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Version 2 of the SSH protocol has various security and other enhancements over SSH-1. We should encourage its use.
One way of doing this is to make SSH-2 the default protocol (currently it's SSH-1). Note that while PuTTY will fall back to SSH-1 if necessary, this is potentially a user-visible change, as if SSH-2 is chosen users will be prompted about new host keys. (Perhaps the host key dialogue should indicate which keys we do have? See also hostkey-policy.)
Conversely, many upgrading users won't see this change, as it's only the `factory default' that changes; if they've got saved settings with SSH-1 selected then that won't change.
In future we might consider `turning off' SSH-1 by default (i.e., making `2 only' the default). Can't reasonably do this until SSH-2 is practically ubiquitous.
Our documentation should probably discuss the security implications of using SSH-1, too. (For a starting point see the Snail Book FAQ.)
Update: Even Debian stable includes SSH-2 support now, so we can reasonably get away with this. Fixed in snapshots.