Issue Summary

The Atlassian Rovo MCP Server returns JSON-RPC error -32601: Method not found when MCP clients as IDE perform standard capability discovery calls (resources/list, resources/templates/list). While the tools capability connects successfully (40 tools load), MCP clients (Continue, Cursor) render the -32601 responses as persistent, non-dismissible red error banners, making a working connection appear broken.

Steps to Reproduce

1. Configure an MCP client (e.g., Continue IDE) to connect to the Atlassian MCP Server:

{
  "command": "npx",
  "args": ["mcp-remote", "https://mcp.atlassian.com/v1/mcp/authv2", - --resource]
}

1. Complete the OAuth authentication flow in the browser

1. Observe the IDE's MCP connection panel after successful authentication

Expected Results

• Connection shows as healthy with no errors

• 40 tools load successfully

• No error banners are displayed, since the connection is functional

Actual Results

The following errors are persistently displayed in the IDE:

MCP error -32601: Method not found (resources/list)
MCP error -32601: Method not found (resources/templates/list)

The IDE reports a "configuration error" state despite:

• Green connection indicator showing active

• 40 tools loaded and functional

• OAuth authentication completed successfully

This occurs because MCP clients perform capability discovery for all standard MCP capabilities (tools, resources, prompts) during initialization. The server does not implement resources or resource templates and returns -32601 instead of an empty successful response.

Workaround

Users can remove the -resource flag from their mcp-remote args if present. However, this only addresses cases where -resource was explicitly added — the base -32601 errors for resources/list and resources/templates/list still occur during standard client capability discovery even without the flag, as this is default MCP client behavior.