I just upgraded my system from Lenny to Squeeze following the steps posted here. I followed all the steps using apt-get (in the upgrade from Etch to Lenny i used aptitude as suggested) and the upgrade went fine.

In the daily routine I use aptitude to maintain the system up to date and I really like the automatic handling of unused packages, so if I install package A that depends on B when I remove A, B is removed too keeping my system clean.

My question is the following: do apt-get and aptitude share the automatic handling of packages? I don't think so, because I found a lot of packages not marked as Auto in aptitude after the upgrade via apt-get.

Am I right? How can I fix this in automated way if the answer is yes?