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Claude reads it alright, and then ignores it.

Dev: Why did you run Y command? Doesn’t it clearly say in README.md to use X command instead?

Claude: You are right to be frustrated. I ignored it because “some generic excuse”. It won’t happen again

Narrator: It will happen again

Asking it why it did something will not get you usable data. It will read what it did in the context and hallucinate a reason.

You are right on that, but my point was how it just ignores what it read, even if it is in its context

It read the context and randomly picked a way around what it asked. That's just how it works. Other times, it will follow it.