Claude Code Secretly Hoards 140+ Config Files Behind Your Back. Here's How to Take Control.

I've been using Claude Code for a week. Yesterday I peeked inside ~/.claude/ and found 140 items — memories, skills, MCP server configs, hooks — scattered across folders with names like -home-user-projects-my-app/. I didn't create most of them. Claude did. Every time I said "remember this" or installed a tool, Claude silently dumped files into whatever scope matched my current directory. A preference I wanted everywhere? Trapped in one project scope. A deploy skill that belongs to one repo? Leaked into global, contaminating every other project. The best part: I found three identical MCP server entries across different scopes because I'd added the same server while cd'd into different directories. Claude happily duplicated it each time without telling me. Why This Actually Hurts Your AI's Performance This isn't just messy — it's a technical problem. Every time Claude Code starts a session, it loads all memories, skills, and MCP configs from the current scope plus everything it inherits