fresh-clone`'s `if:` (documented in-file, with the 2026-08-13/14 observations of 7-9s "successes") already forces the full matrix on push/schedule/dispatch; the path filter applies only to `pull_request`. Verified against live runs, not just the YAML: the latest `push` run built for ~19 min and the latest `schedule` run for ~23 min — real two-OS cold builds, not 1-second skips. No change. **Retry half: shipped.** `pnpm install --frozen-lockfile` now retries up to 3 attempts (20s backoff, `::warning::` per miss, `::error::` on exhaustion) in **both** places that build better-sqlite3 natively: - the root install (better-sqlite3 is a direct root dependency), and - the `mcp-4da-server` install line (a direct dependency there too — the open 13.x bump PR #446 targets exactly that package; only the install line is retried, build and tests stay single-shot because a failure there is real signal). better-sqlite3 falls back to a node-gyp source build whenever no prebuilt binary matches the image's Node ABI (the 13.x line in particular), and that native build flakes on windows-latest. Three attempts separates network/toolchain weather from a genuine fresh-clone break; anything still failing after 3 tries IS the finding. ## Hole 4 — `check-remove-by.cjs` unenforced (FIXED: wired into `Repo guards`) Shipped in #421 and wired to nothing — verified by grep across package.json, `.husky/`, and `.github/`: zero references. (`.husky/pre-commit` runs the *staged-files-only* cousin `check-dead-code-expiry.cjs`, which covers only `#[allow(dead_code)]`; the whole-tree `REMOVE BY <date>` gate never ran anywhere, so an expired marker could never fail anything.) Now a step in `repo-guards` — the unfiltered job that runs on every PR — invoked as `node scripts/check-remove-by.cjs --ci` for GitHub annotations. Exits 0 on the current tree (49 markers, all future-dated, 0 expired, 0 allowlisted), so this ratchets from a clean baseline. ## Verification performed - `node scripts/check-file-sizes.cjs --ci` — exit 0 - `node scripts/check-remove-by.cjs` — exit 0 (49 upcoming, 0 expired) - `pnpm install --frozen-lockfile --ignore-scripts` + `node scripts/generate-notice.cjs` (write mode) — NOTICE byte-identical, diff-detector confirmed - `node scripts/check-workflow-shell-syntax.cjs` — 53 inline scripts (including the new run blocks) parse cleanly - Both workflows parsed with a YAML parser (actionlint not installed on this box); job graphs confirmed: validate = `changes, frontend, mcp-server, relay, repo-guards, dependabot-notice, rust, validate-success`; hermetic = `changes, fresh-clone, hermetic-success` - Live-state checks: ruleset required checks, failing step identification on #457/#516, passing repo-guards on #517/#518, hermetic push/schedule run durations ## Out of scope (deliberately untouched) Frontend job's npx/audit steps and its 30-min timeout; release.yml (signing owned elsewhere). ## Residual risks, disclosed - The heal costs ~4-8 hosted-runner minutes per Dependabot PR sync (toolchain + install + `cargo metadata`); dev-dep bumps pay it only to conclude "no diff". Acceptable against 27 rotting PRs. - After the bot pushes to a Dependabot branch, Dependabot treats the PR as externally modified and stops auto-rebasing it; `@dependabot rebase` still works and simply re-triggers the heal on the recreated branch. - The dispatched Validate run executes the FULL suite (dispatch runs all heavy legs) — heavier than the path-filtered PR run, but the only dispatch-shaped trigger that exists, and correctness beats economy at a required gate. 🤖 Generated with [Claude Code](https://claude.com/claude-code) https://claude.ai/code/session_01LrXvdHoDGUj99Fqf1fCYJY Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
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Bumps [better-sqlite3](https://github.com/WiseLibs/better-sqlite3) from 12.11.1 to 13.0.3. - [Release notes](https://github.com/WiseLibs/better-sqlite3/releases) - [Commits](WiseLibs/better-sqlite3@v12.11.1...v13.0.3) --- updated-dependencies: - dependency-name: better-sqlite3 dependency-version: 13.0.3 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
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Bumps better-sqlite3 from 12.11.1 to 13.0.3.
Release notes
Sourced from better-sqlite3's releases.
... (truncated)
Commits
dbc2ea113.0.3b872585use Ubuntu 22.04-arm (#1510)569e85a13.0.2df1324bfix: this dependabot configuration does not set a co... in... (#1508)b9fbe5ffixed segfault from making calls while worker thread is terminating71707c4validate the parameters of table properly (#1504)6478c99Update SQLite to version 3.53.4 (#1506)6d24034add gypfile option to package.json (#1505)ab6232efixed typo in docs57d751cupdated readme