I’ve been advised that MyEclipse forces a particular project layout and hierarchy
Almost every IDE forces a certain layout, MyEclipse is so far the most flexible in this regard in that it just needs you to have a layout that atleast ‘makes sense’. In future releases we will completely remove the need for a specific structure; but that is still down the road aways.
As far as the structure, have a look at this FAQ entry:
http://www.myeclipseide.com/FAQ+index-myfaq-yes-id_cat-30.html#111
The reason for this is just to follow an exploded WAR format which is defined by the web application spec from Sun. That way our deployment and development model can stay conceptually in sync with eachother; it makes it easier for people to use.
I would mention that we have added over the last 6 months major enhancements to the deployment tool to handle resource and inter-project references during deployment allow you to shift and shape your project into most any form as needed. THe format above, is a good suggestion for a project layout even if you are not using MyEclipse, it will be understood and easily handled by most all IDEs because it follows the WAR layout.