I assume with 1000 agent jobs you mean completed jobs, not jobs running in parallel.
My solution for keeping the historical context of my projects: In docs/plan/, I have plans currently being executed. They get deleted when the work is done, and their contents gets folded into the permanent documentation in docs/.
I have the rule for the agents to put into the long-living documentation only that which is
1. not obvious from the source code (surprisingly much is obvious for agents),
2. information that an experienced engineer would not to rebuild the project (ignoring if it would look different).
Your 1000 changes in a few weeks matches the order of magnitude of changes that I did in a recent project of mine. It's a tool for managing agents, so a bit of a circular example, but anyway, if you want to take a look at the layout and CLAUDE.md instructions, it's open source: https://github.com/sadilek/obeya