Codex_CLI-Atlassian MCP.md

Atlassian MCP for Codex CLI on Ubuntu

1. Prerequisites

• codex installed and working (codex --version)
• Node.js + npm/npx installed (node -v, npx -v)
• Atlassian Cloud access (Jira/Confluence) with browser login available

2. Configure Codex

Edit ~/.codex/config.toml and add:

[mcp_servers.atlassian]
command = "npx"
args = ["-y", "mcp-remote@latest", "https://mcp.atlassian.com/v1/mcp"]
startup_timeout_sec = 90

Validate config:

codex mcp list
codex mcp get atlassian

Expected:

• atlassian appears as enabled
• transport is stdio
• Auth: Unsupported is expected for this mcp-remote setup

3. Test the Integration

Run:

codex exec --skip-git-repo-check "Use atlassian MCP and list available tools."

Expected:

• mcp: atlassian ready
• tool call succeeds (for example getAccessibleAtlassianResources)
• tool list is returned (Jira + Confluence tools)

4. Functional Test (Real Query)

Example:

codex

Then prompt:

The Atlassian MCP was just installed. Use the Atlassian MCP to test and search for any topic. 

Expected:

• search returns matching Confluence/Jira results
• fetch can open specific page/issue ARIs
• returned data matches your Atlassian permissions

5. Troubleshooting

• Startup timeout: increase startup_timeout_sec (for first-time npx bootstrap).
• If auth/session is stale: remove old ~/.mcp-auth/mcp-remote-* cache and retry.
• If org policy blocks access: verify Atlassian domain allowlist and site permissions.