store: MCP manager was writing to wrong config path - ~/.claude/.mcp.json instead of project .mcp.json

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

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