git says “not under version control” for just-checked-out file

Question

I have the distinct impression my Git repo is somehow mangled.

Here\'s the sequence I\'m doing:

1. git clone [remote\'s clone string]

   This creates,

Answer 1

Maybe App/android/AndroidManifest.xml does exist, but with a diferent case (like App/android/androidmanifest.xml, which would mean that App/android/AndroidManifest.xml isn't versioned (hence the error message):

Doing the git mv with the right case should then be enough.

The OP explains in the comments:

What happened was that there were two folders in Git, "App" and "app".
When I checked out the repo under Windows, because of the case-insensitivity of Windows, it actually overlayed the two folders into one into "App".
Which meant, the directory structure was fine, but half of the files (the ones coming from the "app" side) had an invalid Git path!