Makefile fixes and cleanups

- Distinguish between CC/CFLAGS, CPP/CPPFLAGS and CXX/CXXFLAGS.
  Do not store compiler flags in CPPFLAGS, which is for preprocessor,
  and do not try to link files using a preprocessor.
- Use COMMON_FLAGS for flags that are for both C and C++.
- Drop -m64 flag which is wrong on 32-bit systems.
- Use $(MAKE) instead of make, so that parallel building works.