Flarum/flarum is the skeleton. It's like a preset, if you're a familiar with Laravel. It contains the basics to boot Flarum, it has flarum core, several of our first party Extensions and its dependencies as dependencies.
The flarum framework repository contains the source code of Flarum, including core, extensions, utilities and mithril code. You will not need that repository unless you want to contribute to Flarum.