Further to Martin's post...

Using the included java admin client can be clunky for frequent use, so I've written a bash script that uploads the most recently modified files to the database. It's been tested on Ubuntu 11.10 and Mac OS X (10.6 and 10.7).

To use it, provide values for the variables at the top of the script and set the script to be executable. It is only designed to work in a very specific context (one local directory, one remote db, etc.) so you'll need a copy for each project. It is also utterly dependent upon accessing a script inside the eXist DB that provides the timestamp of the most recently modified file in the DB. Martin wrote one and posted about it here: http://hcmc.uvic.ca/blogs/index.php?blog=11&p=8947

Extra info
In Gnome-Shell I installed an extension called Quick Launch that allows me to add functionality similar to the old Gnome Drawers applet, providing me with a fast, gui-based method of launching the updater from the Gnome panel.

I've added a quicklaunch for the admin client (sometimes you need it) using javaws. The essential command is:

javaws http://your.server.here/exist/webstart/admin-client.jnlp

Works a treat.