MyEclipse requires the classes to be built into the [WebRoot]/WEB-INF/classes directory, otherwise the application server doesn’t find them during runtime.
MyEclipse requires them to be built there ONLY if you want to use our deployment tool, if you are using a custom Ant script, you can build your classes to [WebRoot]/some/random/directory if you prefer 😉
I don’t see why there is the possibility (necessity?) to define two different output folders.
This is currently a limitation we will correct later in the year, the issue is that the deployment tool does a straight-packaging of the [WebRoot] dir and doesn’t go hunting down the output dir to *build* the /classes folder (As it should). We appologize for this inconvenience.
This would ease the setup of our Maven build configurations very much!
Not currently, again we will fix this later this year with version 5.0 release.