We have bunch of autogenerated classes which are mostly Axis2 stubs, skeletons etc. For some complicated wsdls, Axis2 generates a TON of java-beans, stubs etc. And I am sure there are other cases too when auto generation is used.
For now we treat these as other first class members of our code-base and they are stored in the same packages.
However when doing refactoring, cleanups etc it becomes hard to weed out the warnings that are coming from these auto-generated classes. For example, if I am trying to clean up the code so as to use Java1.5 generics, there is no good way to know how many of these offending classes are ours vs being auto-generated.
Should I be separating these autogenerated parts out into a different package? How do you guys store such artifacts in the repository?
EDIT: I see 'generate during build process' in quite a few answers below. While I see the benefits of doing that, I dont quite see how I can get away from a repository checkin.
My code has compile time dependencies on some of these classes and for me, a build during development is a 'ctrl-s' in eclipse. We use ant-scripts to generate the compile, run tests and generate deliverables.