There should be a central location where you set the timeout for SSH Commands and Logins

 

If you go Manage System -> Configure System -> Publish over SSH and then to Advanced Settings there is a SSH timeout that is defaulted to 300K seconds (5 minutes)

 

When you create a build and then add a step of "Send files or execute commands over SSH" under advanced there is another timeout setting (defaults to 120 seconds).  

 

It would be nice to centrally configure the initial setting of timeout for the build at the overall SSH Server level