During my incarceration period in Windows, the biggest reason I used Ccleaner was to clean up the Registry.
Fortunately, Linux doesn’t have a Registry (a chest of dark secrets) to worry about.
Pudge
EDIT:
Since linux does not have a Registry, I agree with @Kresimir
Yes exactly. That is the biggest problem with Windows. Registry issues are common.
The closest thing to a registry in Linux maybe the dconf user file that stores tons of settings in GTK desktops. It’s not really a registry, but it does have a nice gui editor tool to poke around and change various settings.
I tried it today on a chrooted micro SD card
rm -rf /
didn’t work so I had to do
rm -rf / --no-preserve-root
I think it removed everything except proc (I think that is mounted by arch-chroot)
Here is the result
rm: cannot remove '/proc/143125/loginuid': Operation not permitted
rm: cannot remove '/proc/143125/sessionid': Operation not permitted
rm: cannot remove '/proc/143125/coredump_filter': Operation not permitted
rm: cannot remove '/proc/143125/io': Operation not permitted
rm: cannot remove '/proc/143125/uid_map': Operation not permitted
rm: cannot remove '/proc/143125/gid_map': Operation not permitted
rm: cannot remove '/proc/143125/projid_map': Operation not permitted
rm: cannot remove '/proc/143125/setgroups': Operation not permitted
rm: cannot remove '/proc/143125/timers': Operation not permitted
rm: cannot remove '/proc/143125/timerslack_ns': Operation not permitted
^C
[root@sra-odr /]# rm -rf
bash: /usr/bin/rm: No such file or directory
[root@sra-odr /]# rm -rf /
bash: /usr/bin/rm: No such file or directory
[root@sra-odr /]#
[root@sra-odr /]# pacman -Syy^C
[root@sra-odr /]# ls
bash: /usr/bin/ls: No such file or directory
[root@sra-odr /]#
Then there is always Bleachbit Very effective for cleaning up according to one former US polîtician 
didn’t Snowden recommend this as well?
I think Bleachbit mention Snowden on their page.