What does a conflicting instruction set cost you? For one, time and tokens, not to mention the constant headache to figure out the "why?". An instruction you wrote and rely on heavily gives contradicting results, the only tell-tale that something is going wrong. No other warning present. Say your CLAUDE.md carries code under scratchpad/ ships without tests in one section and, further down, write a test for every function . The first time the agent works in scratchpad/ , the two collide...