There are two ways how content roots are registered in compiler configuration
in JVM CLI compiler:
1. Directly from arguments
2. From Module, which build from arguments
And there was a problem that both ways used at the same time in some
circumstances (regular compilation without .xml module file) which
caused duplication of all content roots.
Ideal solution for this problem is removal of Module usages at all,
because it looks like redundant abstraction which just complicate
things, but it's too scary to remove it, because it hove some none
trivial usages inside compiler. So to fix problem with duplicated
roots this commit just removes registration of roots from arguments
if Module is used
Dmitriy Novozhilov
faba9c4272