MacOS – Permissions won’t let me delete a file on a shared school server

Permissions repair only affects folders and packages installed by apple and during software updates and it leaves most user folders alone.

You should be able to run it again to fix anything not correct. If there are still issues, you likely have a user definition corruption issue and might have to attack that head on. Which specific app it folder has these issues? Edit your question and this can also be edited once more detail is provided.

From debugging a different problem (which showed up as deny file-read-data in the Console, see the other answer), it seems that sandboxd prevents sandboxed applications from reading quarantined data, so I think you'd need to remove the attribute with: xattr -d com.apple.quarantine /path/to/file (see for instance https://superuser.com/a/28394/46794). You'd need to prefix the command with sudo if the file didn't belong to your user, but according to your info it does.

The other user reported that using a non-sandboxed application fixed the problem, and this would confirm that sandboxing is at fault.

An aside: When ls reports extended attributes with @ next to the permission field, you don't need ls -le file, but instead ls -l@ file.