0.5.3: MCP initialize fails with "name 'LLM_SYSTEM_PROMPT' is not defined" — stdio server unusable #1451

Summary

codegraphcontext 0.5.3 cannot complete the MCP initialize handshake over stdio. Every initialize request returns a JSON-RPC internal error, so no stdio MCP client can connect (Claude Code, Cursor, etc.). 0.5.2 is unaffected — this is a regression introduced and released on the same day.

{"jsonrpc": "2.0", "id": 1, "error": {"code": -32603, "message": "Internal error: name 'LLM_SYSTEM_PROMPT' is not defined"}}

Reproduction

pip install codegraphcontext==0.5.3
echo '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"t","version":"1"}}}' \
  | cgc mcp start

Observed:

Starting CodeGraphContext Server...
MCP Server is running. Waiting for requests...
{"jsonrpc": "2.0", "id": 1, "error": {"code": -32603, "message": "Internal error: name 'LLM_SYSTEM_PROMPT' is not defined"}}

Expected: an initialize result containing serverInfo and instructions.

Root cause

src/codegraphcontext/server.py references the module-level LLM_SYSTEM_PROMPT when building the initialize response, but no longer imports it:

• L19: from .prompts import build_system_prompt
• L808: "instructions": LLM_SYSTEM_PROMPT,

Introduced by c9a9f7e ("feat: Add cgc prompt command for custom LLM prompts (#583)", #613), which changed the import from LLM_SYSTEM_PROMPT to build_system_prompt and left the L808 reference in place.

Both names are needed — build_system_prompt() is called at L795, and LLM_SYSTEM_PROMPT is still used at L808.

Scope

• The initialize handler at L793 is the only one and is unconditional, so the failure is total for stdio — not intermittent or config-dependent. The server starts and logs normally, which makes it look healthy.
• The SSE transport (api/mcp_sse.py) does not reference either symbol and is unaffected. That is plausibly why this got through.
• No test covers the initialize handshake — tests/integration/mcp/test_mcp_server.py exercises tool routing only.

Affected versions

Verified by grepping server.py in each published wheel:

main currently carries the bug as well.

Fix

One line:

from .prompts import LLM_SYSTEM_PROMPT, build_system_prompt

PR follows, with a regression test that drives _run_loop with a real initialize request (fails before the fix with the exact error above, passes after).

Workaround meanwhile: pin codegraphcontext==0.5.2.

Environment

• codegraphcontext 0.5.3 (pip)
• Python 3.13, macOS 15 (arm64)
• Client: Claude Code (stdio transport)