Import very specifically does not rename or delete items. Per the docs:
Import does not purge unknown items
If a template or route is removed from the manifest, it is not deleted from Sitecore on the next import.
If you want to follow default conventions and have Sitecore look entirely like your manifest and nothing else, consider using wipe import (
-w on the CLI) which will purge imported items before recreating them all. Wipe will prompt by default;
--unattendedWipe will disable the prompt for CI scenarios.
If you're going to get advanced with your items though, use an item serialization tool to maintain the app's state from the Sitecore side.