Previously, we created this weird bare repo that didn't do set all the normal git config. This change switches to cloning the local temp directory, fixing the `receive.denyCurrentBranch` property that blocked pushing to this weird bare repo after calling git:from-image or git:from-archive.
Additionally, since we now use a git clone, we set the default branch correctly, ensuring git pushes later on that branch work as expected (and not on master if it was customized prior to app creation).
Closes#5601Closes#5662