Repro:

1. gbrain serve (stdio MCP server, no flags)
2. From MCP client (Claude Code), call mcp__gbrain__whoami

Expected: {transport: "local", scopes: []}

Actual:

{
  "error": "unknown_transport",
  "message": "whoami called over a remote transport that did not thread ctx.auth. This is a transport bug — every remote call site must populate ctx.auth or set ctx.remote === false."
}

Other tools work fine over the same stdio transport — find_orphans, takes_list, sources_list, get_stats, list_pages all return correct responses. Only whoami mis-detects the transport.

Likely cause (from quick grep on src/mcp/server.ts):

• Line 36 sets remote: true (HTTP server context)
• Line 58 sets remote: false (stdio context)

The whoami handler probably checks ctx.remote === true first and bails into the unknown_transport branch before reaching the local-shape return — OR the stdio entry point doesn't actually reach line 58 in some code path.

Environment: gbrain v0.28.6 (commit b325f28) / Bun 1.3.13 / Linux (Ubuntu 22.04, Vertex AI ADC fork) + Windows 11 client. Both clients exhibit the same error over their respective stdio MCP server.

Happy to PR a fix if you confirm the diagnosis direction.