Added some comments to things in options.hpp.
Fixed parse_commands_deep so that default values do not override config file values.
Made parse_config_file_flat just return the options map instead of taking it as an output parameter.
Made options::parse_command_line return by value instead of passing a reference.
Made options::parse_command_line return by value instead of reference parameter.
Replaced options::merge_new_values with the pure function options::merge.
Made parse_command_line_and_collect_unrecognized return options dict by value, made main_rethinkdb_admin actually verify options.