Self-hosted runners now skip re-copying already-synced skills into session containers, and exclude daemon/agent-memory folders
When a self-hosted runner prepares a session container, it copies over a snapshot of the host's ~/.claude configuration directory. That snapshot now leaves out dotfiles in general, plus any paths starting with daemon or agent-memory, and checks a new bookkeeping file to avoid re-copying skills that were already synced in from an organization.
If that bookkeeping file can't be read or is malformed, the runner seeds no skills into the session at all, and logs a warning telling the operator to delete the stale file.
This avoids duplicating skills that are already managed centrally by an organization, and keeps daemon and memory state out of session snapshots where it doesn't belong. The warning matters because a corrupted bookkeeping file silently disables all skill seeding until it's cleaned up.