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Hence the shutdown

Notice they're closing?

Trello's integration is an afterthought and I never found it as useful or simple as Waffle's; they'll be missed.

They're not "closing"; CA Technologies bought them a while back and now CA is selling to Broadcom, who's killing the product.

Exactly.

It didn't always. Products like Waffle and ZenHub came about to meet market needs for better project management with Github. (Waffle launched in 2013)