On installation, BNS Buddy would then apply a sym link to CookedPC_mod.
That's not always true as of 5.9.7.8:
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www.bnsbuddy.com
The sym application method has the limitation of forcing all your mods be stored on the same path of your game.
That's pure and simply not true.
I don't know where you read this, but it is wrong.
When you google for "symbolic link windows" (
http://google.com/search?q=symbolic+link+windows), you will have over 71.7 million results.
Fear not, because this is the first result:
https://www.howtogeek.com/howto/16226/complete-guide-to-symbolic-links-symlinks-on-windows-or-linux/
Quoting from there:
Symbolic links are basically advanced shortcuts. Create a symbolic link to an individual file or folder, and that link will appear to be the same as the file or folder to Windows—even though it’s just a link pointing at the file or folder.
For example, let’s say you have a program that needs its files at C:\Program. You’d really like to store this directory at D:\Stuff, but the program requires that its files be at C:\Program. You could move the original directory from C:\Program to D:\Stuff, and then create a symbolic link at C:\Program pointing to D:\Stuff. When you relaunch the program, it will try to access its directory at C:\Program. Windows will automatically redirect it to D:\Stuff, and everything will just work as if it were in C:\Program.
This has been known for years, but the legacy name is "junction", up until Windows 10 build 14972.
(
https://blogs.windows.com/windowsdeveloper/2016/12/02/symlinks-windows-10/)
A workaround to this limitation is to assign a storage destination path, and having BNS Buddy looking that up and copying folders from that path into CookedPC_mod.
You can apply a custom mod folder in settings:
With this, you can create a folder wherever you want.
Using the new knowledge in this answer, you can create multiple symbolic links to the folders where you have the mods.
BnSBuddy has support for subfolders for a year or so, so, you can easily have a CookedPC_mod folder with mods, a Nude folder with mods, a CookieCutter folder with mods .... and that custom folder simply has symbolic links to each of those folders.
Remember this: BnSBuddy only supports 1 level of sub-folders.