This tool will remove all extra files and folders in the fallout 4 directory (it will only leave vanilla files and folders for the beta 1.3.47 Fallout 4. It will delete the rest)

Real easy to use either paste the location of your fallout 4 directory into the textbox or browse for it then hit clean.



This should now be compatible with any modded game. Steps to add a new game

•   1. Backup your original FileMasterlistDoNotEdit.txt
•   2. create a batch file in the root directory of the new game with forfiles /s /m *.* /c "cmd /c echo @file" >> FileMasterlistDoNotEdit.txt then run it.
•   3. remove all quotation marks from the generated FileMasterlistDoNotEdit.txt that is these "
•   4. place your newly generated FileMasterlistDoNotEdit.txt in the same folder as Fallout4Cleaner.exe.
•   5. use as you would normally for fallout 4.
  

A little more detail.

• It has an FileMasterlistDoNotEdit.txt list of all the files included in Fallout 4 beta 1.3.47.
• It also has a KeepList.txt that you can add file names to.
• It looks at the content of the directory and compares each file to those lists.
• If it is not in that lists it removes it.
• When it has finished it finds folders with no content then removes those too =)
  

To generate a quick filelist text of everything in your Fallout directory
create a batch file with

forfiles /s /m *.* /c "cmd /c echo @file" >> FileList.txt


Move it to your Fallout directory and run. It will generate a filelist.txt
with a complete list of all of your Fallout files. kinda good for keeping
a keeplist.txt that can revert your Fallout directory to a fixed state.

The filelist.text will have " either side of the filename Use notepad++ and
find/replace with nothing (No space just leave it blank) then replace
all

Source included with download and also here
https://github.com/Nixsy4/Fallout-4-Beta-1.3.47-folder-cleaner