This is unlike other mod managers that delete overwritten files from the data directory and revert them back if mods are uninstalled. The only difference is, because of the virtual file system used by MO2 (which essentially compiles your data folder at launch) redundant files are always kept in their separate mod data folders.
The modlist is no different in that regard, the assets of mods towards the bottom of the list will overwrite any that are above them. What do I mean by this? Basically if you were installing mods to your Skyrim data folder manually or through the use of older mod managers like Nexus Mod Manager, you would be overwriting asset files from conflicting mods in your data directory with mods installed last overwriting those installed first. What you need to know is that not only is it a list of all the mods you’ve installed through Mod Organizer or any other means but it is also a dynamic installation order. Ok, the mod list, this is the left pane of your MO2 window and I have referred to it by many names throughout the course of my guides but the final name I will be settling on is mod list.
