mpy-cross: Make build independent of extmod directory.

mpy-cross doesn't depend on any code in the extmod directory so completely
exclude it from the build (extmod may still be scanned for qstrs but that
is controlled by py/py.mk).  This speeds up the build a little, and
improves abstraction of this component.

Also, make -I$(BUILD) take precedence over -I$(TOP) in case there are stray
files in the root directory that would be picked up.