I don't know what you're talking about. We've had these Eclipse projects for over three years, with many CVS branches and released versions behind us. A new branch in CVS usually equates to a new product release (possibly either major or minor version). When we branch in CVS we create new Eclipse workspaces, and new classpath variables prefixed by the branch name. Launch configurations are copied and updated to reflect the branch. It’s all very simple and enables us to load up a workspace (or individual projects) for any given CVS branch at any time.
As for your question of how we can manage this... huh? Are you referring to the fact that we have stuff outside of Eclipse? We've got a lot of stuff outside of Eclipse - shell scripts, configuration files, C++ code, SQL scripts, Perl scripts, LDAP schema modifiers, documentation, etc. All of this stuff exists in CVS and is built by Ant scripts on a build server.
The reason is that it is a fairly large system, with multiple Java-based modules. Each of these has its own Eclipse project, but shares a common config directory. This is where hibernate.cfg.xml lives, along with other items. You can't have multiple Eclipse projects share a directory, so that is why it is not in the source tree.
The solution you propose is an obvious one, and one that we've considered. We may, in fact, do it - adding the hibernate.cfg.xml to our 'common' module (which is also where most of our Hibernate domain classes are). The only way that we would though is if we really need the Hibernate Console functionality. It is not a burning desire at the moment - just a 'nice to have' test/prototype tool that is not worth tweaking our directory structures and build scripts over. That is why I was inquiring about a way to make it work with our existing environment.
Anyways, thanks for the comments and sorry if this response sounds harsh. I wasn't looking for ways to set up a development environment - we have had a very successful one using Hibernate for several years. I just had a simple question.
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