i understand what you're saying, but I believe that creates other problems. historically the non-java EHR module and java-EHR module were separate folders in /server/customModules/. here's how my machine is configured:

I checked out a copy of labkey from svn to D:\labkey_trunk\. This is what I used to build. My external modules folder is set to: d:\labkey_trunk\server\customModules. Using this approach, I can make changes in the files and any changes will be live in the local instance of labkey i'm running. If I do what you suggest, I dont think that live development will work, since /build/... is going to have a snapshot of them. I also probably dont want to actually develop using the files in /build/ since I assume those can get overwritten easily.

can the java and non-java modules be made to better co-exist? otherwise i think we might need to re-split the java and non-java parts.