Guys, I don't know whether this information deserves a new topic but yesterday I've found a way to clean the N900 rootfs that worked fine on my device. Please handle this information with care, since I've read about people running ubuntu or debian who got the system erased by this command.
I've typed this (as root):

apt-get autoremove

my free rootfs increased by 8% but before I recommend to try this:

apt-get --simulate autoremove

this command simulates the autoremove action so, you can check the output in order to be sure that only useless packages will be removed.

Try also: apt-get moo

This won't help you in rootfs cleaning but is absolutely safe! ;-)

I accidentally extracted NITDroid to my root directory (for got a cd /And). Is this a good way to clean out the excess files?

ive done the exact same thing grrrrr lol

how to remove useless config.files ? the packages i have already uninstalled through HAM ,but still i can see some of their files in Filebox..
how to get rid of all of them ?
how to do this safely ?

Try something like:

it says ..
''Eackage couldnt find, <app> not installed so not removed ''
nothing happened i guess,still files can be seen in filebox,rootfs hasnt freed too.

Yes, use purge for installed apps...

thanks but what about those config.files appearing in the filebox,i already have uninstalled those apps through HAM..so any solution for that buddy ?

dpkg -l | grep ^rc (this command will show you a list of apps configuration files still left in the system from uninstalled app)
dpkg --purge <appname> (This will remove it)

so what you both did to solve this because I also did this but now can't solve this problem