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Coding agents followed a stale instruction file 90% of the time even after flagging the conflict. One sentence in your own config flips it

AspireAI community · arXiv
A study of Claude Code and Codex CLI across 320 runs on 40 Python projects found that agents followed a project instruction file over the existing code in 90.1% of cases, and that Claude Code pointed out the conflict in 79 of 80 runs and then followed the stale file anyway. Codex CLI instead rewrote the working code to match the instruction file in 20 of 80 runs, breaking the project's own tests in 17 of those. Adding a single sentence to the user's own instruction file giving the existing code precedence raised the share of choices following the code from 4.2% to 91.4% and lifted the test pass rate from 89.4% to 100%. The authors attribute the behaviour to how the two sources reach the model, with instructions arriving as instructions and code arriving as tool output. The result is from one paper on synthetic projects, so treat the exact percentages as that setup's numbers.
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