Use GNU autoconf and automake! They are your friends :) Automake examines C files, determines how they depend on each other, and generates a Makefile so the files can be compiled in the correct order. Autoconf permits automatic configuration of software installation, handling a large number of system quirks to increase portability..

Subclass Widgets to better organise your code. You should probably subclass your main Window at least. Then you can make your child Widgets and signal handlers members of that class.