When you create a program or library for Linux you may need GNU auto tools (automake, libtool, configure etc) to detect environment settings. These tools may become a pain in the ass when you start with them (and probably later too). Something I recommend that has worked for me is to create a bootstrap.sh script like this:
#!/bin/bash autoheader libtoolize --force --copy aclocal automake -f --copy --add-missing autoconf
The –force –copy for libtoolize and -f –copy –add-missing for automake will help you to not depend on symbolic links that are created by libtoolize and automake and that may not be present on the target machine where your code will be built.
I suppose there is a valid reason to not use those options, but for me, that saved me a lot of hassle.