Preserve git repos when cloning
The clone process should preserve any git repos on the server.
Right now, the .git directory and .gitignore file is excluded from a clone.
This means, in order to restore the repo after a clone, we need to remove the existing files and pull the repo down again from the origin (github in our case).
This should not be necessary when cloning a server, which is supposed to make an identical copy.
A clone (that is, making an identical copy) should preserve any git repos present on the server as these are a key part of many workflows.