Hang on, you say your autotools animosity derives from attempts to cross-compile? And you push *pkg-config*? pkg-config is *immensely* worse than autotools at cross-compilation: it barely supports it at all, and tends to cause silent horrible failures if it doesn't (picking up .pc files for entirely the wrong architecture, with no understanding of sysroots nor any of the other delicacies involved in cross-compilation).
Your claim that code generation is an amateur's tool is also laughable in the extreme.
As for resetting things, 'make distclean' is your friend (assuming you're either following the GNU Coding Standards or using Automake, which lets you follow them automatically).