Fixes parameters of ls, create-table and delete to use kiji uris.

Updates the parameters to some commandline tools to correctly use kiji uri's.

This should be the last change needed for docs-21 since @jhlch re-added the JSON section.

I have not extensively tested any of this except for the JSON table creation command and a few of the ls's. This is pending someone running through the tutorial, but I expect this change will save people time.