I think it would be better to adopt the Maven-style directory layout e.g src/main/java and src/test/java. It would allow the flexibility to move to other build systems in the future, if desired. Plus it seems quite a logical arrangement.
I also agree, that such a big change should form a separate patch that only performs the directory modifications, to confirm all permutations of the existing build creates the same artifact after the re-arrangement.
Thanks
Stephen
