Atlassian Rovo MCP Server connector fails auth probe with HTTP 400, blocking all Atlassian tool calls #5118

Summary

The built-in Atlassian Rovo MCP Server connector is failing its authorization probe with an HTTP 400 Bad Request, and every Atlassian tool call (Jira/Confluence) returns 401 Unauthorized as a result. This is blocking an in-progress agent session that needs to edit a Confluence page.

Environment

• Copilot CLI app version: 1.0.94-3
• Platform: macOS
• MCP server: Atlassian Rovo MCP Server (built-in/first-party connector, shown in Settings → MCP Servers as "Custom configuration")

Steps to reproduce

1. In an active session, call any Atlassian Rovo MCP tool, e.g. atlassianUserInfo or getAccessibleAtlassianResources.
2. Observe the tool call fails.
3. In the app UI, an authorization check also fails with a toast: "Could not check authorization" — WsCommandError: invalid argument: MCP server probe returned HTTP 400 Bad Request (screenshot captured by user in session).

Expected behavior

Tool calls to the Atlassian Rovo MCP Server should succeed (as they did earlier in the same session — multiple successful Confluence page reads/edits/creates occurred before this started).

Actual behavior

• atlassianUserInfo → {"code":401,"message":"Unauthorized"}
• getAccessibleAtlassianResources → {"error":true,"message":"Failed to fetch accessible resources: 401","statusCode":401}
• getConfluencePage (for a previously-accessible page) → 404 Not Found (likely a downstream symptom of the same broken auth state)
• The in-app connector health probe itself fails with HTTP 400 Bad Request (not 401), suggesting the probe request the client is sending is malformed or rejected before Atlassian even evaluates the token.

Troubleshooting already attempted (did not resolve)

• Removed and re-added the Atlassian MCP plugin/connector 3 times, each time completing sign-in successfully.
• Fully restarted the GitHub Copilot CLI app.
• Removed and re-added the app sign-in itself.
• Disconnected from a corporate VPN (Haivision VPN) in case it was interfering with the probe request — no change.
• Connector shows as enabled/green-check in Settings → MCP Servers → Atlassian Rovo MCP Server throughout.
• Retried the failing tool call repeatedly over ~15 minutes; consistently 401.

Since re-authentication (multiple times, including a full app restart, re-sign-in, and VPN disconnect) did not change the outcome, and the in-app probe reports a 400 (not a 401/expired-token-style error), this looks like a server-side or connector-level bug rather than a user credential/network issue.

Impact

Any session relying on the Atlassian Rovo MCP Server for Jira/Confluence work is fully blocked until this is resolved.