Using different versions of dependencies in separated Java platform modules
Java 9 doesn't solve such problems. In a nutshell what was done in java 9 is to extend classic access modifiers (public, protected, package-private, private) to the jar levels.
Prior to java 9, if a module A depends on module B, then all public classes from B will be visible for A.
With Java 9, visibility could be configured, so it could be limited only to a subset of classes, each module could define which packages exports and which packages requires.
Most of those checks are done by the compiler.
From a run time perspective(classloader architecture)
, there is no big change, all application modules are loaded by the same classloader, so it's not possible to have the same class with different versions in the same jvm unless you use a modular framework like OSGI or manipulate classloaders by yourself.
Theoretically it is possible to use different versions of the same library within your application. The concept that enables this: layering!
When you study Jigsaw under the hood you find a whole section dedicated to this topic.
The idea is basically that you can further group modules using these layers. Layers are constructed at runtime; and they have their own classloader. Meaning: it should be absolutely possible to use modules in different versions within one application - they just need to go into different layers. And as shown - this kind of "multiple version support" is actively discussed by the people working on java/jigsaw. It is not an obscure feature - it is meant to support different module versions under one hood.
The only disclaimer at this point: unfortunately there are no "complete" source code examples out there (of which I know), thus I can only link to that Oracle presentation.
In other words: there is some sort of solution to this versioning problem on the horizon - but it will take more time until to make experiences in real world code with this new idea. And to be precise: you can have different layers that are isolated by different class loaders. There is no support that would allow you that "the same object" uses modV1 and modV2 at the same time. You can only have two objects, one using modV1 and the other modV2.
( German readers might want to have a look here - that publication contain another introduction to the topic of layers ).
Version Conflicts
First a correction: You say that modules have their own class path, which is not correct. The application's class path remains as it is. Parallel to it the module path was introduced but it essentially works in the same way. Particularly, all application classes are loaded by the same class loader (by default at least).
That there is only a single class loader for all application classes also explains why there can't be two versions of the same class: The entire class loading infrastructure is built on the assumption that a fully qualified class name suffices to identify a class with a class loader.
This also opens the path to the solution for multiple versions. Like before you can achieve that by using different class loaders. The module system native way to do that would be to create additional layers (each layer has its own loader).
Module Hell?
So does the module system replace class path hell with module hell? Well, multiple versions of the same library are still not possible without creating new class loaders, so this fundamental problem remains.
On the other hand, now you at least get an error at compile or launch due to split packages. This prevents the program from subtly misbehaving, which is not that bad, either.