Fix security pr

Fix Security PR

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

Covers npm/pnpm/yarn/bun audit failures, CVE alerts, Dependabot merge conflicts, Snyk failures, and GitHub security advisory blocks. Use when asked to fix the security PR, resolve a vulnerability failure, or unblock a Dependabot PR.

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.