Copilot cloud agent: connect to the Atlassian MCP server directly over HTTP

[playb0t]

Why:

Closes: #46357

The Atlassian MCP server is a remote server. Copilot cloud agent supports remote servers on this very page: "type": "http", url, headers, secrets via $COPILOT_MCP_*. The current example reaches the server through a local npx mcp-remote@latest process on the v1/mcp endpoint. Atlassian's API-token documentation configures clients with a direct url and an Authorization header on v2/mcp. Its README recommends v2/mcp while keeping v1 supported.

What's being changed (if available, include any code snippets, screenshots, or gifs):

• The Atlassian example moves from "type": "local" with command, args and env to "type": "http" with url and headers.
• The endpoint changes from https://mcp.atlassian.com/v1/mcp to https://mcp.atlassian.com/v2/mcp, the address in Atlassian's current documentation.
• The secret keeps its name and meaning: COPILOT_MCP_ATLASSIAN_API_KEY, the base64 of email:token. It is now referenced in the header value. This follows the substitution rule under "Remote MCP specific keys" and the in-string substitution of the Sentry example.
• One sentence is added to the intro, scoped to API token authentication: configure the server as a remote HTTP server. "API key" becomes "API token", matching the linked Atlassian page.

Sources: Atlassian, "Configuring authentication via API token"; the atlassian/atlassian-mcp-server README (endpoints and client snippets); this page's "Remote MCP specific keys" and "Variable substitution" sections.

I did not run this configuration inside Copilot cloud agent. The change follows the page's documented keys and Atlassian's published configuration. If header values accept only a whole substitution reference, the alternative is a secret that holds the full Basic <base64> value, referenced as "Authorization": "$COPILOT_MCP_ATLASSIAN_AUTH". Happy to switch on review.

Check off the following:

• A subject matter expert (SME) has reviewed the technical accuracy of the content in this PR. In most cases, the author can be the SME. Open source contributions may require an SME review from GitHub staff.
• The changes in this PR meet the docs fundamentals that are required for all content.
• All CI checks are passing and the changes look good in the review environment.

[github-actions]

How to review these changes 👓

Thank you for your contribution. To review these changes, choose one of the following options:

• Spin up a codespace
• Set up a local development environment

A Hubber will need to deploy your changes internally to review.

Table of review links

Note: Please update the URL for your staging server or codespace.

The table shows the files in the content directory that were changed in this pull request. This helps you review your changes on a staging server. Changes to the data directory are not included in this table.

Source	Review	Production	What Changed
copilot/how-tos/copilot-on-github/customize-copilot/configure-mcp-servers.md	fpt ghec	fpt ghec

Key: fpt: Free, Pro, Team; ghec: GitHub Enterprise Cloud; ghes: GitHub Enterprise Server

🤖 This comment is automatically generated.