Cyrus Setup Github

CRITICAL: Never use Read, Edit, or Write tools on ~/.cyrus/.env or any file inside ~/.cyrus/. Use only Bash commands (grep, printf >>, etc.) to interact with env files — secrets must never be read into the conversation context.

Setup GitHub

Configures GitHub CLI and git so Cyrus can create branches, commits, and pull requests. Optionally creates a GitHub App so Cyrus can receive and respond to @mentions in PR comments and reviews, automate rebases and merges, and auto-fix based on CI failures (coming soon).

Part A: GitHub CLI + Git Config (Outbound)

Step 1: Check Existing Configuration

Check if gh is already authenticated:

gh auth status 2>&1

If authenticated, check git config:

git config --global user.name
git config --global user.email

If both gh auth and git config are set, inform the user:

GitHub is already configured. Skipping to webhook setup.

Skip to Part B.

Step 2: Authenticate GitHub CLI

If gh is not authenticated:

gh auth login

This opens an interactive browser flow. Let the user complete it.

After completion, verify:

gh auth status

Step 3: Configure Git Identity

If git user name or email are not set, ask the user for their preferred values:

What name should appear on commits made by Cyrus? (e.g., your name, or "Cyrus Bot")

What email should appear on commits? (e.g., your email, or a noreply address)

Then set them:

git config --global user.name "<name>"
git config --global user.email "<email>"

Step 4: Verify

gh auth status
git config --global user.name
git config --global user.email

Part B: GitHub App + Webhooks (Inbound — Optional)

Ask the user:

Do you want Cyrus to respond to GitHub @mentions in PR comments and reviews?

• Yes — enable @mentions: Creates a GitHub App so Cyrus can receive PR comments and reviews via webhooks, respond when @mentioned, and act on "changes requested" reviews.
• No — PRs only: Cyrus will create branches, commits, and PRs but won't respond to comments.

If No → skip to Completion.

Step 5: Check Existing Webhook Config

grep -c '^GITHUB_WEBHOOK_SECRET=.' ~/.cyrus/.env 2>/dev/null
grep -c '^GITHUB_APP_ID=.' ~/.cyrus/.env 2>/dev/null
grep -c '^GITHUB_APP_INSTALLATION_ID=.' ~/.cyrus/.env 2>/dev/null
test -f ~/.cyrus/github-app.pem && echo "PEM exists" || echo "PEM missing"

If all four checks pass (1, 1, 1, "PEM exists"), skip to Completion — webhooks are already configured.

Step 6: Collect Inputs

Read the webhook base URL:

grep '^CYRUS_BASE_URL=' ~/.cyrus/.env | cut -d= -f2-

If CYRUS_BASE_URL is not set, stop and tell the user to run the endpoint setup step first.

Use the AGENT_NAME value from the orchestrator (set in Step 0 of /cyrus-setup). If not available, ask:

What should the GitHub App be named? (e.g., "Cyrus", "My Code Agent")

Important — GitHub @mention autocomplete quirk: GitHub's autocomplete in PR comments only suggests real GitHub user accounts, not App bots. This means @your-bot won't appear in the autocomplete dropdown unless a GitHub user with that exact name exists. The mention still works if typed manually, but for the best experience:

Before choosing a name, check if the same name is available as a GitHub username at https://github.com/<name>. If it is:

1. Create a free GitHub user account with that name
2. Invite it to your org and/or repo as a collaborator
3. Set GITHUB_BOT_USERNAME to that username (the one users will type in @mentions, not <slug>[bot])

This is the simplest way to get autocomplete working — a silly GitHub limitation, but the known workaround.

Without a matching GitHub user, @mentions still work if typed manually, but won't autocomplete. In that case users would need to set up co-authorship (via a git message template or prepare-commit-msg hook adding Co-authored-by:) to get the bot's name showing as a repo contributor, which is more involved.

Ask:

Where should the GitHub App be created?

• Personal account (github.com/settings/apps)
• Organization — which org? (github.com/organizations/<ORG>/settings/apps)

Store the org name if applicable.

Ask:

What homepage URL should the GitHub App use? This is displayed on the app's settings page as its website. It has no functional impact — GitHub just shows it as a link. Most users use their company website, GitHub org page, or any placeholder URL.

(e.g., https://github.com/your-org, your company URL, or just https://example.com)

Step 7: Build Manifest JSON

Construct the manifest, substituting AGENT_NAME, HOMEPAGE_URL, and CYRUS_BASE_URL:

{
  "name": "<AGENT_NAME>",
  "url": "<HOMEPAGE_URL>",
  "redirect_url": "http://localhost:8976",
  "hook_attributes": {
    "url": "<CYRUS_BASE_URL>/github-webhook",
    "active": true
  },
  "public": false,
  "default_permissions": {
    "contents": "write",
    "issues": "write",
    "pull_requests": "write",
    "repository_hooks": "write"
  },
  "default_events": [
    "issue_comment",
    "pull_request_review",
    "pull_request_review_comment",
    "repository"
  ]
}

Note: redirect_url is required by GitHub's manifest flow. The actual redirect will include a ?code= parameter appended to this URL — the code is what matters, not the destination page.

Step 8: Create GitHub App via Manifest

GitHub's manifest flow works by POSTing a form with a manifest field to the app creation URL. After the user approves, GitHub redirects to a URL containing a code parameter.

Determine the creation URL:

• Personal: https://github.com/settings/apps/new
• Organization: https://github.com/organizations/<ORG>/settings/apps/new

GitHub's manifest flow requires a form POST with a manifest field to the creation URL — the page itself does not have a manifest input field. All paths use the same helper HTML page approach.

First, create the helper page and serve it via a local web server. This works for both local and remote/headless setups (e.g., tmux/SSH into a server). The manifest JSON must be HTML-entity-escaped (replace " with ") since it's placed in an HTML attribute:

# Escape the manifest JSON for safe embedding in an HTML attribute
MANIFEST_HTML_ESCAPED=$(echo '<MANIFEST_JSON>' | sed 's/"/\&quot;/g')

cat > /tmp/github-app-manifest.html << HTMLEOF
<form method="post" action="<CREATION_URL>">
  <input type="hidden" name="manifest" value="$MANIFEST_HTML_ESCAPED">
  <p>Click the button to create the GitHub App:</p>
  <button type="submit" style="font-size:18px;padding:12px 24px;">Create GitHub App</button>
</form>
HTMLEOF

# Serve the page on a local port (works for headless/remote setups)
python3 -m http.server 8976 --directory /tmp &
HTTP_SERVER_PID=$!
echo "Serving at http://localhost:8976/github-app-manifest.html"

After the user completes the flow, stop the server:

kill $HTTP_SERVER_PID 2>/dev/null

Choose the automation path based on what's available:

1. If claude-in-chrome MCP tools are available → use Path A-1
2. If agent-browser is installed and a Chrome debug session is connected → use Path A-2
3. Otherwise → use Path B (manual)

Path A-1 (claude-in-chrome):

1. Navigate to http://localhost:8976/github-app-manifest.html
2. Click the submit button to POST the manifest to GitHub
3. GitHub shows a confirmation page — click Create GitHub App
4. After redirect, extract the code parameter from the URL

Path A-2 (agent-browser):

Same flow via agent-browser — navigate to the helper page, click submit, then click Create.

Path B (manual):

Tell the user:

1. Open http://localhost:8976/github-app-manifest.html in your browser and click the button
2. Review the permissions on GitHub and click Create GitHub App
3. After redirect, copy the entire URL from the browser address bar and paste it here

Extract the code parameter from the redirect URL.

Step 9: Exchange Code for Credentials

IMPORTANT: The /app-manifests/<CODE>/conversions endpoint is one-time-use. Call it exactly once.

# Store the full response temporarily (one-time-use endpoint — do NOT call twice)
gh api /app-manifests/<CODE>/conversions --method POST > /tmp/github-app-response.json

# Extract values (these are all secrets — handle via Bash only)
GITHUB_APP_ID=$(cat /tmp/github-app-response.json | jq -r '.id')
GITHUB_APP_SLUG=$(cat /tmp/github-app-response.json | jq -r '.slug')
GITHUB_WEBHOOK_SECRET=$(cat /tmp/github-app-response.json | jq -r '.webhook_secret')
GITHUB_APP_PEM=$(cat /tmp/github-app-response.json | jq -r '.pem')

# Clean up
rm /tmp/github-app-response.json

Step 10: Write Credentials to Env

# Ensure directory exists (may not if running standalone outside cyrus-setup)
mkdir -p ~/.cyrus

# Webhook secret (for signature verification)
printf 'GITHUB_WEBHOOK_SECRET=%s\n' "$GITHUB_WEBHOOK_SECRET" >> ~/.cyrus/.env

# App ID (for token minting)
printf 'GITHUB_APP_ID=%s\n' "$GITHUB_APP_ID" >> ~/.cyrus/.env

# Bot username (for mention filtering — see note below about GitHub autocomplete)
printf 'GITHUB_BOT_USERNAME=%s\n' "$GITHUB_APP_SLUG" >> ~/.cyrus/.env

# Private key (multi-line — stored as a separate file)
printf '%s\n' "$GITHUB_APP_PEM" > ~/.cyrus/github-app.pem
chmod 600 ~/.cyrus/github-app.pem

# Ensure self-hosted mode is active (required for signature verification)
grep -q '^CYRUS_HOST_EXTERNAL=' ~/.cyrus/.env || printf 'CYRUS_HOST_EXTERNAL=true\n' >> ~/.cyrus/.env

Verify all values were written:

grep -c '^GITHUB_WEBHOOK_SECRET=.' ~/.cyrus/.env
grep -c '^GITHUB_APP_ID=.' ~/.cyrus/.env
grep -c '^GITHUB_BOT_USERNAME=.' ~/.cyrus/.env
test -f ~/.cyrus/github-app.pem && echo "PEM exists" || echo "PEM missing"

All checks must pass (return 1, 1, 1, "PEM exists").

Step 11: Install App on Repositories

The GitHub App must be installed on the repositories Cyrus will monitor.

Go to: https://github.com/apps/<GITHUB_APP_SLUG>/installations/new

Select which repositories (or "All repositories") and click Install.

Or via browser automation (navigate to URL, select repos, click Install).

After installation, capture the installation ID:

# Re-read GITHUB_APP_ID from .env (shell vars don't persist between blocks)
GITHUB_APP_ID=$(grep '^GITHUB_APP_ID=' ~/.cyrus/.env | cut -d= -f2-)

# Generate a JWT to authenticate as the app
GITHUB_APP_JWT=$(node -e "
const crypto = require('crypto');
const fs = require('fs');
const key = fs.readFileSync(process.env.HOME + '/.cyrus/github-app.pem', 'utf8');
const now = Math.floor(Date.now()/1000);
const header = Buffer.from(JSON.stringify({alg:'RS256',typ:'JWT'})).toString('base64url');
const payload = Buffer.from(JSON.stringify({iat:now-60,exp:now+600,iss:'$GITHUB_APP_ID'})).toString('base64url');
const sig = crypto.createSign('RSA-SHA256').update(header+'.'+payload).sign(key,'base64url');
console.log(header+'.'+payload+'.'+sig);
")

# List installations — if multiple, show all and let user pick
INSTALLATIONS=$(curl -s -H "Authorization: Bearer $GITHUB_APP_JWT" -H "Accept: application/vnd.github+json" https://api.github.com/app/installations)
echo "$INSTALLATIONS" | jq '.[] | {id, account: .account.login}'

If there are multiple installations, ask the user which one to use. Then write the installation ID:

printf 'GITHUB_APP_INSTALLATION_ID=%s\n' "<INSTALLATION_ID>" >> ~/.cyrus/.env

Verify:

grep -c '^GITHUB_APP_INSTALLATION_ID=.' ~/.cyrus/.env

Must return 1.

Completion

✓ GitHub CLI authenticated ✓ Git identity configured: <name> <email>

If webhooks were enabled:

✓ GitHub App created: <GITHUB_APP_SLUG> ✓ Webhook secret and app credentials saved to ~/.cyrus/.env ✓ Private key saved to ~/.cyrus/github-app.pem ✓ App installed (installation ID: <GITHUB_APP_INSTALLATION_ID>) ✓ Cyrus will respond to @<GITHUB_BOT_USERNAME> mentions in PR comments

Note: The webhook URL will only respond successfully once Cyrus is running. If GitHub shows a webhook delivery failure during setup, it will retry automatically once Cyrus starts.