Have you looked into debootstrap? It allows you to build a complete GNU/Linux system inside of another. I also dont think you use ./configure in this case directly, I could be wrong though. Debian/Ubuntu is supposed to have tools that detect which packages are needed for building. they are contained in the build-essential package.

This page might help:
http://www.debian.org/doc/manuals/maint-guide/build.en.html
and here:
http://wiki.debian.org/HowToPackageForDebian#Building_Debian_packages

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