Atlassian & GitHub MCP CLI Tool

A Model Context Protocol (MCP) CLI tool for accessing Atlassian services (Jira, Confluence) and GitHub repositories using OAuth2 authentication and Bearer Token REST API access.

Overview

This skill enables AI agents to interact with Jira issues, Confluence pages, and GitHub repositories through a standardized MCP interface. It supports both OAuth2 and Basic authentication (PAT tokens) for flexible deployment scenarios.

Prerequisites

Before using this skill, you must:

1. **Register OAuth applications** (if using OAuth mode):

- Atlassian: https://developer.atlassian.com/console/myapps/

- GitHub: https://github.com/settings/developers

2. **Create Personal Access Tokens** (if using Basic mode):

- Atlassian: https://id.atlassian.com/manage-profile/security/api-tokens

- GitHub: https://github.com/settings/tokens

Installation Steps

1. Install the Package

```bash

npm install -g boilerplate-mcp-tool --registry=https://artifactory.cathaypacific.com/artifactory/api/npm/npm-common/

```

2. Authenticate

Choose one authentication method:

**OAuth2 Login (Recommended):**

```bash

Opens browser for OAuth flow

boilerplate-mcp-tool login

Force re-login

boilerplate-mcp-tool login -f

Clear credentials

boilerplate-mcp-tool login -c

```

**Basic Authentication (PAT):**

```bash

Login with Personal Access Tokens

boilerplate-mcp-tool login -b

```

**Note:** OAuth and Basic tokens cannot be mixed. The login method will overwrite previous authentication.

3. Configure MCP Server

```bash

Auto-configure VSCode mcp.json

boilerplate-mcp-tool install

Display config for manual setup

boilerplate-mcp-tool config

```

Add to your `mcp.json`:

```json

{

"servers": {

"boilerplateMcpTool": {

"command": "node",

"args": ["/path/to/boilerplate-mcp-tool/dist/app.js"]

}

}

}

```

Available Tools

Once configured, the following MCP tools are available:

Jira Tools

Confluence Tools

GitHub Tools

Utility Tools

Available Prompts

Usage Instructions for AI Agents

When using this skill, follow these steps:

1. **Verify Authentication:**

- Use `#cx_health_check` to confirm the tool is properly authenticated

- If authentication fails, instruct the user to run `boilerplate-mcp-tool login`

2. **Fetch Jira Issues:**

- Use `#cx_my_jira_issue` to list user's assigned issues

- Use `#cx_fetch_jira_issue` with issue key (e.g., "PROJ-123") for detailed information

3. **Search Confluence:**

- Use `#cx_search_confluence` with search queries

- **Note:** Due to Atlassian API restrictions, OAuth tokens may have limited access to full Confluence content. Search functionality is available, but full body content may be restricted.

4. **Access GitHub Repositories:**

- Use `#cx_fetch_github_repository_info` to get repository metadata

- Use `#cx_fetch_github_repository_code` to fetch specific files

- Use `#cx_search_github` for code and repository searches

- **Note:** Private repositories require organization admin authorization of the OAuth app

5. **Generate To-Do Lists:**

- Use `/my_todo_list` prompt to create actionable task lists from Jira assignments

Known Limitations

1. **OAuth Token Expiry:**

- Atlassian OAuth tokens expire after 1 hour

- Tokens are automatically refreshed using refresh tokens

- If refresh fails, re-login required

2. **Confluence Content Access:**

- OAuth Bearer Tokens have restricted access to Confluence body content

- Search functionality works, but full page content may be unavailable

- Consider using Basic authentication (PAT) for full access

3. **GitHub Private Repository Access:**

- OAuth tokens cannot access private repositories without admin approval

- Organization admins must authorize the OAuth app:

- Navigate to: Organization Settings → OAuth App Access

- Approve the boilerplate-mcp-tool application

4. **Token Conflicts:**

- OAuth and Basic authentication cannot coexist

- Logging in with one method overwrites the other

Example Workflows

Workflow 1: Daily Standup Preparation

1. Run `#cx_health_check` to verify connectivity

2. Use `#cx_my_jira_issue` to list assigned issues

3. Use `/my_todo_list` to generate prioritized task list

Workflow 2: Code Review Context Gathering

1. Use `#cx_fetch_jira_issue` to get requirement details

2. Use `#cx_fetch_github_repository_code` to fetch related code files

3. Use `#cx_search_confluence` to find relevant documentation

Workflow 3: Bug Investigation

1. Use `#cx_fetch_jira_issue` to get bug report

2. Use `#cx_fetch_atlassian_attachment` to retrieve screenshots/logs

3. Use `#cx_search_github` to find related code patterns

Troubleshooting

Development & Customization

This tool is built on the Model Context Protocol SDK and can be extended with additional tools. The source structure supports:

For development: `npm run dev -- [arguments]`