Huygens, as far as I know and can see from the code, computer-janitor
does remove only the packages it shows. Could you send the
/var/log/dpkg.log file from your computer, and attach it to this bug?
** Changed in: computer-janitor (Ubuntu)
Status: New => Incomplete
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Computer Janitor wiped out most of my packages
https://bugs.launchpad.net/bugs/345939
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