Fix make depend for things being built in subdirectories

Some makedepend mechanisms remove all directory information in the
target, so a dependency can looks like this:

ssl3_record.o: record/ssl3_record.c

However, that doesn't quite suit us, our Makefile has us build
record/ssl3_record.o rather than ssl3_record.o.

To clear this up, a change to util/clean-depend.pl takes care of this
case by looking up the original file in the dependencies and restoring
the directory information from it.

Reviewed-by: Ben Laurie <ben@openssl.org>