Atlassian MCP: headless sessions don't reuse existing mcp-remote auth tokens

Problem

When Claude Code runs in a headless/agent context (e.g. Atlas orchestrator), the built-in HTTP MCP client for Atlassian (https://mcp.atlassian.com/mcp) requires an interactive OAuth flow to authenticate. It does not check for or reuse existing mcp-remote tokens cached in ~/.mcp-auth/ from prior interactive sessions.

This means:

• A user can be fully authenticated via mcp-remote in their TUI session
• An agent session running the same .mcp.json config gets no Atlassian tools at all
• The workaround is to manually switch the config from type: http to command: npx mcp-remote@latest and restart — which then correctly reuses the cached token

Expected Behavior

The built-in HTTP MCP client should detect and reuse valid mcp-remote tokens from ~/.mcp-auth/ when the server URL matches, or at minimum document that headless sessions require the mcp-remote stdio approach.

Workaround

Replace the HTTP-type server entry with the stdio mcp-remote approach:

"atlassian": {
  "command": "npx",
  "args": ["mcp-remote@latest", "https://mcp.atlassian.com/v1/mcp"]
}

This reuses the existing cached auth and works in headless sessions.

🤖 Generated with Claude Code