Does opening an existing folder as a gem modify its files?

It can create or update a small set of user-controlled integration files. crystl ensures .crystl/.gitignore exists, may create .mcp.json from your enabled MCP catalog when that file is absent, and may maintain the marked crystl CLI section in agent instruction files when tell agents about the crystl CLI is enabled. If a project has MCP servers and MCP auto-trust is enabled, crystl may also merge the trust flag into .claude/settings.local.json. It does not initialize Git or create commits merely because the folder was opened.