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MCP Optimization for Agents

MCP (Model Context Protocol) servers can make or break your agent performance. This guide helps you avoid common pitfalls.

The Problem: MCP Token Bloat

Every MCP server you install consumes context tokens before you even ask a question.

200K advertised context window
- 16K model overhead
- 16K harness overhead
= 176K USABLE

With typical MCPs installed:
- GitHub MCP: ~4K tokens
- Chrome MCP: ~5K tokens
- AWS Lambda MCP: ~40K+ tokens (!)
= Down to <100K usable

Real impact: With heavy MCPs loaded, you lose 28%+ of your context before doing any work.

The Rule: CLI > MCP

"Do not install the GitHub MCP server. Just prompt the LLM to use the GitHub CLI." - Geoffrey Huntley

Task MCP Approach CLI Approach Winner
GitHub issues GitHub MCP (~4K overhead) gh issue list CLI
Git operations Git MCP git status CLI
File search Custom MCP rg, fd CLI
API calls Custom MCP curl CLI

Why CLI wins:

  • Zero token overhead
  • Claude already knows these tools
  • No schema bloat

Audit Your Current Setup

Run /context in Claude Code to see token breakdown:

System tools: 16.7k tokens (8.4%)   ← Built-in
MCP tools:    45.0k tokens (22.5%)  ← Problem area

Look for mcp__ prefixed entries to identify culprits.

Config File Locations

Claude Desktop:

Windows: C:/Users/[USER]/AppData/Roaming/Claude/claude_desktop_config.json
Mac:     ~/Library/Application Support/Claude/claude_desktop_config.json

Claude Code:

~/.claude.json        (user config)
.mcp.json             (project config)

Minimal Config (Recommended)

Start with no MCPs, add only what you need:

{
  "mcpServers": {}
}

Then add only project-specific servers via .mcp.json in your project root.

Common Culprits

MCP Token Cost Alternative
GitHub MCP ~4K Use gh CLI
AWS Lambda MCP ~40K+ Use aws CLI
Chrome MCP ~5K Disable when not needed
Memory MCP ~2K Usually unnecessary

Quick Fixes

Disable Chrome MCP

In ~/.claude.json:

{
  "claudeInChromeDefaultEnabled": false
}

Remove GitHub MCP

Just delete it from config. Use gh CLI instead:

gh issue list
gh pr list
gh pr create

Switch Configs Based on Task

Keep multiple configs:

claude_desktop_config.minimal.json   # Daily use
claude_desktop_config.aws.json       # When debugging AWS
claude_desktop_config.full.json      # Rare, specific tasks

Best Practices Summary

  1. Start minimal - Empty MCP config by default
  2. Audit regularly - Run /context to check usage
  3. Prefer CLI - gh, aws, kubectl over MCP equivalents
  4. Load on demand - Switch configs for specific tasks
  5. Project-specific - Use .mcp.json for project needs

Learn More

For advanced MCP optimization including custom server development and token budgeting: