Paul, thank you for your support.
Actually, I'm not sure the Arduino way of compiling a sketch is the most adequate way with so many under-the-hood hidden processes...
The Arduino IDE is lacking a critical feature more powerful MCUs —and thus larger projects— call for: debugging. Only Texas Instruments offers the Arduino-based Energia framework with the debugging tools from Eclipse-based Code Composer Studio 6.
So why not to focus your makefile + utility on a standard IDE-friendly project?
I know that "developing an Arduino sketch is not programming" but let's stop the fairy tales and face the reality: avoiding any reference to C++ makes portability and scalability very difficult to achieve, when the framework is strong enough for large project.