This is a BC breaking change!
Manipulating Pico's $plugins array is a really bad idea. We've introduced the Pico::loadPlugin() method to safely load plugins at any time, however, Pico might do unexpected things when loading plugins too late. See the class docs of Pico::loadPlugin() for more details. Nevertheless, this change breaks BC to Pico 1.0. However, I don't know a single plugin that relies on manipulating the $plugins array. If you just want to load a plugin manually, use Pico::loadPlugin() instead.