We have just started using Git and GitHub at work on windows and whenever git is unable to access a file on checkout it will mark the files as deleted and lists them as changed but not updated. i.e.
error: git checkout-index: unable to create file XXXXX (Permission denied)
Checking out files: 100% (876/876), done.
D XXXXX
Switched to branch 'dev'
It seems to right itself if I checkout random branches a couple of times though.
Is this a problem and is their a nice way to make sure git handles this properly i.e. tells me to make sure that the files aren't locked and aborts the checkout.
EDIT
Actually had git delete a visual studio project file so if anyone knows why git does this and how to tell git not to do it let me know.