Changed CommandConfiguration and Command Design

Eclipse Webmaster requested to merge github/fork/osbornjd/jay/MarkIII into jay/MarkIII

Created by: osbornjd


This PR introduces a change in the design of CommandConfiguration and Command. Much of the functionality of Command was moved into CommandConfiguration. This cleans up Command significantly and also is better design for putting all of the work prior to running the command into CommandConfiguration.

This PR supports issues 405 and 406

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