This ~mods folder sorting baseline requires the ability to READ.
¶ Why sort the ~mods folder?
To keep your ~mods folder sorted properly. Which, in turn, will ensure mods work as intended. Some issues that users encounter are caused by an improper ~mods folder sorting.
¶ How to sort the ~mods folder
By doing folder categorisation. We'll put mods in different folders, based on the category of said mods. As such, I will share my example of sorting the ~mods folder alongside explanations for each folder's purpose below.
I will explain each folder's purpose, starting with the bottom one; UI.
¶ UI
As you guessed it, it's for UI-related mods. Mods that belong to this category include mods that modify the colour of the HUD, or portrait icons, etc.
An example of my UI folder. The .PAKX File type serves to disable the .PAK files from being readable by the game. Essentially, just another way of disabling mods without removing them.
¶ Skins, VISMODs
For skin mods and visual mods, be it mesh or VFX. To go further, make folders inside for each aircraft (excluding add-ons) and NPCs.
This way, you can sort each skin mod to their respective aircraft folders. The tildes (~~) on the NPC folder serve to override anything inside these tilde-less folders, just in case a skin mod also includes NPC textures. It's a rare occurrence, but nonetheless, just in case.
¶ Gameplay
Gameplay mods. Mods that modify plane capabilities, weapon capabilities, buffs or debuffs the NPCs, weapon swaps, etc. I also personally consider model-swap mods as gameplay mods, since, technically speaking, they're replacing existing plane files, be it capabilities, weapon capabilities, alongside mesh and textures.
I split Mission and NPC gameplay mods under their subfolders, with NPC folder having three tildes to override any mods that may also include NPC files.
¶ ~Add-Ons
2023 saw the rise in add-on mods; mods that include new planes without replacing any existing ones. Add-on mods work rather different than model-swaps. That is because, again, add-ons do not replace existing plane files, and also require 4 essential files known as PlayerPlaneDataTable, SkinDataTable, AircraftViewerDataTable and localisation. PlayerPlaneDataTable in particular, it's the file that control each plane's ammo counts. This means that ammo buffing mods may override add-on mods. Thus, add-on mods need a folder that can override the three previous folders.
Anything add-on-related needs to go into this folder. As for skin mods made for add-ons, it's recommended to make a subfolder with a lot of tildes to make sure it can override said add-on's textures.
¶ ~~Skies Restored
18th January 2024 saw the release of Calamitous' anticipated Skies Restored mod, which brings about cut-contents, alongside various QoL improvements to the main campaign and DLC missions. This mod also replaces a lot of things, including localisation, which is integral for add-ons, and, as such, deserves it's own folder. If you don't use the mod, well, you don't need to make this folder.
I recommend extracting the folders from the ZIP file as is, and then deleting unwanted modules from each folder. That way, whenever Skies Restored is updated, you can just check the folders on your ~~Skies Restored folder, and drag and replace the updated modules.
A reminder that this is only my way of sorting the ~mods folder. You may follow this one-by-one, or use it as a baseline to sort your ~mods folder, your own way.