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claude-memory/graph/fixes/mcp-manager-was-writing-to-wrong-config-path-claudemcpjson-i-b3c2d4.md

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id type title tags importance confidence created updated
b3c2d454-3b8e-4d3d-b24c-6241f12d03e6 fix MCP manager was writing to wrong config path - ~/.claude/.mcp.json instead of project .mcp.json
mcp
claude-code
mcp-manager
fix
configuration
0.9 0.8 2026-02-20T03:52:57.247423+00:00 2026-02-20T03:52:57.247423+00:00

Problem

The mcp-manager skill's mcp_control.py was reading/writing ~/.claude/.mcp.json, but Claude Code does NOT read that file. Claude Code reads MCP config from two locations:

  1. Global: ~/.claude.json → mcpServers key (always-on MCPs like cognitive-memory)
  2. Project: <project-root>/.mcp.json → mcpServers key (on-demand MCPs)

This meant n8n-mcp was correctly configured in ~/.claude/.mcp.json but never loaded by Claude Code, even after multiple session restarts.

Root Cause

The original mcp_control.py had hardcoded:

MCP_CONFIG = CLAUDE_DIR / ".mcp.json"  # ~/.claude/.mcp.json - WRONG

Fix

  1. Updated mcp_control.py to auto-detect project root via git rev-parse --show-toplevel and write to <project-root>/.mcp.json
  2. Added GLOBAL_CONFIG constant pointing to ~/.claude.json for reference
  3. Cleaned up stale MCP registry (removed Daniel Miessler's MCPs: httpx, naabu, apify, brightdata, Ref, stripe, content, daemon, Foundry)
  4. Added n8n-mcp to the registry
  5. Updated SKILL.md to document correct config locations
  6. Also found the project-level .mcp.json at /mnt/NV2/Development/claude-home/.mcp.json had "mcpServers": {} which was overriding global config

Key Lesson

Claude Code MCP config hierarchy:

  • ~/.claude.json → global, always loaded
  • <project>/.mcp.json → project-specific, merged with global
  • ~/.claude/.mcp.json → NOT USED by Claude Code (was a mistake)