How do I restore permissions of my files?

edit

Please keep in mind, running these commands might mess up your system and you may lose all your data. Make a backup of everything right away before attempting anything further. If you choose to follow any of my advice below, you do so AT YOUR OWN RISK.

It looks like most files under /usr are still owned by root, so you do not need to mess with most of /usr. It seems like you actually ran chown on:

• /usr/lib/node_modules
• /usr/bin
• /usr/share

Taking a look at the chown man page (accessible via $ man chown) you will see the -R flag:

-R, --recursive
          operate on files and directories recursively

So to chown every file under /path/to/directory to be owned by user and to be part of group, you would run:

# chown -R user:group /path/to/directory

Of course, the question is, were all the files in those directories owned by root before your ran the command in the first place.

Running the find command on my Fedora 24 system looking for any file or directory in /usr/bin and /usr/share that is not owned by root (I don't have a /usr/lib/node_modules directory because I don't have Node installed), I get these results:

# find /usr/bin /usr/share \! -user root -print
/usr/share/polkit-1/rules.d

That means the only file or directory that is not owned by root in these two directories on my system is the directory /usr/share/polkit-1/rules.d. Of course, there is no guarantee your system should be the same.

The directory /usr/share/polkit-1/rules.d should be owned by user polkitd, as you can see here:

# ls -l /usr/share/polkit-1/
total 8
drwxr-xr-x. 2 root    root 4096 Oct 15 18:36 actions
drwx------. 2 polkitd root 4096 Oct 15 18:25 rules.d

(There are files under /usr/share/polkit-1/rules.d but they are owned by root.)

So, assuming your /usr/bin and /usr/share were the same as mine in terms of file permissions (which, again, may not be true), reversing your original command could be done via:

# chown -R root /usr/bin
# chown -R root /usr/share
# chown polkitd /usr/share/polkit-1/rules.d

Notice that I am using # chown -R root /usr/bin and NOT # chown -R root:root /usr/bin. The second root in the command refers to the group. In your original command you did not modify the groups so there is no need to reverse group ownership.

I can't say anything about the original ownership of /usr/lib/node_modules so I'm skipping that.

Good luck!