Since classpaths work in precedence order, in this case the assembly would take precedence over the binary class files and that wouldn't be what we want. 

But I see your point -- One option is to do the following: 
- check if the assembly-deps jar exists and if so, include the class files and the deps jar.
- If not check for the assembly.jar file and use it if found

This way the development versions are first included if found and we fall back to the assembly jar otherwise.
I'd rather avoid another environment variable if possible. Any thoughts on this ?