Note that the latest npm has changed its behaviour for folder links - if you refer to a dependency by a folder name ("fred":"file:../fred", that sort of thing) rather than npm version or git link (etc.), npm now creates a junction inside node_modules that links directly to the original folder.

Deletion tools that don't know how to distinguish junctions and folders may then find the original files via the junction and delete them...

(del and rmdir don't suffer from this. I did get a strange error message from rmdir, though, and it didn't actually delete the junction. GNU-Win32's rm blithely follows the junction and deletes everything in it.)