Giles,
Good questions. This type of flexibility discussion has come up before. Here are some of the better discussions on it.
https://www.genuitec.com/forums/topic/jsp-debugging/#post-196607&highlight=#524
https://www.genuitec.com/forums/topic/error-when-creating-a-web-module-project/#post-196222&highlight=#121
As entertaining as these threads are, the net-net of it all is this: we’ll add deployment extentions in the future for flexibility, but in order to do so much automation we have to do a bit of imposing on the project structure. That’s just the way it is right now.
In the meantime, you can continue to use all the MyEclipse tools except the deployer. The editors, wizards, and server connectors will continue to work great for you and you can continue to use your ant script for deployment. For new projects though, I’d highly recommend our product structure so you can use our Sync-On-Demand deployer. Very fast.
–Scott
MyEclipse Support