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My supervisor sat with me and did many modifications.
1) He deleted all the copied files to home directories manually
2) Since I used the root. Somehow all users folders permissions changes to root. So He changes user folder one by one to Sudo group
I thought everything is fixed. Now all users are facing issues with login, sending files, and accessing their folders. How can I figure the right permissions for each user?
Since the only thing you want to fix is permissions, I would just LOOK at the backup, and change the permissions on the necessary directories to match. If you copy the backup and replace the current files, anything your users have written, modified, etc. in the last couple of weeks will be gone.
Just to make sure I will not make something wrong again:
I will perform the following:
1) ls -id foldername "to check permission"
Result should be something like "drwx------+ 3 Al staff 102 May 29 2014 movies"
2) chmod foldername 700 "700 is equal to rwx------ this will include subfolders"
3) Repeat the process to all folders
Please confirm or correct me if anything is wrong?