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1) Should the POJOs I create that map to data be simple "Value Objects" (otherwise called Data Transfer Objects) or richer Domain Objects.
We use a rich domain model and implement most of our business logic on the POJOs. We're about to move to a JSF/Seam layered application (from JSP/Struts) and I have a feeling I'm going to be glad I put the logic in the domain model instead of the Struts Actions or in some other type of Command/Script Object.
While we don't use the EJB development model of Stateless/Stateful objects - I having a feeling when we move to EJBs we won't use the SLSB/SFSB objects. I just feel its cleaner to have the logic close to the data it modifies. But I'm sure there are very valid reason that I don't pretend to understand about using SLSBs....we just don't have that level of performance/scalability requirements....
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2) Should I hand-code both the java and hbm.xml mapping files, or build one of the two and generate the other. (I was planning to generate the DDL for the database).
Currently we build both by hand. Very shortely though we are going to start using annotations (see the Annotation Tools project). We also let hibernate generate the ddl.
Good luck!