The emergence command line tool allows you to run emergence function right off the command line. To get going ssh into your emergence server and run the following command. (Be sure to have root access)
emergence-shell sitename
Sitename is the name of the site in emergence.
Using the standard php namespaces you can now being creating objects, running script etc.
php > $build = new \Emergence\Commerce\Build();
php > $build->myTestFunction();