Fix Vulnerabilities

1. Sync main

git checkout main && git pull

2. Create branch

git checkout -b fix/vulnerabilities-$(date +%Y-%m-%d)

3. List Dependabot alerts

Use the repo's actual owner/name (don't leave :owner/:repo). The patched version lives under vulnerabilities[].first_patched_version.identifier.

gh api repos/<owner>/<repo>/dependabot/alerts --paginate \
  -q '.[] | select(.state=="open") | {pkg: .dependency.package.name, severity: .security_advisory.severity, summary: .security_advisory.summary, vulnerable: .security_vulnerability.vulnerable_version_range, patched: .security_advisory.vulnerabilities[0].first_patched_version.identifier, manifest: .dependency.manifest_path}'

Also check code scanning (often catches CI/workflow issues that audit misses):

gh api repos/<owner>/<repo>/code-scanning/alerts --paginate -q '.[] | select(.state=="open")'

4. Run npm audit

npm audit --json

npm audit walks workspaces by default. Treat deprecation notices (e.g. inflight, whatwg-encoding, "Old versions of glob are not supported") as informational — they have no patched version and can't be "fixed" without replacing the upstream caller. Note them in the PR body and move on.

5. Fix in priority order

For each vulnerability, try in order:

1. Bump the direct dependency. Check both root package.json AND every workspace package.json (packages/*/package.json) — the vulnerable transitive may be reachable through a workspace. If a direct dep can be bumped to a version whose transitives no longer carry the vuln, do that:

   npm install <pkg>@<safe-version>
   # or for a workspace:
   npm install <pkg>@<safe-version> -w <workspace-name>
   

   Always verify against npm view <pkg> version — if every direct dep is already at latest and the vuln persists, no direct bump can fix it.

2. Add an overrides entry in the root package.json for transitives with no direct-bump path:

   • Flat keys ("pkg": "version") override every instance — only safe when one version works for all callers.
   • When a package has multiple incompatible major lines in the tree (e.g. minimatch 3.x and 9.x have different APIs), use range-keyed overrides — "pkg@<major>": "<version>" — so each major line is pinned separately. A single flat pin will silently force older callers onto an incompatible API and break the build.
   • npm overrides are nested-friendly: see npm help package-json for parent-scoped overrides if a flat or range-keyed key is too broad.

   Example block from this repo:

   "overrides": {
     "tar": "^7.5.11",
     "minimatch@3": "^3.1.4",
     "minimatch@9": "^9.0.7"
   }
   

   Then npm install and confirm with npm ls <pkg> that each major resolves to the pinned version.

3. No fix available — leave it and note it in the PR body.

Re-run npm audit after each change.

6. Verify

Use the validate skill. Overrides can break callers expecting older APIs (especially across major versions). Tests alone aren't enough — build pipelines (rollup, webpack, babel) often hit the bumped transitives at compile time.

If a bump/override breaks the build and the incompatibility can't be reconciled (caller depends on a removed API, peer-dep conflict between two libs, etc.), roll back that specific change — revert the npm install or remove the offending overrides entry, run npm install, and move it to the "Unfixed" section of the PR body with a one-line reason. Do not commit a broken build.

7. Commit, push, open PR

Use the commit skill with title fix: patch dependency vulnerabilities and body:

## Fixed
- <pkg>: <old> → <new> (direct bump / override)

## Unfixed (no patch available)
- <pkg> (<severity>): <summary>