Resolve Github Alerts

Resolve GitHub Alerts

This skill resolves all GitHub security alerts: Dependabot alerts, code scanning alerts, and secret scanning alerts.

Constants

• Label: automated/resolve-github-alerts
• Branch: automated/resolve-github-alerts
• Base branch: detect at runtime — do not hardcode main. Most repos use main, but some use master, develop, or trunk. Run gh repo view --json defaultBranchRef --jq .defaultBranchRef.name once at the start of execution and use the result everywhere a base branch is needed (PR creation, branch creation, etc.).

Setup

At the start of execution, derive the GitHub owner and repo. Use git remote get-url origin from the current working directory (works in both the main checkout and git worktrees):

OWNER_REPO=$(git remote get-url origin | sed -E 's#.*(github\.com[:/])##;s/\.git$//')
OWNER=${OWNER_REPO%/*}
REPO=${OWNER_REPO#*/}

Use $OWNER and $REPO in all gh CLI commands below.

Worktree Awareness

This skill may run inside a git worktree. Observe these rules:

• Derive repo root from git rev-parse --show-toplevel, never hard-code a path.
• All file reads/edits must use paths relative to the worktree root, not the main checkout.
• git remote, git fetch, git push, and gh commands work unchanged in a worktree because they share the main repo's remote configuration.
• Do not run git worktree add/remove — the caller manages the worktree lifecycle.

Resolution Priority

1. Fix the root cause in code — All fixes must be committed as code changes: dependency upgrades in the project's manifest/lockfiles (e.g. requirements*.{in,txt}, pyproject.toml, poetry.lock, uv.lock, package.json, Cargo.toml, go.mod), Dockerfile base image tags, GitHub Actions versions, or application code fixes in the project's source tree. Never apply ad hoc fixes via manual steps. Never add lint exclusions or scanner ignores.
2. Dismiss only for confirmed false positives — Only dismiss alerts for test credentials, false positives, or transitive dependencies with no available patch.
3. Create GitHub issues as last resort — Only when the fix requires human judgment or access you don't have.

PR Management Pattern

Maintain at most ONE open PR at a time for non-Dependabot fixes. Identified by the automated/resolve-github-alerts label.

Before creating or updating a PR

1. Search for an existing open PR:

   gh pr list --repo $OWNER/$REPO --label automated/resolve-github-alerts --state open --json number,title
   

2. If PR exists: Push additional commits to the existing automated/resolve-github-alerts branch and update the PR body.

3. If no PR exists: Create the branch from the detected base branch, push fixes, create the PR, and add labels/assignee:

   • Labels: automated/resolve-github-alerts, security, dependencies
   • Assignees: $OWNER

Execution Phases

Run all four phases in order. Track results for the final summary.

Phase 1: Triage Dependabot PRs

Goal: List open Dependabot PRs, check CI status, and fix ones with CI failures if possible. Never auto-merge — leave merging to the user.

Step 1.1: List open Dependabot PRs

gh pr list --repo $OWNER/$REPO --state open --author "app/dependabot" --json number,title,headRefName

Step 1.2: Check CI status for each Dependabot PR

For each Dependabot PR, check CI status:

gh pr checks <PR_NUMBER> --repo $OWNER/$REPO

Categorize each PR:

• Passing: All required checks are successful — ready for manual merge
• Failing: One or more checks failed
• Pending: Checks still running

Step 1.3: Fix failing Dependabot PRs

For each failing Dependabot PR:

1. Get the PR diff to understand the dependency change:

   gh pr diff <PR_NUMBER> --repo $OWNER/$REPO
   

2. Get the failure details from the checks output.

3. Determine if the failure is fixable:

   • Lint failures (ruff, mypy, type errors): Read the failing files, determine the fix, and push a commit to the Dependabot branch.
   • Test failures: Read the test files, understand the breakage, fix the tests, and push.
   • Security check failures: Do NOT attempt to fix. Skip and report as "unfixable - security check failure".

4. After pushing fixes, re-check CI status and report result.

Step 1.4: Report Phase 1 results

Track counts: passing (ready to merge), fixed (ready to merge), attempted fix (still failing), pending, skipped.

Phase 2: Fix Remaining Dependabot Alerts

Goal: Resolve open Dependabot vulnerability alerts that don't have associated PRs.

Step 2.1: Discover open alerts

gh api repos/$OWNER/$REPO/dependabot/alerts --jq '[.[] | select(.state == "open")] | length'

Get full alert details:

gh api repos/$OWNER/$REPO/dependabot/alerts \
  --jq '[.[] | select(.state == "open")] | .[] | {
    number, state,
    dependency: .dependency.package.name,
    ecosystem: .dependency.package.ecosystem,
    manifest: .dependency.manifest_path,
    severity: .security_advisory.severity,
    summary: .security_advisory.summary,
    fixed_in: .security_vulnerability.first_patched_version.identifier
  }'

If no open alerts, skip to Phase 3.

Step 2.2: Map alerts to files

Each Dependabot alert payload includes a dependency.manifest_path field — that's the ground-truth file holding the vulnerable pin. Always prefer manifest_path over guesswork. The discovery globs below are only for finding related files (e.g. when a requirements.in change cascades into a requirements.txt regen, or when a package.json bump must update its lockfile).

Map by dependency.package.ecosystem:

If the ecosystem isn't in the table, fall back to reading dependency.manifest_path and applying the smallest possible edit that bumps the pin — most ecosystems use a "manifest + lockfile" pair that's straightforward to update once you've read both.

Step 2.3: Apply fixes

For each alert:

1. Read the file at dependency.manifest_path to confirm the current pin.

2. Determine the fix command by dependency.package.ecosystem:

   • pip with pip-tools (detect: any requirements*.in exists alongside its .txt): bump the version pin in the matching .in file. Recompile via the project's lockfile command (see Step 2.4).
   • pip without pip-tools (no .in files): bump the pin directly in requirements.txt / pyproject.toml's [project] dependencies / setup.py install_requires.
   • pip with poetry (detect: pyproject.toml [tool.poetry] with poetry.lock): poetry add <pkg>@<version>, then poetry lock --no-update.
   • pip with uv (detect: uv.lock): edit the dep in pyproject.toml (or run uv pip install <pkg>==<version>), then uv lock --upgrade-package <pkg>.
   • npm (detect: package-lock.json): bump in package.json, then npm install <pkg>@<version> (regenerates the lockfile).
   • yarn (detect: yarn.lock): yarn add <pkg>@<version>.
   • pnpm (detect: pnpm-lock.yaml): pnpm add <pkg>@<version>.
   • cargo: bump in Cargo.toml, then cargo update -p <pkg> --precise <version>.
   • go: go get <module>@<version> && go mod tidy.
   • docker: update the image tag in the Dockerfile at manifest_path. Prefer immutable tags (digest pinning with @sha256:...) when the original used digest pinning.
   • github-actions: update the action version in the workflow at manifest_path. Prefer SHA + comment pinning (e.g. uses: actions/checkout@<sha> # v5.0.1) when the rest of the repo follows that style.

3. Apply edits via the Edit tool. For commands that mutate lockfiles, run them in the worktree root.

Step 2.4: Verify the fix

Before running ANY Python verify command below, detect the project's Python runner. If pip/python isn't on the default PATH, every subsequent make/pip-compile/pytest/ruff invocation will fail with "command not found". Detect in this order — first match wins — and prefix all subsequent shell commands accordingly:

• venv/bin/activate exists → prefix with source venv/bin/activate &&
• .venv/bin/activate exists → prefix with source .venv/bin/activate &&
• poetry.lock exists → wrap commands as poetry run <cmd>
• Pipfile.lock exists → wrap commands as pipenv run <cmd>
• uv.lock exists → wrap commands as uv run <cmd>
• None of the above → assume system Python; run commands as-is

Apply the chosen prefix to lockfile-recompile, lint, AND test sub-steps below. Skip this preamble entirely for npm/yarn/pnpm/cargo/go projects — their tooling is typically on PATH via system package managers.

After detecting the runner, run the project's verify commands in this order — first match wins:

1. Recompile lockfile (only when applicable):

   • Makefile defines compile-deps, compile-requirements, lock, or update-deps → make <target>. Prefer compile-deps if it exists, since it usually compiles BOTH prod and dev requirements.
   • Dev-requirements follow-up: if you ran make compile-requirements (which typically only updates the prod tree) AND a sibling make compile-requirements-dev target exists alongside a requirements-dev*.in file, run that next so the dev lockfile stays in sync.
   • Else if requirements*.in files exist → pip-compile --generate-hashes <input>.in for EACH .in file (production AND dev).
   • Else if poetry.lock exists → poetry lock --no-update.
   • Else if uv.lock exists → uv lock.
   • npm/yarn/pnpm/cargo/go: the install command from Step 2.3 already updated the lockfile — no separate step.

2. Lint:

   • Makefile defines lint → make lint.
   • Else .pre-commit-config.yaml exists → pre-commit run --all-files.
   • Else for Python: ruff check . if available.
   • Else for JS/TS: npm run lint if package.json has a lint script.
   • Else: surface "no lint command detected — manual review needed" in the PR body and continue.

3. Test:

   • Makefile defines test → make test.
   • Else for Python: pytest if available.
   • Else for JS/TS: npm test if package.json has a test script.
   • Else: surface "no test command detected — manual review needed" in the PR body and continue.

A missing lint/test step is not a hard failure for opening the PR — note it in the PR body so the human reviewer knows what wasn't auto-verified.

Step 2.5: Push fixes as a PR

Follow the PR Management Pattern above. Commit all Dependabot alert fixes together with a clear message describing what was bumped and why.

Phase 3: Resolve Code Scanning Alerts

Goal: Fix SAST/code scanning findings in source code.

Step 3.1: Discover open alerts

gh api repos/$OWNER/$REPO/code-scanning/alerts --jq '[.[] | select(.state == "open")] | length'

Get full alert details:

gh api repos/$OWNER/$REPO/code-scanning/alerts \
  --jq '[.[] | select(.state == "open")] | .[] | {
    number, state,
    rule: .rule.id,
    severity: .rule.severity,
    description: .rule.description,
    path: .most_recent_instance.location.path,
    start_line: .most_recent_instance.location.start_line,
    end_line: .most_recent_instance.location.end_line
  }'

If no open alerts, skip to Phase 4.

Step 3.2: Analyze each alert

Read the affected source file at the identified line range to understand the context and determine the correct fix.

Step 3.3: Fix each alert

Apply the appropriate fix based on the alert type:

Apply fixes using the Edit tool.

Step 3.4: Push fixes

Add code scanning fixes to the same PR branch (following PR Management Pattern). If no PR exists yet, create one.

Phase 4: Resolve Secret Scanning Alerts

Goal: Handle exposed secrets detected by GitHub secret scanning.

Step 4.1: Discover open alerts

gh api repos/$OWNER/$REPO/secret-scanning/alerts --jq '[.[] | select(.state == "open")] | length'

If no open alerts, skip to Summary.

Step 4.2: Triage each alert

gh api repos/$OWNER/$REPO/secret-scanning/alerts \
  --jq '[.[] | select(.state == "open")] | .[] | {
    number, state,
    secret_type: .secret_type_display_name,
    created_at
  }'

Step 4.3: Handle each alert

For false positives (test keys, example values, already-rotated secrets):

• Verify the secret is not real/active.
• Note in the summary as "false positive" for manual resolution.

For real credentials:

1. Always create a GitHub issue with:
   • Title: [Secret Scanning] Rotate exposed <secret_type>
   • Body: Details of what was exposed, where, and what rotation steps are needed
   • Labels: security, automated/resolve-github-alerts
   • Assignees: $OWNER
2. Remove the secret from code if still present:
   • Replace with environment variable reference
   • Add the file pattern to .gitignore if it's a credentials file
3. Push the code fix to the PR branch

Guardrails for Phase 4

• Always create a GitHub issue for confirmed real credentials, even after rotation.
• Never log or echo the actual secret value in any output.
• Check if the secret is referenced in other files before removing.

Summary Report

After all phases complete, output a summary table:

## Security Alert Resolution Summary

### Phase 1: Dependabot PRs
| PR | Title | CI Status | Action |
| ---- | ------- | ---------- | -------- |
| #XX | Bump foo from 1.0 to 1.1 | Passing | Ready to merge |
| #YY | Bump bar from 2.0 to 2.1 | Fixed | Ready to merge |

### Phase 2: Dependabot Alerts
| Alert | Package | Severity | Action | Result |
| ------- | --------- | ---------- | -------- | -------- |
| #NN | package-name | high | Version bump | Fixed in PR #ZZ |

### Phase 3: Code Scanning Alerts
| Alert | Rule | File | Action | Result |
| ------- | ------ | ------ | -------- | -------- |
| #NN | rule-id | src/file.py | Fixed pattern | Fixed in PR #ZZ |

### Phase 4: Secret Scanning Alerts
| Alert | Type | Action | Result |
| ------- | ------ | -------- | -------- |
| #NN | secret-type | False positive | Noted for manual review |

### Totals
- Dependabot PRs ready to merge: X
- Dependabot alerts fixed: X
- Code scanning alerts fixed: X
- Secret scanning alerts handled: X
- Items requiring manual attention: X

If no issues were found across all phases, report:

## All Clear

No open security alerts found.
- Dependabot PRs checked: 0 open
- Dependabot alerts: 0 open
- Code scanning alerts: 0 open
- Secret scanning alerts: 0 open

End the summary with: Generated by /resolve-github-alerts

PR Format

When creating or updating the fix PR, use this format:

Title: fix: resolve GitHub security alerts

Body:

## Summary

Automated resolution of GitHub security alerts.

<insert summary table from above>

## Changes

<bulleted list of specific changes made>

## Test Plan

- [ ] CI checks pass
- [ ] No new security alerts introduced
- [ ] Dependency compatibility verified

Generated by `/resolve-github-alerts`