A twelve-factor app is always tracked in a version control system, such as Git, Mercurial, or Subversion.
A copy of the revision tracking database is known as a code repository, often shortened to code repo or just repo.
There is only one codebase per app, but there will be many deploys of the app.
A deploy is a running instance of the app. This is typically a production site, and one or more staging sites.
Additionally, every developer has a copy of the app running in their local development environment, each of which also qualifies as a deploy.