The /migrate command's --yes flag imports only user-level items that have no ⚠ warning. Items flagged as requiring review — such as commands with shell exec (!{cmd}), MCP servers with repo-authored configs, or permission-mode escalations — are held back and must be reviewed individually via the terminal picker (claude migrate without --yes). Project-level items from .codex/ or .gemini/ in your repo are always held back in --yes mode because project config can be authored by anyone with write access to the repository.