fix-security-pr

name	fix-security-pr
description	Fix a PR that is failing due to security or vulnerability issues — npm/pnpm/yarn/bun audit failures, CVE alerts, Dependabot merge conflicts, Snyk failures, or GitHub security advisory blocks. Use when asked to 'fix the security PR', 'resolve the vulnerability failure', or 'unblock the Dependabot PR'.

Fix Security PR

Diagnose and remediate security/vulnerability failures in a pull request so CI passes.

Step 1 — Identify the PR and failure

Detect the PR:

• If a PR URL or number is provided, use it directly
• If on a branch: gh pr view --json number,url,headRefName,baseRefName
• If unspecified: list recent failing PRs: gh pr list --state open --json number,title,url | grep -i -E "security|vuln|cve|dependabot|snyk|audit"

Read the failure:

gh run list --repo <owner>/<repo> --branch <branch> --limit 5 --json databaseId,conclusion,name
gh run view <run-id> --log-failed 2>&1 | head -100

Look for these patterns in the logs:

Pattern	Source	Meaning
npm audit / pnpm audit / yarn audit exit non-zero	Audit step	Vulnerable dep in tree
High / Critical severity advisory	Audit output	Specific CVE needs fixing
merge conflict / conflict in PR	Git	Dependabot PR is stale; needs rebase
Snyk found / snyk test failure	Snyk	Vulnerable dep detected by Snyk
GHSA-* advisory ID	GitHub Advisory	Specific advisory blocking

Step 2 — Understand the vulnerability

Extract from the failure log:

• Package name (e.g. lodash)
• Vulnerable version range (e.g. <4.17.21)
• Safe version (e.g. >=4.17.21)
• Severity (critical / high / moderate / low)
• Advisory ID (CVE or GHSA number)
• Whether it's a direct or transitive dependency

For Dependabot PRs, also check:

gh pr view <number> --json body,title,commits

Step 3 — Detect package manager and repo type

File	Package manager
pnpm-lock.yaml	pnpm
bun.lock / bun.lockb	bun
yarn.lock	yarn
package-lock.json	npm

Check for monorepo: pnpm-workspace.yaml, workspaces in root package.json, or bun.workspace.ts.

Step 4 — Apply the fix

Choose the approach based on whether the dependency is direct or transitive:

Direct dependency

Update the version in package.json to the safe version, then reinstall:

# pnpm
pnpm update <package>@<safe-version>

# npm
npm install <package>@<safe-version>

# yarn
yarn upgrade <package>@<safe-version>

# bun
bun update <package>

Transitive dependency (you don't control the version directly)

Add an override to force the safe version across the entire tree:

pnpm (package.json):

{
  "pnpm": {
    "overrides": {
      "<package>": ">=<safe-version>"
    }
  }
}

npm (package.json):

{
  "overrides": {
    "<package>": ">=<safe-version>"
  }
}

yarn (package.json):

{
  "resolutions": {
    "<package>": ">=<safe-version>"
  }
}

After adding the override, reinstall to regenerate the lockfile:

<pm> install

Dependabot PR with merge conflicts

The PR branch is stale. Rebase it onto the base branch:

git fetch origin
git checkout <dependabot-branch>
git rebase origin/<base-branch>
# resolve any conflicts
git push --force-with-lease origin <dependabot-branch>

If the conflict is in the lockfile, delete it and reinstall after resolving package.json conflicts:

rm <lockfile>
<pm> install
git add <lockfile>
git rebase --continue

Monorepo: vulnerability in a workspace package

Check which workspace contains the vulnerable dep:

<pm> audit --json 2>/dev/null | jq '.vulnerabilities | to_entries[] | {pkg: .key, via: .value.via}'

If the vulnerable dep is a transitive dep of a workspace, add the override to the root package.json (not the workspace's).

Step 5 — Verify the fix locally

# Confirm no remaining vulnerabilities at the severity level that was failing
<pm> audit --audit-level=high   # or: critical / moderate

# If Snyk is used
npx snyk test

If the audit still fails after fixing one package, check for additional advisories in the output and repeat Step 4 for each.

Step 6 — Commit and push

git add package.json <lockfile>
git commit -m "fix: patch <package> vulnerability (<CVE-or-GHSA>)"
git push origin <branch>

For Dependabot PRs where you rebased with --force-with-lease, the push is already done in Step 4.

Step 7 — Re-trigger CI and verify

# Watch the new run
gh run list --branch <branch> --limit 3
gh run watch <new-run-id>

If CI passes, the PR is unblocked. If another security failure appears, return to Step 2 for the next advisory.

Edge cases

Audit level mismatch: CI may fail on moderate while you're checking high. Check the CI command's --audit-level flag and match it when verifying locally.

No safe version exists yet: If the advisory has no fix available, options are:

1. Remove the package entirely if it's not truly needed
2. Add the package to an audit ignore list (.nsprc, auditignore, or --ignore flag) and leave a comment explaining why — inform the user before doing this
3. Wait for upstream to release a fix; inform the user

Private registry: If npm audit / pnpm audit fails to reach the registry, check for .npmrc or .pnpmrc with a private registry URL. The fix process is the same; just ensure the registry is reachable in CI.

Dependabot already auto-merged: Check if the PR is still open before starting. If it merged and CI still fails on main, the vulnerability is in the base branch — treat it as a direct fix to main, not a PR fix.