Yes. I found this quickly after wrapping codex in a launcher that uses bubblewrap to exclude certain files and directories based on a config file at the project root. My best solution so far is to also include instructions for the agent that explain that it is not allowed to see certain files, and that their inaccessibility is not an error, and that it must not attempt to access them through other means (e.g. via git history, etc.).

This has been a major improvement, but it's not foolproof.