Yep, this isn't a great solution for software factories.

As I see it - you need to track spec (a declarative process) and also tasks/progress (an imperative process). You do need to manage blockers so tasks should largely be a dependent graph.

There's also a third thing which emerges - which is "design decisions along the way". I do actually keep this in the repo as well, but I'm not sure this is correct.

Beads combines all three, which I'm not sure is correct, but seems quite brilliant.