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Part A reads .graphify_detect.json and Step 9 deletes it, but the aider
and devin --update sections never wrote it again, so Part A raised
FileNotFoundError after any full build.
The sections now write it from .graphify_incremental.json, as the
generated references/update.md does, with each file's own path
convention.
The test no longer seeds the file; it asserts the update section wrote
it.
(cherry picked from commit ca090b6da5)