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Pin the factory config at run start - #89
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… commands Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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A security review found .factory/config.yaml was read lazily from the working tree, so a build step that edited it could change the commands the gate runs. runIssue now loads and pins it before the first agent call. The test rewrites the file after pinning and asserts the commands do not change.
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