Thank you for your answer and sorry for the delay (I was on vacation...). I am using git 2.9.0.windows.1 (run on Windows 7 via git bash). I tested it on this repo: https://github.com/githubtraining/example-dependency.git The same problem occurs. Here a small script to reproduce the error on my PC: #!/bin/bash git clone https://github.com/githubtraining/example-dependency.git cd example-dependency git submodule deinit js It ends with this error: fatal: Please stage your changes to .gitmodules or stash them to proceed Submodule work tree 'js' contains local modifications; use '-f' to discard them Is the script working on your PC? Thank you in advance. Thomas On Wed, Sep 14, 2016 at 10:29 PM, Heiko Voigt <hvoigt@xxxxxxxxxx> wrote: > On Tue, Aug 30, 2016 at 01:45:56PM +0200, Thomas Bétous wrote: >> Are you able to reproduce this problem? > > No. I just did a clone and an immediate deinit afterwards and no error. > Maybe you can provide a script to reproduce? Which System was this on? > > Cheers Heiko