[TASK] Remove sys_file.deleted flag and it's usage

This also fixes the 'Uncaught TYPO3 Exception #1317178604
No file found for given UID.' that appears when some sys_file
entries have a deleted flag set by mistake.

Resolves: #51562
Releases: 6.2, 6.1, 6.0
Change-Id: Id23636d2732f3562b8a155025656b26041c9a4e2
Reviewed-on: https://review.typo3.org/23748
Reviewed-by: Stefan Neufeind
Tested-by: Stefan Neufeind