Makefile modification to compile with no warning and only the necessary files

[grypoB]

Reviewed the current Makefile and modified how the compilation was done to remove the following issues:

• The warnings due to the usage of wrong flags for compiling C++ (instead of C)
• Not all files would be recompiled each time but only the ones with their dependencies changed

For this, a new set of flags for C++ compilation was created, and the way headercheck.py (for RBSM communication) and fingerprint.py (for compilation time) are run during compilation was modified.

main.cpp was changed to clear some warning due to the presence of the new c++ flag -Wmissing-declarations (equivalent of the c -Wmissing-prototypes).

[ramensandwich]

Has this been tested and its output runs fine on the buggy?

[grypoB]

This branch has been merged into buckley-cpp-changes (see #463)