Or the folder. The way to run a Java application is as follows:
That fully qualified class name means the package name followed by the class name. For example, java.lang.String (of course String has no main method so it won't work, but you get the idea).
You must set the class path (defaults to the current folder only) to be able to run classes located in other folders. The class path should include the root of the package folder structure, not the package folders themselves.
If you don't know what the class path is, it's probably only the current directory. As for how to set it, check our FAQ, it's in there somewhere. But as suggested, don't do it. Use the -cp / -classpath JVM flag.