Hi, please do not top-post the conversation will otherwise get hard to follow. Thank you. On Tue, Oct 04, 2016 at 05:46:45PM +0200, Thomas Bétous wrote: > 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). My initial reaction is that this might be a problem with line endings. Did you check whether you get any diff when you do a 'git diff' after the clone? Maybe the variable 'core.autocrlf' is set to 'input' ? Have a look at 'git help config' > 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 Here I get $ git submodule deinit js Cleared directory 'js' So all seems fine. > Is the script working on your PC? Yes. I am on Mac OS X though. Cheers Heiko