# Claude Desktop - Clean Config Reference
**Date:** 2026-02-09
**Status:** Working — timeouts resolved
## Problem
Claude Desktop was experiencing persistent timeouts due to ~40+ tool sources loading across three layers (Connectors, Desktop Extensions, and Developer config). Each tool source injects schema definitions into the context window before the user types anything.
## Root Cause
Duplicated and excessive tool sources across:
- **Connectors** (cloud, managed by Anthropic)
- **Desktop Extensions** (local, managed in app UI)
- **Developer config** (`claude_desktop_config.json`, manual JSON)
All three inject tool definitions identically. Duplicates = double the payload for the same service.
<!-- atomicity: 1 idea ✓ -->
## Key Rule
- If a **Connector** exists → use that (lightest, works everywhere)
- If no Connector but a **Desktop Extension** exists → use that (easier to manage)
- **Config file** → only for tools that don't exist in the other two places
## Clean Config File
Only two entries should be in `claude_desktop_config.json` — tools that have no Connector or Extension equivalent:
```json
{
"globalShortcut": "Alt+C",
"mcpServers": {
"obsidian": {
"command": "mcp-obsidian",
"args": ["/Users/crobertson/no-icloud/2nd Brain"],
"env": {}
},
"wordpress-trac": {
"command": "npx",
"args": [
"mcp-remote",
"https://mcp-server-wporg-trac-staging.a8cai.workers.dev/mcp"
]
}
},
"preferences": {
"quickEntryDictationShortcut": "capslock",
"localAgentModeTrustedFolders": [
"/Users/crobertson/no-icloud/2nd Brain",
"/Users/crobertson"
],
"coworkScheduledTasksEnabled": false,
"sidebarMode": "chat"
}
}
```
## What Was Removed from Config
| Removed | Reason |
|---|---|
| `github-official` | GitHub Connector handles this |
| `filesystem` | Desktop Extension handles this |
## Duplicates Resolved
| Service | Was In | Kept |
|---|---|---|
| GitHub | Config + Connector | Connector |
| Figma | Extension + Connector | Connector |
| Atlassian | Custom MCP + Connector | Connector |
| Filesystem | Config + Extension | Extension |
## Extensions Disabled
| Extension | Reason |
|---|---|
| Control Chrome | Redundant with Claude in Chrome + Desktop Commander |
| Control your Mac | Redundant with Desktop Commander |
| Figma | Figma Connector covers this |
## Connectors Disconnected
Removed cloud connectors that weren't actively used — each loaded tools into every conversation:
- AWS Marketplace
- Benevity
- Indeed
- PubMed
- Scholar Gateway
- Learning Commons Knowledge Graph
- Play Sheet Music
- Udemy Business
## Troubleshooting History
- **Dec 2025:** Initial freezing issues
- **Jan 10, 2026:** Compaction error identified as Opus 4.5 bug
- **Jan 21, 2026:** Cache clearing
- **Jan 26, 2026:** Context size error on new chat — identified MCP overload
- **Feb 5, 2026:** Timeout testing
- **Feb 9, 2026:** Full audit and cleanup — **timeouts resolved**
## If Timeouts Return
1. Check if new connectors or extensions were added
2. Count total tool sources across all three layers
3. Aim for ~10 total active tool sources max in Desktop Chat
4. Config file should stay at max 2-3 entries (Claude Code config can be heavier)
## Links
- [[CLAUDE]] — companion operational reference for the separate Claude Code configuration
- [[3. Resources/Permanent Notes/Tool-Interface Choice Shapes Agent Architecture More Than Model Choice]] — applies-in: duplicated always-loaded MCP schemas show how interface configuration consumes context and affects reliability before model choice matters
- Chat: https://claude.ai/chat/49fca0cd-9313-4607-88f7-3e090f1807cf (original troubleshooting)
- Chat: https://claude.ai/chat/48790822-8239-46be-beab-756fb476492c (MCP overload identified)
- [[3. Resources/MOCs/AI Agent Safety MOC]] — applies-in: the MOC lists this note under Bounded action & access control.