To package applications as Debian packages for personal use, I need to know what are their dependencies.The auto-apt command installs the dependencies of a ./configure script automatically.  aut-apt has an option to run a simulation, and my understanding is that such simulation will let you know what packages would be installed.  However, as far as I can see, auto-apt will not tell you what dependencies are already installed (because you installed them before for some other software).
Detecting `.configure` dependencies in Debian
debian;configure;deb
The usual way to do this is to start in a clean/minimal chroot. Alternatively, when you have constructed a list of dependencies, check the correctness of the list in a clean/minimal chroot. There are tools like schroot, sbuild, pbuilder, cowbuilder etc. that can help in creating and managing such a chroot.