Hey @Yann_Baelli,
Building on @AllIN’s split: for prefs that should apply to every Cloud Agent run, put them in User Rules (Cursor Settings → Rules). They’re account-scoped, nothing to commit, and Cloud Agents pick them up - see best practices.
For different private rules per team/repo without committing: no first-class surface yet. Keep shared conventions in the repo, personal cross-repo prefs in User Rules, and small repo-specific constraints in that run’s launch prompt. If you need fuller private file rules, a custom Cloud Agent environment can install them outside the checkout and expose them at /.cursor so discovery finds them (layout reference).
No timeline to share on a dedicated private per-repo surface. We’ll keep tracking interest here - if others want the same, chime in.