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Clarify that files modified in prek runs are still failures #1573

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@nathanjmcdougall

Context:
j178/prek#1868

e.g. Files were modified by following hooks...................................Failed is a failure. Just because all the tools "Passed" or were "Skipped" doesn't mean it was a success.

We should update the agent skills for static checks to clarify this edge case, it came up in #1558

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agentConfiguration updates for LLM coding agents

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