Hi, yes you're right that the main repository is
https://github.com/stackalytics/default_data Stackalytics.com uses it directly. However most of the people still use x/stackalytics to update company affiliation.
We can't close x/stackalytics repo because it contains source code of stackalytics itself.
The solution with 2 repositories for companies was temporary to allow people to move to github.
But as we see we need some other way to ask people to use github.
Unfortunately I was busy for a while, that is why we had a lot of open PRs on x/stackalytics.
I merged most of them yesterday. And I'll try to do it more often.
Sergey