Make sure your classpath is set accordingly and just use the javac and java commands on the command line (or better yet, Ant and Ant scripts).
The note merely states that you should have the JAVA_HOME environment variable set appropriately as some software installations expect it to be set.
Hoe does this relate to running Java programs from the command line? That I should put my .java files in Java/Home and all other archive files in Extensions? Good grief. And I thought Macs were user friendly...
Some applications look for Java�s home directory (JAVA_HOME) on the users system, especially during installation. If you need to explicitly set this, in a shell script or an installer, set it to /Library/Java/Home. Setting it to the target of that symbolic link can result in a broken application for your customers. Programatically you can use System.getProperty("java.home"), as you would expect.
/Library/Java/Home also contains the /bin subdirectory where symbolic links to command-line tools like java and javac can be found. These tools are also accessible through /usr/bin.