How to reproduce:

1. Create a new project
2. Open the project /Assets folder using Explorer/Finder
3. Create a folder named '~'
4. Put some files in the '~' folder
5. Open the project in Unity
- Note the warnings for each file in the '~' folder in the Console: "Ignoring asset refresh of <pathtofile> because the folder it is in has not been imported yet!"
- The folder shouldn't be imported as it is a special function, but no warnings should be thrown as well.