Resetting user permissions to their default mode
Here's the tentative solution I have found to my own problem:


print initial state: ls -l
remove ACL permissions: chmod -R -N /Users/fr/
equalize all permissions: chmod -R 755 /Users/fr/
rebuild Spotlight index: sudo mdutil -E /
print new state: ls -l


The -N option, which is well hidden in the man chmod documentation but mentioned here, removes the + sign that indicate ACLs, just like @ indicates a hidden file extension or a custom icon (as far as I can tell). Using Repair Utilities on ACLs should have done that but did not.

By using chmod with the 755 mode, I lost all custom permissions in the process, but did not need any. Rebuilding the Spotlight index then guarantees that all files get properly indexed. That solution worked, through without explaining how the initial problem emerged.