Partial undo of "Makefile: Streamline directory creation"

Commit c964d962 changed the way we create directories, by two things:

- unifying all dependencies and ad-hoc directory creation into a
  single target (all_dirfiles)
- changing how directories are created from a stamp file to .dir files
  in each directory

The first item is a very good one, but the second item is debatable:
there's no per-se advantage of .dir files versus a single one,
top-level, since both the .dir file and stamp-directories creation are
depending on Makefile, which is the only one which can introduce new
directories.

On the other hand, moving back from .dir files to stamp-directories
has an advantage: "make -d | wc -l" does from ~8.7K lines to ~5.3K
lines, because we eliminate the many .dir files and their multiple
implicit and explicit dependencies (the %/.dir files fall under
multiple patterns).

Signed-off-by: Iustin Pop <iustin@google.com>
Reviewed-by: Guido Trotter <ultrotter@google.com>