A simple instruction in AGENTS.md fixed that.
Before LLMs, I found "mostly works" systems like this to be incredibly sketchy and not worth using. The main thing I've had to learn in this past year is that what I thought was an ironclad rule turned out to be only a heuristic that was useful before but not always helpful, because empircally as much as I might find the lack of determinism jarring, in practice these tools are genuinely good enough at what they do to be worthwhile to use, as long as you're making sure not to use them in ways that the occasional failure costs more than just some wasted time.
I have not even really needed a formal memory system. If I see an error happen more than once, I just say "hey add a note on this to agents.md". Tends to be verbose but overall works quite well for the projects I am doing.
For Python, I have the agent use `uv` (even for direct script invocations) so that the agent doesn't need to burn tokens concerning itself with the details that `uv` is managing behind the scenes.