Which format do you use to run a java application? I always pass the fully-qualified class name to java command, namely, java com.whatever.Main. In fact, either way is acceptable:

build/classes > java javahowto.Member
build/classes > java javahowto/Member

I've tried java command with both forms in JDK 1.4, JDK 5, and JDK 6 on Linux without any error. On Windows, you can use either pkg.Main, or pkg/Main, but not pkg\Main:

C:\javahowto\build\classes>java javahowto.Main
In Main.main(String[])
C:\javahowto\build\classes>java javahowto/Main
In Main.main(String[])
C:\javahowto\build\classes>java javahowto\Main
Exception in thread "main" java.lang.NoClassDefFoundError: javahowto\Main (wrong name: javahowto/Main)
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
    at java.net.URLClassLoader.access$000(URLClassLoader.java:56)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
    at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)

In any event, do not include .class in the class name. When running from the root of class directory on Unix, one can use the shell auto-completion to fill the class name, instead of typing the FQN. That's a big plus for the the second format. On Windows, auto-complete doesn't help in this case, since \ is class name is not accepted. I guess from now on, I will be using the slash form more often.

Unlike java command, javac operates on java source files and always takes file paths as arguments.