Hello i had the same problems too.
Some sales-persons on the CeBIT told me that XDoclet ist depricated and replaced by annotations. So when you are going to develop a new Web Application you better should use this kind.
If you need XDoclet for older application there are some IDE-independent ways. You can use ANT to build your application and there are some ANT-Tasks for xdoclet.
I remember that i had the same problems like you, so i decided by building my own build script.