We are upgrading from Hibernate 2.1 to Hibernate 3.1. Using version 2.1 hibernate tools I was able to generate POJO's for HBM files one at time using the class net.sf.hibernate.tool.hbm2java.CodeGenerator with parameters that gave the template name, the output location and the hbm file.

I haven't been able to figure out how to create POJO's one at a time using Hibernate3Tools.

Is there a way?

Use org.hibernate.tool.hbm2x.POJOExporter.

currently no - and it only worked in the "old days" because it would ignore some associations which can/could result in pretty bad code generated.

Today the model has to be sound/complete, meaning if a mapping has an assocation to another mapping both mappings have to be included and we automatically dump all classes.

Anyways, you can write your own Exporter or simply write a template that only exports a set of the pojos. Look at POJOExporter for how it is done programmatically

a thing that might work (as a sideeffect) is that you could put some logic in the top of pojo.vm which would either generate the right contents or let the file be empty. If the output is empty we dont generate a file for it.