The sweep has three steps: read the system prompt, read the context file, compare them. The first two are cheap to mechanize. The third is expensive because a person has to hold both documents in mind and keep hunting for lines where the context file tells the agent to do something the prompt forbids or states a fact that contradicts it.
Spending a little on a model pass is worth it. Research on repository context files found that unnecessary requirements make agent tasks harder, so fixing a contradictory file has value beyond tidiness (Evaluating AGENTS.md, AlphaXiv). The failure modes of models used as judges are documented and predictable, so you can plan a review around them instead of pretending they do not exist (Evaluation-Driven Iteration for LLM Applications, arXiv).
Treat this as an evaluation. You are not asking a model for an opinion about your file. You are scoring a fixed output against fixed labels with a fixed prompt, the same way you would score any prompt change (What is prompt evaluation, Braintrust). That discipline is the difference between a check that improves and a demo that quietly lies.
A working definition: a contradiction exists when a context-file item cannot be true at the same time as a prompt item. Two sentences can mean the same thing in different words, so exact-match tests will not help (Evaluation-Driven Iteration for LLM Applications, arXiv). The task is semantic, which is why a model is the right tool and why its errors are semantic too.



