Coot will occasionally ask you to clear up the coot-backup directory. You can adjust the behaviour in a number of ways:
(define *clear-out-backup-run-n-days* 3) will run the backup clearance every 3 days (the default is every 7).
(define *clear-out-backup-old-days* 1) will clear out files older then 1 day (rather than the default 7 days).
(clear-backups-maybe)
So, if you wanted to clear out everything more than 1 day old, every time, without Coot asking you about it:
(define *clear-out-backup-run-n-days* 0)
(define *clear-out-backup-old-days* 1)
(define (clear-backups-maybe)
(delete-coot-backup-files 'delete)
(coot-real-exit 0))