The correct answer IMO is git clone --mirror. This will fully backup your repo.
Git clone mirror will clone the entire repository, notes, heads, refs, etc. and is typically used to copy an entire repository to a new git server. This will pull down an all branches and everything, the entire repository.
git clone --mirror [email protected]/your-repo.git
Normally cloning a repo does not include all branches, only Master.
Copying the repo folder will only "copy" the branches that have been pulled in...so by default that is Master branch only or other branches you have checked-out previously.
The Git bundle command is also not what you want: "The bundle command will package up everything that would normally be pushed over the wire with a git push command into a binary file that you can email to someone or put on a flash drive, then unbundle into another repository." (From What's the difference between git clone --mirror and git clone --bare)