@runequestor: Which ones? linux, or window-manager? The hidden folders should have .dot folders for all
the window-managers that are installed.
Which filemanager , and which distro? thunar, pcmanfm, nautilus, dolphin, konqueror, rox-filer
are among many filemanagers. For access from a root prompt, some new distros now require
a dbus-launch preface:
[root@localhost username] #dbus-launch konqueror etc to launch certain apps
These are typical folders
cd /usr/bin
cd /usr/share
cd /home/username/.local
cd /etc
Cheers