[BUG] Atlassian MCP Server Tools Not Available in Claude Code 2.0.10 Conversations Despite Successful Connection

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?

Environment:

• Claude Code Version: 2.0.10
• Platform: macOS 15.6.1 (24G90)
• Architecture: ARM64 (Apple Silicon)
• Node.js: v24.9.0
• mcp-remote version: 0.1.29
• MCP Server: Official Atlassian Rovo MCP Server

(https://mcp.atlassian.com/v1/sse)

Configuration:
{
"atlassian": {
"type": "stdio",
"command": "npx",
"args": ["-y", "mcp-remote", "https://mcp.atlassian.com/v1/sse"],
"env": {}
}
}

Issue Description:
The Atlassian MCP server connects successfully and OAuth authentication
completes, but MCP tools are not exposed to Claude in conversation
sessions.

Evidence of Successful Connection:

1. claude mcp list shows: ✓ Connected
2. OAuth tokens are cached in ~/.mcp-auth/mcp-remote-0.1.29/
3. mcp-remote proxy establishes successfully via SSE transport
4. No connection errors in logs

Problem:
Despite successful connection, when asked to "list my recent Jira
issues" or perform any Jira/Confluence operations, Claude reports not
having access to any Atlassian MCP tools.

Expected Behavior:
MCP tools from the Atlassian server should be automatically available in
conversations for Claude to use (similar to how it works in Claude
Desktop/Claude.ai).

Related Issues:

• #2682: MCP Tools Not Available in Conversation Interface Despite

Successful Connection

• #3426: Claude Code fails to expose MCP tools to AI sessions
• #3279: MCP server loses connection
• #1611: MCP servers fail to connect despite correct configuration

Additional Context:

• This is the official Atlassian Rovo MCP Server recommended by

Atlassian

• The same server works in Claude Desktop according to Atlassian

documentation

• Issue affects stdio-based MCP servers with OAuth authentication
• Tools should be discoverable but are not being exposed to the AI

session

What Should Happen?

Please investigate why MCP tools are not being exposed to Claude Code
conversation sessions despite successful server connection and
authentication.

Error Messages/Logs

Steps to Reproduce

Run: claude mcp add --transport stdio atlassian npx -- -y mcp-remote
https://mcp.atlassian.com/v1/sse

1. Complete OAuth authentication (tokens cached successfully)
2. Verify connection: claude mcp list shows ✓ Connected
3. Start conversation and ask Claude to use Atlassian tools
4. Claude reports tools are not available

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.0.10

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_