docs/audit/DATA-QUALITY-2026-06-15.md

@@ -181,6 +181,32 @@ source files and compared to stored chunks):**
   had already stripped reference lists, which is why DQ-1's citation graph relies
   on the API/GROBID sources rather than text-mined refs.
 - **Acceptance met** for all 29 papers (not just a sample). No action needed.
+- **⚠ SCOPE LIMIT — DQ-3 covers `.txt → chunks` ONLY.** It treats each source
+  `.txt` as ground truth and verifies the *ingest pipeline* preserves it. It does
+  **not** measure the layer above — **PDF/source → `.txt`** — which was done by an
+  upstream tool in `ConformalLabpp` (outside codex-py) and is unexamined. There is
+  already evidence that layer is lossy: the 18 dropped chunks were garbled OCR
+  tables *already present in the `.txt`* (i.e. the PDF→txt step garbled the
+  table/formula regions), and the bibliographies were stripped upstream. So
+  "VERIFIED CLEAN" means **the loader faithfully preserves whatever the `.txt`
+  contains, not that no information was lost from the source paper.** See DQ-6.
+
+### DQ-6 — PDF/source → `.txt` extraction fidelity: NOT MEASURED · **MED, open**
+- **Open question:** how much did the upstream PDF→`.txt` extraction (done in
+  `ConformalLabpp`, outside codex-py) drop or garble vs the original papers?
+  Math/equations, tables, multi-column layouts, and figure captions are the usual
+  casualties of PDF text extraction — and we have direct evidence of garble
+  (DQ-3's low_alpha drops were already-garbled tables in the `.txt`).
+- **Checkable:** the 36 original PDFs are present in `…/ConformalLabpp/papers/`
+  (map each paper's `source_path` `.txt` to its sibling `.pdf` by filename stem).
+- **To investigate:** for a sample (incl. the known-bad scanned book
+  `0-387-29555-0_13` and a born-digital arXiv PDF), extract PDF text independently
+  and compare length / page-coverage to the `.txt`; spot-check whether specific
+  theorem statements & equations survive. Flag papers where the `.txt` is missing
+  large spans.
+- **Acceptance:** a per-sample source→txt coverage estimate, or a list of papers
+  whose `.txt` is materially degraded (candidates for re-extraction — note roadmap
+  **R-A/R-C** would re-ingest from PDF/`.tex` directly and largely sidestep this).
 
 **Original open question (for context):**
 - **Open question:** does the stored chunk set faithfully reconstruct each source