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I used to use this approach as well for managing many agents and myself. I do think the bloat problem is real as well as the need to handle multiple disjoint workstreams.

My solution was to put tasks and their dependencies in a sqlite db. https://github.com/mhalstrom/maximizepm take a look if you're interested

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Why not use Linear/Plane/Paperclip?

I built an issue tracker that persists issues as code, which you can run in a separate, linked repo, so you don't need to litter your code repo. If you do run it the same repo it puts it in a state branch, so it isn't really in the way.

https://ljtn.github.io/epiq/

One benefit of persisting issues as code is traceability of intent and keeping track of vision drift. Epiq enables this via time travel, so you can trace the board evolution by going back in time, filtering for specific sessions, etc.

I like it, especially the name :)

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