I wrote a quick and dirty upgrade.sh script that sits in the parent directory of my Known site. I'm using the following directory structure:
The offical Known git repository is checked out in known/. The config.ini and Uploads folder have been moved to the folder to sit alongside it.
The contents of the upgrade.sh script are as follows:
rm -rf old
cp -R known old
ln -sf `pwd`/config.ini `pwd`/known/config.ini
ln -sf `pwd`/Uploads `pwd`/known/Uploads
It's not elegant but it makes updating to the latest Known changes pretty seamless.