doctor

gitto doctor [<name>]

Reports what still points outside a clone: symlinks into the canonical, absolute hook paths, submodule git directories that escaped, and worktrees the clone hosts for someone else.

$ gitto doctor search
storefront-search
  still pointing outside this clone:
    symlink  .agents -> /Users/you/work/storefront/.agents
    hosts    storefront-docs

What it can see

Everything git records: configuration, worktree registrations at every submodule depth, and the git directory each submodule resolves to. Symlinks and virtualenv activation scripts, because both write their own path into a file.

What it cannot see

Any reference that lives outside git. An editor workspace, a launch agent, a line in ~/.ssh/config, the working directory of a shell someone left open.

A clean report therefore means that nothing git knows about points at the canonical. Treating it as permission to delete a directory is a mistake the report cannot warn you about.