Fix the update target and remove duplicate file updates

We had updates of certain header files in both Makefile.org and the
Makefile in the directory the header file lived in.  This is error
prone and also sometimes generates slightly different results (usually
just a comment that differs) depending on which way the update was
done.

This removes the file update targets from the top level Makefile, adds
an update: target in all Makefiles and has it depend on the depend: or
local_depend: targets, whichever is appropriate, so we don't get a
double run through the whole file tree.

Reviewed-by: Rich Salz <rsalz@openssl.org>