Move graph.h functions into graph.c

Move graph.h functions into graph.c

So we only need one copy in the final library, not one copy per time
used. Ensure all necessary includes are in place (especially to get the
right size of off_t each time it is compiled) by including "config.h" in
the new graph.c.

One small adjustment here makes the graph_free code more robust- ensure
we don't have invalid pointers after each iteration by looking at the
parents and children and adjusting accordingly.

Signed-off-by: Dan McGee <dan@archlinux.org>