Adds `tools/benchmark-harness/src/sf1.rs`: a block-weighted F1
implementation matching Kreuzberg's methodology, so SF1 numbers we
publish are directly comparable.

Scoring pipeline:
- Parse markdown via pulldown-cmark (tables, math, GFM) into typed
  blocks: Heading(1..6), Paragraph, CodeBlock, Formula, Table,
  ListItem, Image. Math in a paragraph promotes it to Formula, so
  engines that emit `$\alpha$` inline still score as a formula block.
- Per-block weights: heading=2.0, code/formula/table=1.5, list=1.0,
  paragraph/image=0.5. Heading detection is the highest-signal layout
  decision; the weights reflect that.
- Type-compat matrix for cross-type allowances: heading↔heading by
  level distance (clamped ≥0.6), list↔paragraph=0.5,
  paragraph↔heading=0.25, code↔formula=0.3, code↔paragraph=0.2,
  table↔paragraph=0.25.
- Greedy matching on (content_tf1 × type_compat) with threshold 0.10
  (0.20 for short blocks <5 tokens) and no-replacement assignment by
  descending score.
- Weighted precision/recall/F1 using the matched weights on both sides.
- Order score = LIS length of matched ext indices (sorted by gt index)
  / match count. 1.0 = perfectly preserved order; 0.5 = half the
  matches are out of place.

The per-fixture report gains sf1, sf1_precision, sf1_recall,
order_score, matched_blocks. Aggregate gains sf1_mean/p50/p90 and
order_mean. `diff` prints mean TF1, SF1, order deltas — gate
thresholds still TF1-only for now (SF1 gating needs calibration on
a real corpus first to avoid false positives from parser differences).

10 new unit tests cover block parsing (headings/paragraphs/code/tables),
identical-input SF1=1, disjoint content SF1≈0, heading-level-mismatch
partial compat, reversed-order order_score=0.5, LIS basics, weight
taxonomy, and h1↔h2 / h1↔h6 compat values.

 phases 4–8)

Finishes the benchmark harness. Phases 4–8 in one commit.

Engine adapters (phase 4)
- `pdftotext` subprocess adapter wrapping poppler's `pdftotext -layout`.
  Probes the binary once at startup so a missing install fails fast,
  not per fixture. Honours `PDFTOTEXT_BIN` for non-standard locations.
- `pdfium` adapter behind the `pdfium` feature (default off, since the
  crate needs a prebuilt native library). Uses `pdfium-render` and
  falls back between system library and `PDFIUM_DYNAMIC_LIB_PATH`.

Consensus-baseline ground truth (phase 5)
- `--consensus-peers pdftotext,pdfium` on `run` (mutually exclusive
  with `--ground-truth`). Per PDF, runs the peers, takes the token
  intersection of ≥N (default 2) peers, and scores the target engine
  against it. SF1 is skipped in consensus mode (needs block stream,
  not a token set) so numbers aren't misleading.
- Report gains a `reference` field: `"manual"` vs
  `"consensus(pdftotext,pdfium)"`. Prevents downstream readers from
  confusing inter-engine agreement with absolute quality.
- 3 unit tests on the consensus token set + scoring (min-agree, peers
  exceed threshold, partial overlap).

Fixtures (phase 6)
- `scripts/fetch-fixtures.sh`: clones Kreuzberg (pinned via
  `KREUZBERG_REF`, default `main`) into `.fixture-src/`, symlinks
  `tools/benchmark-harness/fixtures/kreuzberg → tools/benchmark-harness/fixtures`
  from the upstream. Re-runnable; idempotent. Don't vendor PDFs
  directly — per-fixture licenses inside Kreuzberg's corpus vary.

Makefile + README (phase 8)
- `make benchmark-fetch`      — runs the fetch script
- `make benchmark-run`        — `cargo run --release -p benchmark-harness
                                 -- run --engine $(ENGINE) …`
- `make benchmark-compare`    — diff with regression gate
- README documents scoring formulas, invocation, engine matrix, JSON
  report schema, and license posture.

Tests: 18 total (5 TF1 + 10 SF1 + 3 consensus). Clippy clean under
`-D warnings`. Release branch build path unaffected — crate is a new
workspace member behind a cfg-less `cargo run -p benchmark-harness`.

Release-validation workflow this enables:
  git checkout main && make benchmark-run OUTPUT=base.json
  git checkout feat/X && make benchmark-run OUTPUT=head.json
  make benchmark-compare BASE=base.json HEAD=head.json
→ non-zero exit on meaningful TF1 regression, tuneable thresholds.

Two bugs found by the first local run on the Kreuzberg corpus:

- Fetch script pointed DEST at the upstream's fixture *metadata*
  directory, but the PDFs and ground-truth markdown actually live
  under test_documents/{pdf,ground_truth/pdf}. Flatten both into
  ${DEST}/pdfs and ${DEST}/gt as symlinks so the harness's
  stem-matching loader just works.
- walkdir by default skips symlinks, so every stem-matched pair was
  invisible. Enable follow_links(true) on both walkers.
- Makefile CORPUS/GROUND_TRUTH point at the flattened subdirs.
- Add .gitignore for the upstream clone + generated symlink forest so
  re-running the fetch script never contaminates the working tree.

First numbers on the 102-pair intersection (TF1 mean):
  pdf_oxide : 0.919   pdftotext : 0.946   Δ: -2.7pp

Detailed analysis follows in a separate artefact.

Running the harness end-to-end on Kreuzberg's 102-pair PDF corpus
turned up real pdf_oxide bugs, which is the whole point. Captured the
findings in BASELINE_ISSUES.md:

Headline numbers (engine vs pdftotext, TF1):
  mean   0.919 / 0.946  (Δ -2.7pp)
  p50    0.965 / 0.984  (Δ -1.9pp)
  p10    0.776 / 0.881  (Δ -10.5pp)   ← biggest gap on hard fixtures

Four issues identified, ranked by blast radius:

- B1: extract_text(n) returns identical content per page on some
  linearized PDFs (nougat_005.pdf: TF1 0.254 vs pdftotext 0.924).
  Page index appears to resolve to page 0 for every call.
- B2: empty-page false positives on text-heavy pages (pdfa_010 pages
  2/9/11 return 0 bytes; pdftotext emits 400–2000 each).
- B3: running-artifact detector suppresses cover-page titles when
  they happen to overlap with per-page running headers (pdfa_010
  loses "University of Oklahoma 2009"; same class as the 5PFVA6
  case from the v0.3.31 sweep).
- B4: XY-cut reading-order loses content on multi-column /
  dashboard layouts (order_mean 0.80 vs 0.86, nougat_026, pdfa_001,
  etc.).

All four are existing pdf_oxide bugs that the 170-PDF byte diff
couldn't catch (bytes matched across branches because both carry the
bug). Now we have a verification pipeline with numbers.

…harness

Numbers on the Kreuzberg 102-fixture corpus with the B1 fix merged in:

  TF1 mean 0.919 → 0.925   (+0.64pp)
  TF1 p10  0.776 → 0.848   (+7.2pp)  ← hard-tail improvement
  SF1 mean 0.337 → 0.339   (+0.22pp)
  runtime  8.3 s → 5.7 s   (−31%)

Zero per-fixture regressions. The worst-in-corpus fixture nougat_005
moved from TF1 0.254 to 0.901 — now essentially at parity with
pdftotext's 0.924 on that file.

This validates the harness workflow end-to-end: harness found a bug,
fix landed with TDD coverage, rerun quantifies the improvement, diff
subcommand gates against any accidental regression.

Drop tools/.gitignore that came in from the fix branch — on the
benchmark-harness branch the tools/benchmark-harness/ crate is the
whole point and must stay tracked.

…harness

After merging B1 and B3 into the harness branch, the Kreuzberg
102-fixture benchmark shows:

  TF1 mean 0.919 → 0.927 (+0.77pp)
  TF1 p10  0.776 → 0.849 (+7.3pp)   ← hard tail
  SF1 mean 0.337 → 0.343 (+0.54pp)
  order    0.804 → 0.819 (+1.5pp)
  runtime  8.3s → 5.6s (-33%)

Zero per-fixture regressions at either fix. Supersedes B1_RESULTS.md.

B2 closed as not-a-bug — post-B1 no fixture has pdf_oxide returning
empty where pdftotext succeeds; pdfa_010's empty pages turned out to
be genuinely empty in both tools.

B4 deferred — multi-column reading-order wants XY-cut promoted to
default in extract_text, which is an architectural change with
enough blast radius to warrant its own validation cycle. Tracked;
nougat_026/pdfa_001 at order_score ~0.4 are the canaries for it.

…harness

XY-cut as default reading order for multi-column pages is correct
(synthetic TDD test passes) but the Kreuzberg corpus aggregate shows
neutral impact:

  TF1 mean  0.927 → 0.927 (+0.04pp)
  SF1 mean  0.343 → 0.342 (−0.09pp)
  order     0.819 → 0.817 (−0.19pp)

Per-fixture: ~6 wins (nougat_011/012, pdfa_048) at +5..+10pp, ~5
losses (nougat_033, pdfa_008, pdfa_037) at −2..−14pp, and a long
tail of no-ops.

Interpretation captured in RESULTS.md: XY-cut is semantically
right, but Kreuzberg's ground-truth markdown was generated from
content-stream-order serialisers, so on single-column pages where
content-stream ≈ row-aware, our fix loses SF1 points against a GT
that's "less correct in the same way". This is exactly the kind of
corpus-bias artefact the harness exists to surface — no amount of
heuristic tightening will improve the aggregate without disabling
the wins.

No per-fixture TF1 regression > 0.5pp; diff gate passes. Keeping the
fix since the synthetic test proves correctness on clearly-multi-
column input; the real corpus-level improvement needs better GT.