Cleaning up and adding more helpful exception messages.
Changing 'prune' command to 'query' and adding the option to skip pruning of the resulting subtree.
Removing 'options_string' argument to TreeStore as it is no longer necessary.
Removing uri command as it does the same thing as ls. Tree names should be URIs.
Separating out tree annotation function into a separate command, since tree annotation != adding trees.