So the options are a) being a really aggressive stickler for generative hygiene with deterministic rules, b) being massively wasteful about hiring a few machine janitors for every machine coder, or c) humans become the machine's janitor. If I haven't missed an option.. only the first option seems reasonable here.

And here is where naive people will say something like "Why do I care if robots shit all over the codebase? Code is for machines, I don't expect to deal with it much now". But really externalized CoT like this confuses machines too, wastes tokens, and eventually wastes exponentially many tokens. Agents tend to think it's more real grounding than prompts are, even for comments-in-code. One bad comment poisons everything, then gets copied around as a ground-truth assumption everywhere. Hooks are more real to them than prompts or comments, and even then if you add enforced limits and tell them to externalize CoT ONLY in scratch task-tracking docs.. they will violate comment-enforcement hooks about 25% of the time. That tells you everything you need to know: even with constant reinforcement, they just really want to break this kind of rule.