Aurora: how to I configure my project???

I tried adding my root directory, and then source directories inside it...
...it spent over an HOUR trying to "optimize" our massive project (over
4100 classes) then I had to add the source dirs which also took a long
time (covering only a few hundred).

In the end my files couldn't resolve references in other packages.

So I tried it another way, adding one module per directory root that I
wanted to include, and that didn't work either.

Is there any written explanation that I have missed on how the project
configurations work now?

While I like the idea of the project level test dirs and excludes, so
far it doesn't work for me.