Mods that were active before the files were sorted will be active after the files are sorted. In at least Fallout 4 active plugins are preceded with an *, which means that the mod is active. Lines in any of the files that begins with # will be ignores as this indicates it is a comment. It gives a report of what plugins that the user has that aren't in the master and what plugins that is in the master but not in the user load order. What it does: lo_sort simply uses a load order file as a master and reorders plugins in another load order file using the master load order.
This program makes it easy to share your load order and to let others import it. Therefore I prefer to sort the load order manually and place the mods in an order that makes sense to me. This order may change without you knowing it if you run LOOT after you have resolved everything. By reordering the plugins you resolve the conflicts. Resolving conflicts often means that you will have to choose features from one mod or another. With LOOT your load order might suddenly change when the master list gets updated and you have no idea if your patches or mods will work they way you want them too. It is a great program for those that like what it does but I don't. I made a super simple program in c++ but thought I'd share if anyone wants it.
