Visual Studio Code conflict

[iongion]

Windows 10, SourceTree 2.0.20.1

When versioned repo is opened in VS Code as project, SourceTree behaves weirdly, files appear and dissappear in the stage making one unable know what is staged, so, unusable.

I have made a GIF with this behavior:

[iongion]

Also, the issue of non visible checkboxes is still there