GitHub & CodeRabbit

protoLabs integrates deeply with GitHub to automate the full PR lifecycle — from branch creation to merge — and with CodeRabbit to provide AI-assisted code review with automatic thread resolution.

Prerequisites

GitHub account with access to your repository
GitHub CLI (gh) installed and authenticated
Repository access with permission to create PRs and manage branches

Setup

1. Authenticate the GitHub CLI

protoLabs uses the gh CLI for all GitHub operations. Authenticate once and the token is reused automatically:

bash

gh auth login

Select GitHub.com, choose HTTPS, and authenticate via browser or token.

2. Set the GH_TOKEN environment variable

After authenticating, export the token to your environment:

bash

# Add to your .env file
GH_TOKEN=$(gh auth token)

Or set it manually with a Personal Access Token:

bash

GH_TOKEN=ghp_your_token_here

3. Required token scopes

Scope	Required	Purpose
`repo`	✅ Yes	Create/merge PRs, read branches, manage reviews
`workflow`	✅ Yes	Read CI workflow run status
`read:org`	Optional	Access organization-owned repositories

Note: GH_TOKEN is the primary variable used for PR operations and CodeRabbit integration. GITHUB_TOKEN (commented out in .env.example) is used only for optional repository-dispatch and Langfuse sync features.

4. Verify the token

Check that protoLabs can reach GitHub:

bash

gh auth status

You can also use the setup health check endpoint: GET /api/setup/gh-status

Configuration

Environment variables

Variable	Required	Description
`GH_TOKEN`	✅ Yes	GitHub token for PR operations, reviews, and CodeRabbit threads
`GITHUB_TOKEN`	Optional	Alternative token for repository-dispatch / Langfuse sync only

Both variables are set in your project's .env file (see .env.example for the full template).

What protoLabs does automatically

Once GH_TOKEN is configured and an agent completes a feature, the following steps happen without manual intervention:

Overall flow

Agent finishes feature
        │
        ▼
 Create worktree branch
 Commit & push changes
        │
        ▼
  Open pull request
  (title + body generated)
        │
        ▼
  Poll CI checks (60s)  ──── timeout (10 min) ──▶ Escalate
        │
   CI passes
        │
        ▼
  resolve_pr_threads
  (auto-resolve bot threads)
        │
        ▼
  Poll review feedback ◀─────────────────────────┐
  (CodeRabbit, human)                             │
        │                                         │
  Feedback received?                              │
    ├─ No:  merge_pr ──▶ Done                     │
    └─ Yes: agent fixes  ─────(up to 2 iterations)┘
                │
           > 2 iterations ──▶ Escalate to EM agent

Branch management

Creates an isolated git worktree for each feature (.worktrees/<feature-id>)
Commits changes to a feature branch named after the feature slug
Pushes the branch to the remote repository

PR creation

Opens a pull request with a generated title and body summarizing the changes
Sets the base branch from project settings (defaults to main)
Adds labels and links the PR to the feature record

Status checks and CI polling

Polls GitHub for CI check results every 60 seconds (up to 10 minutes)
Waits for all required status checks to pass before attempting merge
Escalates to the EM agent if CI fails repeatedly

Feedback loop

Monitors open PRs for review comments (polling every 60 seconds)
Detects: changes requested, inline comments, CodeRabbit feedback, approvals
Passes feedback to the originating agent for autonomous remediation
Limits remediation to 2 PR iterations and 4 total remediation cycles before escalating

CodeRabbit

CodeRabbit is an AI-powered code review tool that installs as a GitHub App and automatically reviews every pull request. protoLabs is aware of CodeRabbit and handles its feedback natively.

What CodeRabbit does

Posts line-level review comments on every PR
Categorises issues by severity (nitpick, suggestion, issue)
Opens review threads that must be resolved before merge (configurable)

Installing the CodeRabbit GitHub App

Go to coderabbit.ai and sign in with GitHub
Click Add to GitHub and select the repositories to enable
Accept the permissions (read/write access to pull requests and repository contents)
CodeRabbit begins reviewing PRs immediately — no additional configuration in protoLabs is required

A .coderabbit.yaml file in the repository root customises review behaviour (path filters, severity thresholds, language rules). protoLabs ships a default .coderabbit.yaml — edit it to tune review strictness.

How resolve_pr_threads works

The resolve_pr_threads MCP tool (and the underlying CodeRabbitResolverService) automatically resolves review threads created by known bot accounts using GitHub's GraphQL resolveReviewThread mutation.

Bots that are auto-resolved:

Bot account	Description
`coderabbitai`	CodeRabbit AI review bot
`github-actions[bot]`	GitHub Actions automation
`dependabot[bot]`	Dependency update bot
`renovate[bot]`	Renovate dependency bot

Human review threads are never auto-resolved — only threads created by the bot accounts above are eligible.

When resolution runs:

Automatically during the PR merge flow, after CI passes and before the merge attempt
On-demand via the resolve_pr_threads MCP tool

How PRFeedbackService reads CodeRabbit comments

PRFeedbackService polls the GitHub API for review threads and passes them through CodeRabbitParserService, which:

Fetches all review threads on the PR
Identifies threads authored by coderabbitai
Parses the comment body for severity category, file path, and suggested change
Classifies threads as: actionable (the agent should fix) or informational (can be resolved without changes)
Includes the structured feedback in the agent's continuation prompt so it can address each item

The agent then decides whether to accept each feedback item. Accepted items trigger a new commit; resolved threads are marked via GraphQL.

Available MCP tools

Seven MCP tools cover GitHub and CodeRabbit operations. See MCP Tools Reference for full details.

Tool	Description
`merge_pr`	Merge an open pull request
`check_pr_status`	Check PR status: CI checks, reviews, mergeability
`get_pr_feedback`	Retrieve PR review feedback for the agent
`resolve_pr_threads`	Resolve CodeRabbit and other bot review threads

Troubleshooting

PR creation fails with "authentication required"

Symptom: Agent log shows gh pr create failing or a 401 error from the GitHub API.

Fix:

Verify GH_TOKEN is set: echo $GH_TOKEN
Re-authenticate: gh auth login
Re-export the token: GH_TOKEN=$(gh auth token)
Confirm the token is in .env and the server has been restarted

PR creation fails with "Resource not accessible by integration"

Symptom: 403 error when creating a PR or accessing reviews.

Fix: The token is missing required scopes. Generate a new Personal Access Token with repo and workflow scopes:

Go to GitHub Settings > Developer settings > Personal access tokens
Click Generate new token (classic)
Select repo (full) and workflow
Copy the token and update GH_TOKEN in .env

CI checks never complete / merge is blocked

Symptom: protoLabs waits for CI but the PR is never merged. Logs show repeated Waiting for CI checks....

Checks:

CI maximum wait is 10 minutes. If your pipeline takes longer, the check times out and the PR is flagged for review.
Verify the GitHub Actions workflow is actually running (check the Actions tab on the PR).
If CI is passing but the check name doesn't match, ensure required status check names in branch protection match what the workflow reports.

CodeRabbit threads are not being resolved

Symptom: After running resolve_pr_threads, CodeRabbit threads remain open.

Checks:

Confirm GH_TOKEN has repo scope (GraphQL mutations require it)
Verify the CodeRabbit bot account name is coderabbitai — custom installations may use a different handle
Check server logs for CodeRabbitResolver errors; a 401 or 403 indicates token scope issues
Threads created by human reviewers are intentionally left open

Agent exceeds PR iteration limit

Symptom: Agent stops and an escalation is raised after two rounds of fixes.

Behaviour: protoLabs limits autonomous PR remediation to 2 iterations to prevent infinite loops. After the limit is reached, the feature is escalated to the EM agent for human review. Resolve the escalation and restart the agent to continue.

MCP Tools Reference — Full tool catalog including GitHub Operations
CI/CD — GitHub Actions pipeline configuration

GitHub & CodeRabbit ​

Prerequisites ​

Setup ​

1. Authenticate the GitHub CLI ​

2. Set the GH_TOKEN environment variable ​

3. Required token scopes ​

4. Verify the token ​

Configuration ​

Environment variables ​

What protoLabs does automatically ​

Overall flow ​

Branch management ​

PR creation ​

Status checks and CI polling ​

Feedback loop ​

CodeRabbit ​

What CodeRabbit does ​

Installing the CodeRabbit GitHub App ​

How resolve_pr_threads works ​

How PRFeedbackService reads CodeRabbit comments ​

Available MCP tools ​

Troubleshooting ​

PR creation fails with "authentication required" ​

PR creation fails with "Resource not accessible by integration" ​

CI checks never complete / merge is blocked ​

CodeRabbit threads are not being resolved ​

Agent exceeds PR iteration limit ​

Related Documentation ​

GitHub & CodeRabbit

Prerequisites

Setup

1. Authenticate the GitHub CLI

2. Set the GH_TOKEN environment variable

3. Required token scopes

4. Verify the token

Configuration

Environment variables

What protoLabs does automatically

Overall flow

Branch management

PR creation

Status checks and CI polling

Feedback loop

CodeRabbit

What CodeRabbit does

Installing the CodeRabbit GitHub App

How resolve_pr_threads works

How PRFeedbackService reads CodeRabbit comments

Available MCP tools

Troubleshooting

PR creation fails with "authentication required"

PR creation fails with "Resource not accessible by integration"

CI checks never complete / merge is blocked

CodeRabbit threads are not being resolved

Agent exceeds PR iteration limit

Related Documentation