Previously, drush allowed only one file to be specified via the --config option, and setting $options['config'], $options['include'] or $options['alias-path'] in one configuration would overwrite the settings from configuration files with lower precedence. Now, these options are merged together from all configuration files they appear in, and the command line, if applicable.
* Any of these options can be set on the command line using a list of files/directories separated by PATH_SEPARTOR.
* Any of these options can be set in a drushrc.php file; if they are, the values set in one location will merge together with the values set in other locations.
* Backend invoke will correctly forward these settings values to invoke calls on the local machine, but will not automatically include them on remote calls. If --alias-path is specified on the command line, only the values provided on the command line will be sent; the default locations will not be sent.
* Long/short options (e.g. '--include' vs. '-i') are now converted to the long form at context-initialization time. The was done for all options with long and short forms for consistency, so there is no longer any need to call drush_get_option(array('r', 'root')); drush_get_option('root') will now suffice.
* When calling drush_set_option, it has always been preferred to use the long form option name; however, it is now required. drush_set_option('r', ...) would previously work, but will now fail.
