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What I'm gonna say is linux specific possibly, but the concepts are pretty much the same regardless
You've created a public private key pair using ssh-keygen so that you have a id_rsa, and id_rsa.pub (Use your preferred too here, on windows I always use cygwin ssh-user-config script and then import into other tools as required)
sftp id_rsa.pub onto your target machine.
ssh onto your target machine (which is of course Unix style)
cat ~/id_rsa.pub >> authorized_keys2
chmod -R 700 .ssh
The last step is possibly optional depending on your umask, but I do tend to find that ssh servers get a bit uppity if the .ssh directory and contents are group/world readable.
Logout and Login.
authorized_keys2 is for ssh2 authentication, authorized_keys for ssh1 authentication. ssh2 is more secure than ssh1, and most servers should support it.
I have no java certifications. This makes me a bad programmer. Ignore my post.