Automatically track per-file dependencies

This is enabled for platforms/compilers that support the -MMD
option, which creates a dependency file named out.d when compiling
to a file named out.o, only including local, not system headers.

The additional -MP option adds phony targets for all included
headers, to avoid having make error out due to "no rule to make
target foo.h" if a header is renamed/removed.

This makes sure that all the right files are rebuilt if a header
is changed, avoiding the need for a full rebuild if only a few
files are affected.