Add dependency commands back to CLI

In d6fb898 we removed old migration commands, and accidentally
removed some commands we want to keep. This commit adds those
commands back to the CLI.

src/Whippet.php

@@ -25,6 +25,8 @@ public function commands()
 		$this->command('init [PATH]', 'Creates a new Whippet application at PATH. NB: this is a shortcut for whippet generate -d PATH whippet.', function ($option_parser) {
 			$option_parser->addRule('r|repository::', 'Override the default application.json WordPress repository with this one');
 		});
+		$this->command('dependencies SUBCOMMAND', 'Manage dependencies (themes, plugins)');
+		$this->command('deps SUBCOMMAND', 'Alias for dependencies');
 	}
 
 	public function plugins($plugin_command)