What I do is to import the whole tree (therefore including src/etc),
and make changes.  I use a script 'etcmanage' that will automatically
merge a $DESTDIR/etc tree into /etc.  The basic rule is to record
files as 'automatically managed', either manually, or from a previous
merge.  Then, a file which is auto-managed and has the same md5 sum as
when it was enrolled or last installed, will be auto-updated (or
removed if not in $DESTDIR - be careful!).

The code below is in perl, and rough, but given my spare time level I
think it is more useful to share it than try to make it nicer first.

http://www.ir.bbn.com/~gdt/etcmanage/index.html
http://www.ir.bbn.com/~gdt/etcmanage/etcmanage-0.0.tar.gz

If you aren't comfortable with existing tools and doing etc upgrades
by hand, you shouldn't try to use this tool.  But if you find these
processes simple, but overly time consuming, and you can recover from
a trashed / partition, etcmanage may be helpful.

    Greg Troxel <gdt@ir.bbn.com>