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Correct: the flags live in a separate repo.

That’s really an 80/20 situation. The flag repo fixes several large problems around visibility, coordination and state tracking of flag status, but introduces more friction into the system.

I’m not sure I have a comprehensive solution. I just know which ones I hate more than which others. The repo is the least obnoxious of the options.

Can you say more? I think i'm missing the point, in my mind that would make it even worse because you have all the problems I mentioned + merge conflicts being a possibility

Well I don't think you are doing active development on your flags repo. I think it's just using Git as a database for the what are your current feature flags.

One repo is actual flags control-like-database.

So instead of controlling flags from a website, you get the benefits of git merge, PR's, reviews, documentation etc without having to rebuild it.

I like the concept since it brings accountability. But it's just a need that larger orgs have, but by that point have likely internally built a flag system and so transitioning is difficult.

We do this at my company and another huge benefit is the ability to test config at a particular point in time. You can even git bisect to find which flag flip caused a regression.