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