Useful commands

List installed packages having Recommended dependencies which are not installed:

aptitude search '~i ~BRecommends'

List recommended dependencies which are not installed, related to installed packages:

aptitude search '~RBRecommends: ~i' 

Save the list of manually installed packages:

aptitude search '~i !~M' -F '%p' > packages.lst

Install packages from the above list:

aptitude install $(cat packages.lst)

Check altered packages

Altered packages can be found with the debsums tool:

aptitude install debsums

List altered files:

debsums --changed

List altered files + configuration files:

debsums --changed --all

Use dpkg to find the package related to a given file:

dpkg -S /path/to/file