The above command just changed all files ownership to root (privileged user)
Hey uhm, are you sure? That seems wrong.
For me, the command removes read, write, and execute permissions of the user, and read and execute permissions for everyone else. Which would be expected.
chown would be the command to change ownership...
To run any app now, you need to open a new terminal and type sudo -E app-name &,
You could also try and fix the permissions by running sudo chmod -R u+rwX g+rX /home/user. That will fix all access permissions first of all. Then, you might have to fix execute permissions (but do this only on files that are meant to be executed!) using chmod +x path/to/file.
Solutions Be extra extra careful while running sudo commands
Yes. But you (as the owner) would not even have needed sudo for the chmod command to succeed. I think you might have just slightly misunderstood chmod's syntax. Your command as given means "recursively, remove the permissions 755 (you have a - in front of them!). It sounds like you probably wanted chmod -R 755 ... (without -, giving read/write/execute to the owner and read/execute to everyone else). But the descriptive notation above is probably easier to remember. Read the manpage maybe...
A pull request for that issue is open since April with no comments from the developers. Not a good sign :/
https://github.com/FossifyOrg/Clock/pull/62
EDIT: Looking further into it, the only merges and commits seem to be translations and GitHub metadata stuff, there has been no development since the fork :( - https://github.com/FossifyOrg/Clock/commits/master/