[BUG] Title: Atlassian remote MCP OAuth token always has empty scope, causing connection failure

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Description

After completing the OAuth flow for the Atlassian remote MCP server (https://mcp.atlassian.com/v1/sse), the stored token in .credentials.json always has "scope": "" (empty string). As a result, the MCP server rejects the
connection despite authentication appearing to succeed.

Steps to Reproduce

1. Add the Atlassian MCP server at user level:

claude mcp add --transport http --user atlassian https://mcp.atlassian.com/v1/sse

1. Run /mcp → select Atlassian → authenticate
2. Browser OAuth flow completes successfully
3. Claude Code reports "Authentication successful, but server reconnection failed"
4. Inspect ~/.claude/.credentials.json → mcpOAuth entry has "scope": ""
5. Restart Claude Code → /mcp still shows connection failure

Expected Behavior

OAuth scopes should be captured and stored after the authorization flow. The MCP connection should succeed after authentication.

Actual Behavior

• "scope": "" in stored token after every auth attempt
• /mcp shows "Authentication successful, but server reconnection failed"
• After restart: "Failed to reconnect to atlassian"
• Re-authenticating multiple times does not fix the issue

Environment

• Claude Code version: 2.1.71
• OS: Ubuntu (Linux 6.8.0)
• MCP config (~/.claude.json):

{
"type": "http",
"url": "https://mcp.atlassian.com/v1/sse"
}

• Stored token (redacted, ~/.claude/.credentials.json):

{
"serverName": "atlassian",
"serverUrl": "https://mcp.atlassian.com/v1/sse",
"accessToken": "...",
"expiresAt": 1773068958380,
"scope": "",
"clientId": "...",
"refreshToken": "..."
}

Additional Notes

The Atlassian server is reachable (returns HTTP 401 without auth). The issue is that the OAuth callback is not extracting or storing the granted scopes, so the token has no permissions when used against the MCP endpoint.
Clearing the token and re-authenticating multiple times does not resolve the issue.

What Should Happen?

MCP server authenticated and working.

Error Messages/Logs

Steps to Reproduce

1. Add the Atlassian MCP server at user level:

claude mcp add --transport http --user atlassian https://mcp.atlassian.com/v1/sse

1. Run /mcp → select Atlassian → authenticate
2. Browser OAuth flow completes successfully
3. Claude Code reports "Authentication successful, but server reconnection failed"
4. Inspect ~/.claude/.credentials.json → mcpOAuth entry has "scope": ""
5. Restart Claude Code → /mcp still shows connection failure

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.71

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

PyCharm terminal

Additional Information

_No response_