IMHO the best and most relevant part of fossil these days is the ticket system, which is in every single way almost completely ideal for coding agents. Some features are: single-binary, in-repo, CLI or web UI, and offline / sql / markdown-friendly.

Since the whole tracker is just a thin front on sqlite with the above features there's many options. Use it per-project persistently so as to include co-workers, or only locally for your own agents to "think" inside of so they are less likely to dump CoT all over the code-comments. Use it even at a per task granularity, and throw it away afterwards. Do all three, fossil doesn't care! And the agents will love it.