To host javadocs in your www direcotry, you need to do three steps:
You already know how to do the first step using the javadoc command (I strongly suggest using the -d option to javadoc). The second step can simply be accomplished using the cp command.
You can set the permissions by using the following commands:
find ~/www -type d -exec chmod 775 {} \;
find ~/www -type f -exec chmod 664 {} \;
I wrote a script that you can use to do all three steps. Just run this script in your project base directory.