Yes, the tool takes that into account and transforms mcps/permissions/rules to different tool formats. Sadly some tools might not support fine-grained permissions (e.g. Codex) in which case a warning will be displayed but everything else will get transformed/symlinked. Additionally you can put per-tool overrides in ‘.ai/{codex/claude/cursor/etc.}/‘ if needed and lnai will automatically symlink those overrides to respective tools.