STR:

1) Have a maven project with modules.
2) One module will be "assembling" module, which creates a jar with all app's .jars and it's dependencies. Use maven-assembly-plugin for that.
3) On this project, open Project -> Properties -> Run -> Main class -> Browse
4) No classes are listed - because this project has no sources.

The classes which can be run, however, are in the produced jar.
For larger Maven project, it's quite common that such assembly-making module is present.
Other such use case is when there are multiple modules which add different configuration, but again, uses the same .jar's built by other modules.


Therefore, I suggest this:

In the Browse dialog, add "Include dependency classes" checkbox;
when checked, the deps would be also searched for the "Main candidates".

If it's not that easy to add such checkbox, I suggest to include dependency classes by default. Usually, it would not list a lot of classes, so it would not confuse user. Classes from dependencies might be differentiated somehow - e.g. italics or such.