Address

Everything inside a checkout that records where the checkout lives.

core.hooksPath when it was set to an absolute path. The registrations under .git/worktrees, and the same registrations inside every submodule's git directory. Symlinks whose target is the directory the copy came from. A virtualenv's activation script, which exports the path it was created at.

A plain cp leaves every one of them pointing at the original, which is how a copy runs the original's hooks and claims the original's worktrees. Handling them is most of what gitto does; How it works lists the three dispositions it applies.