This may not be the perfect solution you're looking for, but I ran into an almost identical issue. This is how I solved it,
1) Open Solution Explorer in Visual Studio
2) Find your Project ( Angular Project )
3) Right click on it, and click Compare changes.
4) In compare options see View Options and check the following:
- Show items that exist only in source path
- Show items that exist only in target path
- Show items that are different
5) Then find all the files that are in your local mapping that are missing from your server version, right click on them and click "Add file". You should be able to do this for entire folders / groups of files using shift + click .
6) Once you've added all your missing files, make sure they're being tracked in Team Explorer -> Pending changes, then check in your files.
I haven't figured out how to get Visual Studio to track these files automatically as I believe it requires a solution file like in normal C# projects to track them, but I could be wrong.