I have two solutions. I wrote the following script:
================
#!/usr/bin/env bash
svn status | egrep "[.](pages|key|numbers|graffle)/" | egrep "^[?]" | cut -c 2- | sed -e 's/^\ *//' | while read line
do
svn add "$line"
done
svn status | egrep "[.](pages|key|numbers|graffle)/" | egrep "^[!]" | cut -c 2- | sed -e 's/^\ *//' | while read line
do
svn rm "$line"
done
if [ -n "$1" ]
then
svn commit $@
else
svn commit -m"proof reading"
fi
================
Use this script to do commits. It deletes from svn any file that appears to have been deleted by an iworks app (or omnigraffle). It adds newly discovered files.
But I actually have a different solution: so many things are broken in the latest Keynote (most importantly Magic Move annimations) that I have downgraded to the earlier version.
Hope this helps, and of course I make no guarantees that this script will work for you.
Also, make sure you have a relatively recent version of svn, since older versions put a .svn directory in every folder, and this will be a problem for the script I've included.