Folders Copilot CLI trusts without asking.
Copilot CLI keeps trusted folders in its own state file, config.json inside programs.github-copilot-cli.configDir, which it also uses for login and plugin state. These folders are merged into its trustedFolders list at activation, and the rest of the file is left alone. Folders trusted from inside Copilot CLI are kept, and removing a folder here does not untrust it.