Ok, here's what I've done:

- Added the boolean prop "nukes.pk-auto-increment" for each database conf in:

/build/etc/*

- Added the prop "build.gen.src" to set the filter copy destination directory in:

/tools/etc/buildfragents/defaults.ent

- Added the target "_default:filter-sources" to perform the Ant filter pass in:

/tools/etc/buildfragents/targets.ent

- Modified the per module build.xml "generate-classes" target to add a dependency on "_default:filter-sources"

- Modified the ejbdoclet fileset tag in the per module build.xml to use the filtered ${build.gen.src} sources instead of ${source.java}

I'm not sure if / where we document this, and I've put comments in the affected files where appropriate, but this is a good description of the process.