Fallout 4 mod cleaner
Only for beta 1.3.47 This will break other versions of fallout 4
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.
A little more detail.
It has an internal master list of all the files included in Fallout 4 beta 1.3.47.
It looks at the content of the directory and compares each file to that list.
If it is not in that list it removes it.
When it has finished it finds folders with no content then removes those too =)
Source included with download and also here