Got rid of extra subdirectory

I didn't like having a directory containing just a README file and another
directory.

Signed-off-by: Morten Hustveit <morten.hustveit@gmail.com>
Use dependency graph in Makefile

The original Makefile was basically just a list of commands split into multiple
targets, and might just as well have been a shell script.

Signed-off-by: Morten Hustveit <morten.hustveit@gmail.com>