I'm creating a Debian package for a piece of software that has no usable makefile at all. Should I put the building instructions into debian/rules or a separate Makefile? I'm tending towards the latter.
If I do create a separate Makefile, how do I properly include it in my source package?
If there's any actual building commands (rather than simply installation) to do, my instinct would be to treat the lack of a makefile infrastructure as a bug in the upstream distribution and patch it by providing a makefile in the Debian diff like I'd fix any other upstream bug. Be sure to feed your fix upstream.
However, if it just a matter of running a number of cp commands to get the various parts of the software into the right locations in the file system when building the package, then I'd just put those in debian/rules.