I've written a little bash script that makes updating an eXist db trivial.

The update script relies on a publicly accessible xquery script inside the target database that can return the timestamp of the most recently updated file in the /db collection. Martin wrote one that looks like this. You need to get it in to the db before the rest will work.

The update script itself is written in bash, and uses curl to interact with eXist. You can find the script itself here. It is fairly well documented, and only requires a few settings adjustments to work. It works by checking the local tree for the latest timestamp, compares it to the timestamp it got from the exist db, then creates a list of all local files that need to be pushed to the remote db.

To launch it in Ubuntu I use a Gnome launcher that invokes the script (the 'Exec=' line) like this:
Exec=gnome-terminal --title="Upload files to DB" -e "/complete/path/to/update-script.sh"
which opens a terminal and then runs the script.