Update jay/MarkIII

Eclipse Webmaster requested to merge jay/MarkIIIMina into jay/MarkIII

Created by: osbornjd

This PR updates the jay/MarkIII branch to all of the features that have been added to Commands in the past ~6 months. These features were put into the jay/MarkIIIMina branch to avoid conflicts with other code using Commands that was dependent on JSch, since one of the features introduced was to change to sshd mina dependency.

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