Will crystl overwrite an existing AGENTS.md, CLAUDE.md, or MCP configuration?

It does not replace whole agent instruction files. The CLI primer is enclosed by crystl-cli markers, and crystl updates only that managed section while preserving the rest of the file. On ordinary gem open, an existing .mcp.json is left alone. Explicit MCP changes from Gem Settings update crystl-managed entries while preserving entries outside crystl’s catalog.