Added detailed user manual. Analyze and explain commands now properly reject count queries. Analyze queries can only be run in interactive mode. Made explain command output work in batch mode. Added warnings about limit when running non-using analyze commands. Renamed the values for the parameter to make more sense for non-log probabilities. Removed explain from list of parameters since that should only be accessible via the explain command. Disallowed values of 0 for limit since that is ambiguous and confusing. Refactored some more code to make it more pythonic