The plugin allows ssh to be used for Linux.

However, if I manually setup ssh (plus ssh keys and java) on Windows beorehand (baked into the AMI) I can get the plugin to connect to Windows (by selecting the "unix" as the type of agent).

This works - but the plugin tries to run various Linux commands on the Windows server prior to the agent being started. 

Would it be possible to have an option that prevented any commands being run over and above those needed that actually start the agent (ie the "java" commands).

This would make it possible for the user to manually setup Linux and Windows ssh/java on the agent, and then the plugin could just copy across the agent file and start it.