I did 2 things: installed this pack of new light-themes http://www.omgubuntu.co.uk/2017/05/install-improved-ambiance-gnome-theme (which is for 16.10 and 17.04, and I'm on 16.04, I haven't noticed it was incompatible) and updated mesa drivers by adding their ppa and running dist-upgrade.
After reboot the clock indicator has disappeared, nautilus is displaying like in gnome, with csd (with ubuntu theme's black corners), desktop icons became enlarged, only "files" section is in global menu, and right click menu wouldn't display some sections, leaving blank space (you can press it, it would work but no text).
After running sudo apt remove light-themes=16.10+17.10.20170515.1-0ubuntu1 and installing 14.04+16.04.20160415-0ubuntu1 it solved only the right click menu problem. Does anybody know what may have caused these problems and how to fix them?
Upd: Running sudo ppa-purge ppa:ubuntu-x-swat/updates returns:
Updating packages lists
W: The repository 'http://download.opensuse.org/repositories/home:/Horst3180/xUbuntu_15.04 Release' does not have a Release file.
W: The repository 'http://ppa.launchpad.net/hamish-twaddle/ppa/ubuntu xenial Release' does not have a Release file.
W: GPG error: http://download.opensuse.org/repositories/home:/Horst3180/xUbuntu_16.04 Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 5A7D1D38BEB6D886
W: The repository 'http://download.opensuse.org/repositories/home:/Horst3180/xUbuntu_16.04 Release' is not signed.
E: Failed to fetch http://download.opensuse.org/repositories/home:/Horst3180/xUbuntu_15.04/Packages 404 Not Found
E: Failed to fetch http://ppa.launchpad.net/hamish-twaddle/ppa/ubuntu/dists/xenial/main/binary-i386/Packages 404 Not Found
E: Some index files failed to download. They have been ignored, or old ones used instead.
Warning: apt-get update failed for some reason
Upd2:
W: The repository 'http://download.opensuse.org/repositories/home:/Horst3180/xUbuntu_15.04 Release' does not have a Release file.
N: Data from such a repository can't be authenticated and is therefore potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: The repository 'http://ppa.launchpad.net/hamish-twaddle/ppa/ubuntu xenial Release' does not have a Release file.
N: Data from such a repository can't be authenticated and is therefore potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: GPG error: http://download.opensuse.org/repositories/home:/Horst3180/xUbuntu_16.04 Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 5A7D1D38BEB6D886
W: The repository 'http://download.opensuse.org/repositories/home:/Horst3180/xUbuntu_16.04 Release' is not signed.
N: Data from such a repository can't be authenticated and is therefore potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration details.
E: Failed to fetch http://ppa.launchpad.net/hamish-twaddle/ppa/ubuntu/dists/xenial/main/binary-i386/Packages 404 Not Found
E: Failed to fetch http://download.opensuse.org/repositories/home:/Horst3180/xUbuntu_15.04/Packages 404 Not Found
E: Some index files failed to download. They have been ignored, or old ones used instead.