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The --update runbook's Step 9 stamped the entire detected corpus into the manifest, so a semantic file (doc/paper/image) whose chunk failed or was omitted was recorded as done and never re-queued on the next update — losing its content permanently. The runbook now builds the manifest the way the library extract path does: cli._stamped_manifest_files stamps only files that actually produced nodes/edges/hyperedges, dispatched-but-empty files have their stale hash cleared, and scan_corpus drops newly-excluded in-root rows. Applied to the Claude, Aider, and Devin skill bodies and the shared update reference; all 134 artifacts regenerated. gen.py gains a sanctioned monolith- diff predicate for the new stamping lines.