I would write a small shell script for this.

The script should do "diff --brief --recursive olddir newdir" and then parse the output into pathnames, and feed that as a filelist into "xargs tar cvf newdir.tar"

The output of diff will be a bunch of lines that look like this:

Only in olddir: Makefile
Only in newdir: morejunk
Files olddir/README and newdir/README differ

The script will have to convert that into this:

newdir/morejunk
newdir/README

Cheers