Go to Admin → Modules. Each application that is switched on has a Make front page button beside it, and the one currently holding it is marked Front page.
Only its index moves. Everything else stays where it was — make Downloads your front page and /downloads keeps working exactly as before.
An application that is switched off cannot hold the front page, and one that is switched off while holding it hands the front page back to the welcome page rather than leaving visitors on an error.
Choose Use the welcome page to go back to having no application at the root. That is what a fresh install does, because it should not guess.