<p>I'm just starting out with WiX as I need to be able to automate building an MSI on our CI server.  Is there anyway to automatically include all the dependencies of a project?</p>

In my experience, Wix is a still a very manual process.  You have to add each dependency singly - I think the idea was that you would build the Wix installer at the same time you are building your project and add each item in as you are adding it in the code.  This way it seems less daunting than having to go back and do a retrospect on the project.  It certainly would be a great suggestion for an enhancement though!