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CLI: Audit StoreCommands #50

@jjg-123

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@jjg-123

Since we can now use result sets, it turns out that several of the oldest commands are not using the built in system for resolving references to the store, just rolling their own. This must change and everything should access th store in a uniform way.

Also, a lot of the help online is not quite accurate or can be substantially streamlined. A thorough review of that is in order.

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