Companies like CoreOS, Mesosphere, all fall under this umbrella, where you could technically glue all their open source components together to form their main product, but it would take you quite a bit of time to support.
Github is sort of like this. They contribute a ton to open source, and are built mostly out of open source components (that ARE open source). But their website is really just a glue to all their infrastructure, and that's closed source.
That's not true, they have lots of open source projects under their organization: https://github.com/github. It's not enough to build your own GitHub clone, but some significant parts are being developed in the open (jekyll, hubot, linguist, ..)
This makes it sound like Github develops and open sources git, which it doesn't. They just built on top of it and have no control over the roadmap.