app_loader Makefile: Add -d param to install call

This fixes the calls to make sure that the $(PREFIX)/lib and include
directories exist.

Signed-off-by: Frank Hunleth <fhunleth@troodon-software.com>
app_loader Makefile: clean up header file handling

Removed Makefile targets that would never be called and added the public
header files to the dependency list so that changes to them would
trigger .c file recompilation.

Signed-off-by: Frank Hunleth <fhunleth@troodon-software.com>