Assess GitHub Repository Security

Audit a GitHub repository's security posture, read-only, and classify it against tiered best practices. This skill only reads — it never enables, disables, or changes any setting. Remediation is a separate concern (see harden-github-repo-security).

When to Use

• Reviewing a repo before open-sourcing it or cutting a release
• Auditing a public, user-owned repo whose CI auto-commits to the default branch (e.g. via stefanzweifel/git-auto-commit-action + the default GITHUB_TOKEN)
• Verifying that a hardening change actually took effect
• Producing a baseline posture report to track over time

Inputs

• Required: Target repository as OWNER/REPO
• Required: gh CLI authenticated with an account that has the admin repository role on the target repo (some endpoints 403 otherwise). This is a role requirement, not a need for a broad write-capable token: a fine-grained, single-repo PAT scoped to read-only Administration / Actions / Secret-scanning permissions satisfies the same admin check with far less blast radius if the audit credential is ever leaked or reused in automation
• Optional: Branch to check for classic protection (defaults to the repo's default_branch)
• Optional: security_events token scope — needed only to count open Dependabot alerts; the rest works without it

Set a shorthand for every command below:

R="OWNER/REPO"   # e.g. pjt222/agent-almanac

Procedure

Step 1: Preflight — auth and admin

Confirm the CLI is authenticated and the account has admin on the repo. Non-admins get partial data (403 on rulesets, Actions, and security endpoints), which silently understates the posture.

gh auth status
gh api "repos/$R" --jq '{full_name, admin: .permissions.admin, visibility}'

Expected: gh auth status shows a logged-in account; the second call prints admin: true.

On failure: If not authenticated, run gh auth login (or set GH_TOKEN). If admin: false, stop and note in the report that findings are incomplete — a non-admin cannot read ruleset internals or Actions permissions, so absence of a control cannot be distinguished from lack of access.

Step 2: Repo basics — visibility, merge toggles, collaborators

gh api "repos/$R" --jq '{visibility, private, allow_forking,
  default_branch, allow_merge_commit, allow_squash_merge,
  allow_rebase_merge, delete_branch_on_merge}'

# Direct collaborators and their effective role
gh api "repos/$R/collaborators?affiliation=direct" \
  --jq '.[] | {login, role_name}'

Expected: JSON for the repo toggles plus one line per direct collaborator with role_name (admin/maintain/write/triage/read).

On failure: A 403 on collaborators means the token lacks admin; note it and continue. Record visibility — it changes which features are free: on public repos secret scanning, push protection, CodeQL, and dependency review are free; the paid GHAS/Secret Protection products are private/org-only, so their absence on a public repo is not a gap.

Step 3: Ref protection — check rulesets AND classic (both)

A repo can be protected by a ruleset, by classic branch protection, by both, or by neither. Rulesets are the actively-developed path and are free on public user-owned repos. You MUST check both — a repo with only a ruleset returns 404 on the classic endpoint and vice versa.

b=$(gh api "repos/$R" --jq '.default_branch')

# (a) Rulesets — list, then inspect each active one's rules + bypass list
gh api "repos/$R/rulesets" --jq '.[] | {id, name, enforcement, target}'
# For each id from above:
#   gh api "repos/$R/rulesets/<id>" \
#     --jq '{name, enforcement,
#            rules: [.rules[].type],
#            bypass: [.bypass_actors[] | {actor_type, bypass_mode}]}'

# (b) Classic branch protection on the default branch (404 = none)
gh api -i "repos/$R/branches/$b/protection" 2>/dev/null | head -1
gh api "repos/$R/branches/$b/protection" \
  --jq '{required_status_checks: .required_status_checks.checks,
         strict: .required_status_checks.strict,
         enforce_admins: .enforce_admins.enabled,
         required_reviews: .required_pull_request_reviews.required_approving_review_count,
         linear: .required_linear_history.enabled,
         signatures: .required_signatures.enabled,
         allow_force_pushes: .allow_force_pushes.enabled,
         allow_deletions: .allow_deletions.enabled}' 2>/dev/null \
  || echo "no classic branch protection"

Aggregate ALL rulesets, not just the first. Several rulesets can target the same branch at once; GitHub applies them together (most-restrictive-wins), and a common pattern splits ref protection (deletion/non_fast_forward, no bypass) and a required check (required_status_checks, with bypass actors) into separate rulesets. The branch's true posture is the union of every active ruleset plus classic protection — inspect each id from step (a); never conclude from one ruleset alone. A rule absent from ruleset X may be enforced by ruleset Y.

Expected: Either a ruleset with rules such as deletion, non_fast_forward, pull_request, required_status_checks, or a classic protection object, or an explicit "none" from both.

On failure: A 404 on either endpoint means that mechanism is not configured — it is a valid data point, not an error; record "none" for that mechanism. Note the rule set from the ruleset rules[].type list and the bypass_actors. Remember: the default GITHUB_TOKEN / github-actions[bot] can never be a bypass actor by design — if the repo auto-commits AND has required_status_checks/pull_request rules with no Integration (GitHub App) or DeployKey bypass actor, flag that the bot push must be 403ing (a real finding).

Step 4: Actions security — token defaults and PR approval

# Actions enablement + allowed-actions policy (+ SHA-pinning policy)
gh api "repos/$R/actions/permissions" \
  --jq '{enabled, allowed_actions, sha_pinning_required}'

# Default GITHUB_TOKEN permissions + can-the-bot-approve-PRs
gh api "repos/$R/actions/permissions/workflow" \
  --jq '{default_workflow_permissions, can_approve_pull_request_reviews}'

Expected: default_workflow_permissions is read (hardened) or write (permissive default), and can_approve_pull_request_reviews is false (hardened) or true (a review-bypass vector).

On failure: 403 means non-admin — note it. If allowed_actions is all, any action can run (looser); selected with a pinned allow-list is tighter — but note that selected + github_owned_allowed still blocks non-GitHub actions like stefanzweifel/git-auto-commit-action unless explicitly allow-listed. sha_pinning_required may be absent/null on repos that never set the 2025-08 policy — record as "not enforced". Per-workflow permissions: blocks live in the YAML, not the API; note that the API shows only the repo default, which is a default (not a cap) for same-repo push events.

Step 5: Code and supply-chain features

# Dependabot alerts + dependency graph (204 = ON, 404 = OFF)
gh api -i "repos/$R/vulnerability-alerts" 2>/dev/null | head -1

# Dependabot security updates (auto fix PRs) — separate toggle
gh api "repos/$R/automated-security-fixes" \
  --jq '{enabled, paused}' 2>/dev/null || echo "automated-security-fixes: off/unavailable"

# Secret scanning + push protection status (security_and_analysis has NO
# code-scanning field — CodeQL is probed separately below)
gh api "repos/$R" --jq '.security_and_analysis'

# CodeQL code scanning — default setup state (its own endpoint)
gh api "repos/$R/code-scanning/default-setup" --jq '.state' 2>/dev/null \
  || echo "code-scanning default setup: not configured / no access"

# Dependabot version updates config present?
gh api -i "repos/$R/contents/.github/dependabot.yml" 2>/dev/null | head -1

# SECURITY.md — GitHub auto-detects it at root, docs/, OR .github/.
# Present if ANY of the three returns 200; only a GAP if all three 404.
for p in SECURITY.md docs/SECURITY.md .github/SECURITY.md; do
  echo "$p: $(gh api -i "repos/$R/contents/$p" 2>/dev/null | head -1)"
done

# Private vulnerability reporting — status is a 200 body {"enabled": bool},
# NOT a 204/404 toggle, so read the field directly.
gh api "repos/$R/private-vulnerability-reporting" --jq '.enabled' 2>/dev/null \
  || echo "PVR: not accessible"

# Open Dependabot alert count — needs security_events scope; may 403
gh api "repos/$R/dependabot/alerts?state=open" --jq 'length' 2>/dev/null \
  || echo "dependabot/alerts: 403 (needs security_events scope) — skipped"

Expected: vulnerability-alerts → HTTP/2.0 204 when enabled; security_and_analysis shows secret_scanning.status and secret_scanning_push_protection.status as enabled on a hardened public repo; code-scanning/default-setup .state is configured when CodeQL default setup is on; automated-security-fixes → enabled: true; the dependabot.yml probe returns 200 when present; at least one of the three SECURITY.md paths returns 200 when a policy file exists; private-vulnerability-reporting .enabled prints true when PVR is on.

On failure: vulnerability-alerts returning 404 = Dependabot alerts OFF (a gap). Remember alerts != fixes: alerts on with automated-security-fixes off means nothing is auto-remediated — flag both separately. On public repos secret_scanning is usually already enabled by default; if security_and_analysis omits the field entirely, treat it as advisory (public-repo default on) but note the API did not confirm it. code-scanning/default-setup 404/non-configured = CodeQL default setup not enabled (a recommended-tier gap on a public repo, where code scanning is free). For SECURITY.md, record a GAP only if all three paths 404 — a 200 on root, docs/, or .github/ all count as present. private-vulnerability-reporting empty/false = PVR off; a non-JSON or error response = not accessible. dependabot/alerts 403 is expected without security_events scope — record "not assessed", not "0".

Step 6: Produce the tiered PASS/GAP report

Classify every gathered fact into three tiers and mark PASS (control present), GAP (control absent), or N/A (not applicable, e.g. a paid private-repo feature on a public repo). Distinguish a required check from an advisory one: a status check that runs but is not listed in the ruleset's required_status_checks does not gate anything — it is advisory only.

Interpret the solo-maintainer lockout. Cross-reference the Step 2 direct-collaborator count with the Step 3 required_approving_review_count. On a single-maintainer repo, required_approving_review_count >= 1 (and require_code_owner_review with a sole owner) is unsatisfiable — you cannot approve your own PR — so on an auto-commit repo it is a self-lockout / functional breakage, not a PASS. Flag it as a GAP-with-caveat, and note that a ruleset (unlike classic branch protection's enforce_admins) does not auto-exempt the admin: the sole maintainer stays blocked unless explicitly added to the ruleset bypass_actors.

Do not publish the raw report into the audited repo. The PASS/GAP list enumerates exact, admin-only-visible gaps (no ruleset, GITHUB_TOKEN can approve PRs, no push protection) — a pre-remediation vulnerability roadmap. While any GAP is open, keep the findings local/private (a gitignored file, a private gist, or a draft GitHub Security Advisory); never commit it into the public repo being audited (contrast security-audit-codebase, which writes SECURITY_AUDIT_REPORT.md into the project root — do NOT copy that pattern here). Redact ruleset / App ID / bypass-actor identifiers before any public write.

# GitHub Repo Security Assessment — OWNER/REPO
Date: YYYY-MM-DD   Visibility: public   Auditor role: admin

## Essential
- [PASS] Ruleset with deletion + non_fast_forward on default branch
- [GAP]  default_workflow_permissions = write (should be read)
- [PASS] can_approve_pull_request_reviews = false
- [GAP]  actions/checkout pinned to @v4 tag, not a 40-char SHA
- [PASS] Dependabot alerts (204) + security updates (enabled)
- [GAP]  No .github/dependabot.yml (version updates off — keeps
         github-actions action pins fresh; essential supply-chain hygiene)
- [PASS] Secret scanning + push protection enabled

## Recommended
- [N/A]  required_status_checks — none (no CI gate configured)
- [PASS] CodeQL default setup: configured
- [PASS] SECURITY.md present (.github/) + PVR enabled

## Advanced
- [GAP]  sha_pinning_required: not enforced
- [N/A]  Required signed commits — would block the auto-commit bot
- [N/A]  Paid GHAS / Secret Protection — public repo, features free

## Notes
- Auto-commit bot: ruleset has NO App/DeployKey bypass actor; if
  required_status_checks were added the github-actions[bot] push would 403.
- Solo maintainer (1 direct collaborator): required_approving_review_count
  is 0 — correct; any value >= 1 would be an unsatisfiable self-lockout and
  a ruleset would NOT auto-exempt the admin.
- Dependabot open alerts: not assessed (token lacks security_events).
- This report is kept local/private — not committed into the audited repo
  while GAPs remain open.

Expected: A written report with every fact placed in a tier and marked PASS / GAP / N/A, plus a Notes section for auth gaps, advisory-only checks, and the auto-commit-bot bypass interaction.

On failure: If some endpoints 403'd, still emit the report but mark those rows "not assessed" and state the missing scope/role at the top — never record an unreadable control as a GAP (absence of access is not absence of the control).

Validation

• gh auth status confirmed and admin on the repo verified (or the report is explicitly flagged incomplete)
• visibility recorded (drives which features are free vs N/A)
• BOTH rulesets AND classic branch protection were queried (not just one), and EVERY active ruleset was inspected + aggregated (not just the first)
• Actions permissions and permissions/workflow both read
• Dependabot alerts, security updates, secret scanning, and push protection each checked as separate toggles
• CodeQL default setup queried via code-scanning/default-setup (not inferred from security_and_analysis, which has no such field)
• SECURITY.md checked at all three auto-detected paths (root, docs/, .github/) — GAP only if all three 404
• Private vulnerability reporting read from the .enabled body field (not a 204/404 toggle)
• Solo-maintainer lockout interpreted: collaborator count cross-referenced with required_approving_review_count
• Every finding is tiered and marked PASS / GAP / N/A
• Report kept local/private while GAPs are open — NOT committed into the audited public repo
• No setting was changed — this audit is strictly read-only

Common Pitfalls

• Checking only rulesets or only classic protection: They are independent mechanisms. A repo protected by a ruleset returns 404 on branches/{b}/protection; concluding "unprotected" from that alone is wrong. Always query both.
• Some endpoints 403 without security scope/admin: dependabot/alerts needs security_events; rulesets and Actions permissions need admin. A 403 is "not assessed", not a GAP — recording it as a gap fabricates a finding.
• Misreading the auto-commit-bot bypass: The default GITHUB_TOKEN / github-actions[bot] can never be a ruleset bypass actor. If a repo auto-commits to a branch that has required_status_checks or a pull_request rule with no Integration/DeployKey bypass actor, the bot push is being rejected — surface it as a real finding.
• Reading the API default as a hard cap: default_workflow_permissions is the repo default; per-job permissions: in the workflow YAML can raise or drop it for same-repo events. The API cannot show the effective per-workflow grant — note that limitation.
• Inferring CodeQL from security_and_analysis: that object carries secret_scanning*, dependabot_security_updates, and advanced_security — but no code-scanning field. CodeQL default-setup state comes only from the code-scanning/default-setup endpoint; never claim a CodeQL PASS/GAP the skill did not actually probe.
• Marking a solo review requirement as PASS: on a one-maintainer repo, required_approving_review_count >= 1 is an unsatisfiable self-lockout, not a protective control — and a ruleset (unlike classic enforce_admins) will not auto-exempt the admin. Report it as a functional-breakage GAP.

Related Skills

• harden-github-repo-security - apply the fixes this audit surfaces
• security-audit-codebase - complementary in-tree secret/dependency scan
• configure-git-repository - foundational repo + .gitignore setup