[BUGFIX] sys_file record doesn't get flagged as delete

File is deleted by driver and deleted property of FileObject is set by
ResourceStorage but new state is not persisted.

Update deleted property in updateProperties array in FileObject and
persist change.

Fixes: #48336
Releases: 6.2, 6.1, 6.0
Change-Id: I6cac106dcf89125e0b98b8b12a03c0b3f56d484f
Reviewed-on: https://review.typo3.org/22024
Reviewed-by: Steffen Ritter
Tested-by: Steffen Ritter
[BUGFIX] Add advice to RTEmagic wizard

The update wizard that migrates RTE magic images relies on
sys_refindex for finding the magic images. There should be
a warning in the wizard description that users should be sure
their reference index is up to date.

Resolves: #49727
Releases: 6.1, 6.2
Change-Id: I7301a4a52174424655a76b58c7b7856f5f5209a2
Reviewed-on: https://review.typo3.org/22026
Reviewed-by: Wouter Wolters
Tested-by: Wouter Wolters