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The SSH options in 4.1EA2 are very handy. It would be more useful if it could connect to a running ssh-agent(1) (of openssh-client or such, accessible through socket given in environment variable SSH_AUTH_SOCK) and use keys loaded to the agent.
This makes a huge difference if the private key if locked with a passphrase. When I fire up my X session, I load my key to the agent once (and unlock it with the passphrase, as well). If SQL Developer would utilize the ssh-agent, it would not ask me for the passphrase for all the SSH hosts I'm using.