Harden GitHub Repository Security

Apply GitHub protections in order of blast radius: assess, then a zero-downside baseline that never breaks CI, then a gated decision on required checks / PR. Every mutating step is confirmation-gated. Running example: a public, user-owned repo whose CI auto-commits to the default branch via stefanzweifel/git-auto-commit-action with the default GITHUB_TOKEN.

Throughout, R = OWNER/REPO (e.g. pjt222/agent-almanac). Set it once: R=OWNER/REPO. All gh api writes require repo admin.

When to Use

• Hardening a public user-owned repo after assess-github-repo-security
• A repo has no ruleset / branch protection and you want a safe baseline
• Adding required status checks or required PR without breaking a bot that pushes to the default branch
• Provisioning a GitHub App (or deploy key) bypass actor for trusted automation

Inputs

• Required: OWNER/REPO and admin access (gh auth status shows admin)
• Required: whether a CI bot pushes to the default branch (and which action/identity)
• Optional: assessment report from assess-github-repo-security
• Optional: exact CI check context name(s) to require (must run on push)
• Optional: GitHub App id + private key if going to required checks/PR

Procedure

Step 1: Assess First and Confirm Scope

Never mutate blind. Run the read-only assessment and confirm the plan with the user.

# 1. Run the companion read-only skill first (or its core probes):
gh api /repos/$R --jq '{visibility,default_branch,is_org:.organization!=null}'
gh api /repos/$R/rulesets --jq '.[] | {id,name,enforcement}'
gh api /repos/$R/actions/permissions/workflow

# 2. Confirm the two decisive facts before any write:
#    - Is the repo PUBLIC and USER-OWNED?  (rulesets are free here)
#    - Does a bot push to the default branch?  (gates Step 3 entirely)

Confirm with the user: baseline (Step 2) is always safe; Step 3 (required checks / PR) is a separate opt-in that will block a default-branch bot unless a bypass is provisioned first.

Expected: You know visibility, owner type, current rulesets, current token default, and whether a bot pushes to the default branch. The user has approved applying at least the baseline.

On failure: If the repo is private and user-owned, rulesets need GitHub Pro — stop and surface that. If not admin, stop (writes will 403). If a bot pushes to the default branch, flag that Step 3 is blocked until Step 3a runs.

Step 2: Apply the Zero-Downside Baseline (never breaks a CI auto-commit)

This tier hardens the repo without breaking a direct-push bot. Apply after confirmation. Force-push/deletion protection, a read-only token default, the free security features, and policy files.

# 2a. Default-branch ruleset: force-push + deletion protection ONLY.
#     These do NOT block the bot's direct push.
gh api --method POST /repos/$R/rulesets --input - <<'JSON'
{
  "name": "protect-default",
  "target": "branch",
  "enforcement": "active",
  "conditions": { "ref_name": { "include": ["~DEFAULT_BRANCH"], "exclude": [] } },
  "rules": [ { "type": "deletion" }, { "type": "non_fast_forward" } ]
}
JSON

# 2b. Actions token: read-only default + no token PR approval.
#     A DEFAULT (not a cap) for same-repo push events, so the bot still works
#     once its job declares contents: write.
gh api --method PUT /repos/$R/actions/permissions/workflow \
  -f default_workflow_permissions=read \
  -F can_approve_pull_request_reviews=false

# 2c. Free security features (all free on public repos):
gh api -X PUT repos/$R/vulnerability-alerts          # alerts + dependency graph
gh api -X PUT repos/$R/automated-security-fixes      # Dependabot fix PRs (separate toggle!)
gh api -X PATCH repos/$R --input - <<'JSON'
{"security_and_analysis":{"secret_scanning":{"status":"enabled"},"secret_scanning_push_protection":{"status":"enabled"}}}
JSON
gh api -X PUT repos/$R/private-vulnerability-reporting

Leave Settings > Actions > General fork-PR approval at the public-repo default ("Require approval for first-time contributors"). Fork pull_request runs already receive a read-only GITHUB_TOKEN with no access to secrets, so a fork cannot auto-commit to the default branch (no REST toggle — this is a UI setting; tighten to "all external contributors" only if the repo has secrets or self-hosted runners).

Then add two tracked files (commit them):

.github/dependabot.yml — include a github-actions block so action SHAs stay fresh:

version: 2
updates:
  - package-ecosystem: "github-actions"
    directory: "/"
    schedule:
      interval: "weekly"

.github/SECURITY.md — a short disclosure policy pointing reporters at the "Report a vulnerability" button (private vulnerability reporting, enabled above).

Flipping the token default to read silently strips write from every workflow that assumed a write default, not just the auto-commit job. Audit all files in .github/workflows/ and declare the minimal permissions: each job actually needs — common scopes are contents, packages, pull-requests, pages, and id-token. For the running example: top-level permissions: {}, contents: write only on the auto-commit job, and every uses: pinned to a full 40-char commit SHA with the version in a trailing comment.

Expected: gh api /repos/$R/rulesets shows protect-default active; .../actions/permissions/workflow shows default_workflow_permissions: read and can_approve_pull_request_reviews: false; secret scanning + push protection

• Dependabot + private reporting are on; .github/dependabot.yml and .github/SECURITY.md are committed. The bot's next run still pushes.

On failure: If 2b makes an existing bot push 403 — or any other workflow fails after losing a write scope it silently relied on — the job is missing the explicit permissions: it needs (e.g. contents: write, packages: write, pull-requests: write); add the minimal scope back (the read-only default is not a hard cap for same-repo pushes). If automated-security-fixes seems to do nothing, verify vulnerability-alerts (2c line 1) ran first — alerts are a separate prerequisite toggle from fixes. If push protection later fails a bot run, treat the flagged secret as a real finding — the bot cannot click the interactive web bypass.

Step 3: Decision Gate — Required Status Checks / Required PR

STOP. Required checks and required PR block direct pushes to the ref, not just PR merges. If a bot pushes to the default branch, turning either on will break it unless you first provision a bypass. The default GITHUB_TOKEN / github-actions[bot] cannot be a bypass actor (GitHub design). Do not enable this tier on a bot-pushing branch without a bypass in place.

Also, on a solo repo, required_approving_review_count >= 1 is a self-lockout (you cannot approve your own PR) — keep it 0. And a required check that only runs on pull_request never reports on a direct push, so it permanently blocks the bot. Ensure the check runs on push.

Step 3a — provision the bot bypass FIRST (if a bot pushes to this branch). Recommended: a GitHub App installation token. (Deploy key is a narrower single-repo alternative: add an SSH deploy key with write access and use actor_type: DeployKey in 3b.)

# Create a GitHub App (personal account, Settings > Developer settings >
# GitHub Apps), permission Repository > Contents: Read and write; install it
# on THIS repo. Store the App id as a repo variable and the private key as an
# Actions secret. In the workflow, mint a token and pass it to checkout + the
# commit action:
#   - uses: actions/create-github-app-token@<sha>   # v2
#     id: app-token
#     with: { app-id: ${{ vars.APP_ID }}, private-key: ${{ secrets.APP_KEY }} }
#   - uses: actions/checkout@<sha>
#     with: { token: ${{ steps.app-token.outputs.token }} }
#   - uses: stefanzweifel/git-auto-commit-action@<sha>
#     with: { ... }   # inherits the app token via the checkout credentials
#
# The numeric App id used in Step 3b is shown on the App's own page:
# Settings > Developer settings > GitHub Apps > <your app> > About ("App ID").
# It is unrelated to the repository id and cannot be derived from /repos/$R.

Higher-assurance alternative (no standing bypass actor). If a manual merge click is acceptable, convert the job to open a PR with the App token (e.g. peter-evans/create-pull-request) and let a human merge. No bypass actor is needed and every rule stays enforced even against the automation's identity. The App token is still required: a PR opened with the plain GITHUB_TOKEN does not trigger pull_request/push workflows, so required checks never run and it sits expected forever (see Common Pitfalls).

Step 3b — apply the hardened ruleset with the App as an Integration bypass actor. Replace RULESET_ID with the id from Step 2a, <APP_ID> with your App id, and build with your real check context. bypass_mode: always because the action pushes directly (use pull_request only if the bot opens PRs).

gh api --method PUT /repos/$R/rulesets/RULESET_ID --input - <<'JSON'
{
  "name": "protect-default",
  "target": "branch",
  "enforcement": "active",
  "conditions": { "ref_name": { "include": ["~DEFAULT_BRANCH"], "exclude": [] } },
  "bypass_actors": [ { "actor_id": <APP_ID>, "actor_type": "Integration", "bypass_mode": "always" } ],
  "rules": [
    { "type": "deletion" },
    { "type": "non_fast_forward" },
    { "type": "pull_request", "parameters": { "required_approving_review_count": 0, "dismiss_stale_reviews_on_push": true, "require_code_owner_review": false, "require_last_push_approval": false, "required_review_thread_resolution": false, "allowed_merge_methods": ["merge"] } },
    { "type": "required_status_checks", "parameters": { "strict_required_status_checks_policy": true, "do_not_enforce_on_create": true, "required_status_checks": [ { "context": "build" } ] } }
  ]
}
JSON

# Verify the bypass actor is present:
gh api /repos/$R/rulesets/RULESET_ID --jq '.bypass_actors'

do_not_enforce_on_create: true avoids the new-branch catch-22 (CI can't have run on a branch that does not exist yet). If there is no bot on this branch, you may skip 3a and omit bypass_actors.

Trade-off: strict_required_status_checks_policy: true ("branch must be up to date") forces every open human PR to be re-updated each time the bot auto-commits to the default branch, and dismiss_stale_reviews_on_push: true compounds the churn — a chatty bot can make PRs perpetually unmergeable. On a frequently-auto-committed branch prefer strict_required_status_checks_policy: false (loose) unless up-to-date-before-merge is genuinely required.

Expected: The ruleset now enforces the required check and required-PR rule for humans and forks, .bypass_actors lists the App (Integration), and the bot's next run still lands on the default branch (via the App token). Humans must open a PR; the check must be green.

On failure: If the bot 403s after 3b, the App identity is not actually the bypass actor — confirm the workflow passes the App token to checkout (not just to the commit action) and that <APP_ID> in bypass_actors matches. If the bot's push sits expected/pending forever, the required check does not run on push — make it trigger on push or drop it from the required list. If the bypass-actor picker does not appear on your personal repo, the required-PR + auto-commit combination is unsatisfiable here; GitHub's workaround is a free org. If merges are blocked on a solo repo, required_approving_review_count is >= 1 — set it to 0.

Step 4: Optional Advanced Hardening

Apply individually, each still confirmation-gated. None of these are needed for the baseline; several have sharp edges.

# 4a. Tag ruleset — protect release tags (classic tag protection is deprecated):
gh api --method POST /repos/$R/rulesets --input - <<'JSON'
{ "name": "protect-tags", "target": "tag", "enforcement": "active",
  "conditions": { "ref_name": { "include": ["refs/tags/v*"], "exclude": [] } },
  "rules": [ { "type": "deletion" }, { "type": "non_fast_forward" } ] }
JSON

# 4b. Merge-method toggles (e.g. merge-commits-only to preserve per-commit history):
gh api -X PATCH repos/$R -F allow_merge_commit=true -F allow_squash_merge=false \
  -F allow_rebase_merge=false -F delete_branch_on_merge=true

# 4c. CodeQL "default setup" (server-managed — commits NO workflow YAML):
gh api -X PATCH repos/$R/code-scanning/default-setup -f state=configured -f query_suite=default

# 4d. sha_pinning_required — ONLY after every `uses:` is a full 40-char SHA,
#     or every workflow run fails (including actions/checkout):
gh api --method PUT /repos/$R/actions/permissions -F enabled=true \
  -f allowed_actions=selected -F sha_pinning_required=true
# selected mode also gates WHICH actions may run: github_owned covers actions/*,
# but git-auto-commit-action is NOT GitHub-owned — allow-list it in the SAME
# step or the bot fails with "actions are not allowed":
gh api --method PUT /repos/$R/actions/permissions/selected-actions \
  -F github_owned_allowed=true -F verified_allowed=false \
  -f 'patterns_allowed[]=stefanzweifel/git-auto-commit-action@*'
gh api /repos/$R/actions/permissions --jq '.sha_pinning_required'   # verify

Note: allowed_actions=selected with github_owned_allowed=true still blocks stefanzweifel/git-auto-commit-action until it is in patterns_allowed (the 4d allow-list command handles this). Require-signed-commits and require-linear-history are intentionally omitted here: signing blocks the unsigned git-CLI bot push, and linear history is mutually exclusive with a merge-commits-only policy.

Expected: Each selected advanced control is applied and verified without breaking the bot: tag ruleset lists on .../rulesets, merge toggles reflect on the repo object, CodeQL default setup shows state: configured, sha_pinning_required reads true only after all actions are SHA-pinned, and git-auto-commit-action is in patterns_allowed so the bot still runs.

On failure: If every workflow fails right after 4d, an action is still tag-pinned — convert all uses: to SHAs or revert sha_pinning_required to false. If the bot fails with "actions are not allowed" after restricting allowed actions, add git-auto-commit-action to patterns_allowed. If 4c errors, the repo may have no CodeQL-supported language — skip it.

Validation

• Assessment ran and scope (public/user-owned, bot-on-default-branch) confirmed before any write
• protect-default ruleset active with deletion + non_fast_forward
• default_workflow_permissions=read and can_approve_pull_request_reviews=false
• Secret scanning + push protection + Dependabot alerts + fixes + private reporting enabled
• .github/dependabot.yml (github-actions ecosystem) and .github/SECURITY.md committed
• Auto-commit bot's next run still pushes successfully (baseline did not break it)
• Required checks/PR enabled ONLY with a GitHub App (or deploy key) bypass in place first
• Solo repo keeps required_approving_review_count: 0; required checks run on push
• Loop guard added if a bot now pushes with an App token or PAT

Common Pitfalls

• GITHUB_TOKEN is not a bypass actor: github-actions[bot] / the default token cannot be added to any ruleset bypass list and cannot push to a protected branch, by design. "Just add the Actions bot to the bypass list" has no such option — the push 403s. Use a GitHub App or deploy key.
• PAT bypass is an anti-pattern: an admin/personal PAT in the bypass list (or classic BP with enforce_admins=false) exempts ALL admin actions including your own interactive pushes — role-wide, not automation-scoped, and long-lived. Prefer an App (Integration) or deploy key (DeployKey).
• Required checks only on pull_request: a check that never runs on push never reports on the bot's direct push, so it permanently blocks the bot and new-branch creation. Make the check run on push and set do_not_enforce_on_create: true.
• Loop guard once an App token replaces GITHUB_TOKEN: the default token suppresses downstream push/pull_request triggers; an App token or PAT does not, so the auto-commit workflow can re-trigger itself indefinitely. Guard with if: github.actor != '<app>[bot]', paths-ignore, or [skip ci].
• PR via the default GITHUB_TOKEN is a false fix: a PR opened by GITHUB_TOKEN does not trigger pull_request/push workflows, so required checks never run and it sits expected forever. Create the PR with the App token.
• Alerts != fixes: vulnerability-alerts and automated-security-fixes are separate toggles; enabling alerts opens no PRs. Enable both.
• Don't buy GHAS on a public repo: secret scanning, push protection, CodeQL, and dependency review are already free on public repos; the paid Secret Protection / Code Security products target private/org repos.

Related Skills

• assess-github-repo-security - the read-only companion; always run this first
• configure-git-repository - baseline .gitignore, branches, remotes, hooks
• setup-github-actions-ci - the CI workflow whose token/permissions this hardens