Provide a way to disable hermit shell hooks

I can't seem to find a way to disable the hermit shell hooks. It would be nice if there were a `hermit shell-hooks --remove` or such to disable them. In particular this is useful for testing flows that are executed without shells and so don't have the shell hooks.

Start with the `hermit shell-hooks` command and trace how shell hooks are installed or managed. Done means there is a supported way to disable or remove the hooks, including for flows executed without shells, with behavior verified by the relevant command tests.

Written by the indexing model from the issue text.