Hmm, that is unusual. DesktopServer removes the .git folder prior to creating an export zip or performing a DirectDeploy. However, the initial operation is a “copy”, which may cause undue stress if the .git archive is very large. After the copy operation completes, DesktopServer purges any project folders and files on the copy: .git, .gitignore, _Notes, .svn, etc. However, we will make a note of this (ideally it wouldn’t perform the copy from the start on those given folders).

Thank you for your feedback.