Cydia is a front end for an application called Aptitude.
Aptitude is an old and tried package manager, and my favorite from long before the iPhone was released.
If you install a terminal or SSH into your phone you can use this program directly, by typing aptitude and apt commands.
an example of this is
Code:
apt-get clean
which has the description "Erase downloaded archive files"
I am not entirely sure how often Cydia issues like this and similar commands, but at least you can do it your self if you really want to.