git clone vs copy paste, what's the difference?

This answer of mine regarding backup should give you some answer on clone vs copy: Moving a git repo to a second computer?

Main differences:

1. When you clone, you get remote origin setup pointing to original repo, so that you can push to it.
2. You don't get hooks and reflog ( and also old objects) and other remotes when you clone but you do when you copy

Note that when you clone with a folder path, the differences change subtly, as the objects and refs are usually just copied / hardlinked ( equivalent of --local which is the default with local folder paths)

When you use git clone instead of copy paste, the original repository will be the origin.

Besides, when cloning on the same machine you can use --local to make it faster. From the manual page:

--local, -l

When the repository to clone from is on a local machine, this flag bypasses the normal "git aware" transport mechanism and clones the repository by making a copy of HEAD and everything under objects and refs directories. The files under .git/objects/ directory are hardlinked to save space when possible....