How to check if WordPress is updating plugins?

Instead of re-ordering your plugins to load in a specific order, have each of them that requires some other plugin to be loaded to defer their initialization until the “plugins_loaded” action hook.

In other words, when a plugin with a dependency is included and ran, it shouldn’t do anything directly. Instead, it should have functions, and then add_action calls to hook those functions to plugins_loaded. That function that is called later can do the class_exists check and act accordingly.