v0.39.0: full-repository audit and its first-tier fixes

.claude-plugin/marketplace.json

@@ -5,14 +5,14 @@
   },
   "metadata": {
     "description": "Single-plugin marketplace for sci-paper: scientific paper writing, source-traced review, and de-AI rewriting for top-tier journals.",
-    "version": "0.38.0"
+    "version": "0.39.0"
   },
   "plugins": [
     {
       "name": "sci-paper",
       "source": "./",
       "description": "Scientific paper writing, source-traced review, and de-AI rewriting for top-tier journals (ApJ/MNRAS/PRD/JCAP-class) and NSF/NIH proposals. Ships 12 skills and 40 tools under one typed standard: scientific-integrity blockers that cannot be waived as style preferences, a zero-target L0 lexicon, ranked advisories, explicit measurement states so missing calibration never reads as clean, claim-first rewriting gated on hard scientific-fidelity eligibility, a mechanical length budget with a machine-built removal map and a required-shrink gate, corpus-calibrated salience-hierarchy, domain-register (with an exhaustive zero-hit vocabulary audit), collocation, and discourse-texture (given/new cohesion, epistemic hedging) axes, each judged against the field's own per-section distribution at the unit it was calibrated at, a residue axis that gates the trace an edit leaves, A-R review with narrative-spine and adversarial-escalation dimensions, registry-verified bibliographies (CrossRef, DataCite, arXiv), pixel-measured figure review, and isolated multi-reviewer orchestration. Learned scores are field-similarity triage, never an authorship verdict. See CHANGELOG.md for per-version history.",
-      "version": "0.38.0",
+      "version": "0.39.0",
       "author": {
         "name": "skymanbp",
         "email": "skyman.bp@gmail.com"

.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "sci-paper",
-  "version": "0.38.0",
+  "version": "0.39.0",
   "description": "Scientific paper writing, source-traced review, and de-AI rewriting for top-tier journals (ApJ/MNRAS/PRD/JCAP-class) and NSF/NIH proposals. Ships 12 skills and 40 tools under one typed standard: scientific-integrity blockers that cannot be waived as style preferences, a zero-target L0 lexicon, ranked advisories, explicit measurement states so missing calibration never reads as clean, claim-first rewriting gated on hard scientific-fidelity eligibility, a mechanical length budget with a machine-built removal map and a required-shrink gate, corpus-calibrated salience-hierarchy, domain-register (with an exhaustive zero-hit vocabulary audit), collocation, and discourse-texture (given/new cohesion, epistemic hedging) axes, each judged against the field's own per-section distribution at the unit it was calibrated at, a residue axis that gates the trace an edit leaves, A-R review with narrative-spine and adversarial-escalation dimensions, registry-verified bibliographies (CrossRef, DataCite, arXiv), pixel-measured figure review, and isolated multi-reviewer orchestration. Learned scores are field-similarity triage, never an authorship verdict. See CHANGELOG.md for per-version history.",
   "author": {
     "name": "skymanbp",

ACKNOWLEDGMENTS.md

@@ -8,20 +8,26 @@ implicit.
 
 ## AIScientists-Dev/academic-humanizer
 
-<https://github.com/AIScientists-Dev/academic-humanizer> (MIT)
+<https://github.com/AIScientists-Dev/academic-humanizer> (MIT License,
+Copyright (c) 2026 AIScientists-Dev)
 
 **Adopted.** The 2026-07-16 lexicon extensions (`underscore*`, `pivotal`,
 `tapestry`, `testament`, `realm*`, `intricate`, `foster*`); the `serves as`,
 `ing-tail`, and `colon-elaboration` linter rules; the Claim–Evidence Discipline
-and Preserve List sections of [`skills/paper/SKILL.md`](skills/paper/SKILL.md);
+(its Layer 4, recalibrated on the astronomy corpus) and Preserve List (its
+Layer 3) sections of [`skills/paper/SKILL.md`](skills/paper/SKILL.md);
 the [`proposal-polish`](skills/proposal-polish/SKILL.md) skill; and the
 [`de-ai`](skills/de-ai/SKILL.md) skill's Layer 1–5 audit catalog adapt its
-material.
+material. The first five words entered Tier A only after both curated field
+corpora showed zero occurrences of them; `intricate` and `foster*` occur once
+each there, so they entered Tier B.
 
 **Declined.** Venue-specific rules that conflict with astronomy usage —
-`landscape`, and the blanket `demonstrate` / `significantly` bans. Every lexical
-adoption was re-verified against the curated field corpora before tier
-assignment.
+`landscape`, a legitimate field term (`detection landscape`) frequent in the
+corpus, and the blanket `demonstrate` / `significantly` bans: in the combined
+curated astronomy corpus `demonstrate*` runs at 0.147/1k and `significantly` at
+0.274/1k (measured 2026-07-16). Every lexical adoption was re-verified against
+the curated field corpora before tier assignment.
 
 academic-humanizer itself builds on blader/humanizer (MIT).
 
@@ -38,6 +44,12 @@ self-interrogation step, and its false-positive guards.
 chatbot artifacts, curly-quote flags) and its `landscape`-flagging word list.
 Only the academically relevant structural tells were absorbed.
 
+## Project-owner rules
+
+Two rules in [`skills/paper/SKILL.md`](skills/paper/SKILL.md) were set by the
+project owner on 2026-07-16: condense, do not accumulate (改写、删减、精简，而不是堆叠;
+now standard §5.3), and the `colon-elaboration` rule.
+
 ---
 
 Licensing: [MIT](LICENSE) covers code, skills, documentation, and tooling

CHANGELOG-ARCHIVE-EARLY.md

@@ -6,6 +6,7 @@ The earliest history of the plugin, from the first release through v0.21.0
 is edited; the history is verbatim.
 
 - Current releases: [CHANGELOG.md](CHANGELOG.md)
+- **v0.35.0 through v0.35.1**: [CHANGELOG-ARCHIVE-v0.35.md](CHANGELOG-ARCHIVE-v0.35.md)
 - **v0.33.0 through v0.34.0**: [CHANGELOG-ARCHIVE-v0.33-v0.34.md](CHANGELOG-ARCHIVE-v0.33-v0.34.md)
 - **v0.27.1 through v0.32.0**: [CHANGELOG-ARCHIVE-RECENT.md](CHANGELOG-ARCHIVE-RECENT.md)
 - **v0.22.0 through v0.27.0**: [CHANGELOG-ARCHIVE.md](CHANGELOG-ARCHIVE.md)

CHANGELOG-ARCHIVE-RECENT.md

@@ -6,6 +6,7 @@ live changelog passed the repository's 750-line budget. Nothing here is edited;
 history is verbatim.
 
 - Current releases: [CHANGELOG.md](CHANGELOG.md)
+- **v0.35.0 through v0.35.1**: [CHANGELOG-ARCHIVE-v0.35.md](CHANGELOG-ARCHIVE-v0.35.md)
 - **v0.33.0 through v0.34.0**: [CHANGELOG-ARCHIVE-v0.33-v0.34.md](CHANGELOG-ARCHIVE-v0.33-v0.34.md)
 - **v0.22.0 through v0.27.0**: [CHANGELOG-ARCHIVE.md](CHANGELOG-ARCHIVE.md)
 - **v0.21.0 and earlier**: [CHANGELOG-ARCHIVE-EARLY.md](CHANGELOG-ARCHIVE-EARLY.md)

CHANGELOG-ARCHIVE-v0.33-v0.34.md

@@ -6,6 +6,7 @@ archive was within 65 lines of it. Nothing here is edited; the history is
 verbatim.
 
 - Current releases: [CHANGELOG.md](CHANGELOG.md)
+- **v0.35.0 through v0.35.1**: [CHANGELOG-ARCHIVE-v0.35.md](CHANGELOG-ARCHIVE-v0.35.md)
 - **v0.27.1 through v0.32.0**: [CHANGELOG-ARCHIVE-RECENT.md](CHANGELOG-ARCHIVE-RECENT.md)
 - **v0.22.0 through v0.27.0**: [CHANGELOG-ARCHIVE.md](CHANGELOG-ARCHIVE.md)
 - **v0.21.0 and earlier**: [CHANGELOG-ARCHIVE-EARLY.md](CHANGELOG-ARCHIVE-EARLY.md)

CHANGELOG-ARCHIVE-v0.35.md

@@ -0,0 +1,148 @@
+# Changelog archive — v0.35.0 through v0.35.1
+
+Entries moved out of [CHANGELOG.md](CHANGELOG.md) on 2026-09-27 (v0.39.0) when
+the live changelog passed the repository's 750-line budget. Nothing here is
+edited; the history is verbatim.
+
+- Current releases: [CHANGELOG.md](CHANGELOG.md)
+- **v0.33.0 through v0.34.0**: [CHANGELOG-ARCHIVE-v0.33-v0.34.md](CHANGELOG-ARCHIVE-v0.33-v0.34.md)
+- **v0.27.1 through v0.32.0**: [CHANGELOG-ARCHIVE-RECENT.md](CHANGELOG-ARCHIVE-RECENT.md)
+- **v0.22.0 through v0.27.0**: [CHANGELOG-ARCHIVE.md](CHANGELOG-ARCHIVE.md)
+- **v0.21.0 and earlier**: [CHANGELOG-ARCHIVE-EARLY.md](CHANGELOG-ARCHIVE-EARLY.md)
+
+---
+
+## v0.35.1 — 2026-09-03
+
+A post-release audit of the documentation, not of the code. An escape the
+writer lost had truncated the tools table in both READMEs, the one published
+figure with no artifact behind it was wrong, and several figures and dates in
+the record had drifted from what they describe.
+
+### A lost backslash ended the tools table four rows early
+
+The `tools/tex_macros.py` row wrote `\newcommand` without its backslash, and
+the consumed newline split the row, so the table stopped rendering there —
+`retrieve_exemplars`, `fetch_arxiv_abstracts`, `train_ai_ism_classifier` and
+`extract_md_negatives` fell out of it, in both READMEs. The same damage sat in
+the v0.32.0 changelog entry at `\nocite`.
+
+### The worked example published a count the linter does not report
+
+`examples/README.md` said 19 total advisories where `ai_ism_lint` reports 18.
+It was the only published-figure document with no artifact behind it, so
+nothing read it. `tests/test_published_figures.py` now renders both of its
+tables — the before/after summary and the per-rule counts — by running the
+linter on the two shipped manuscripts and looking for the result, the same way
+every other pinned figure is rendered from the artifact it was read from. A
+cell the linter does not produce fails the case, so a document that agrees with
+a stale run and a document nobody updated fail identically.
+
+### Figures and dates the record had drifted from
+
+- **203**, not 200, held-out refereed papers, in the two `DISPOSITIONS.md` rows
+  that still carried the count from before §18 re-measured it.
+- The v0.30.0–v0.33.0 changelog headings were dated 2026-08-27; their tagger
+  dates are **2026-08-26**.
+- The release-gate label in `EVALUATION.md` §12 stamped a version on a suite
+  size measured after it. It now reads "as of 2026-09-03; last tagged release
+  v0.35.1", so the version names the tag and the date names the measurement.
+- Both README latency tables paired 394 tests with 81.4 s, a wall time taken on
+  the 393-test suite. The suite row is re-taken: **73.0 s**, median of 3, the
+  three runs spanning 70.0–86.9 s. Every other row still stands from the
+  2026-08-27 take and the preamble now says which rows carry which date.
+- `docs/README.md` called the evidence record five files where it is eight,
+  gave three of them section maps missing the sections added since, counted
+  four kinds of document where six live there, and described the validator's
+  version and suite-size checks narrower than they are.
+- The unit-pattern anchor in both READMEs pointed at `rewrite_reward.py:41`;
+  the pattern is at `:56`.
+- Both READMEs said CI runs on every push. `ci.yml` filters `branches: [main]`,
+  so it runs on every push to `main` and every pull request.
+
+### Also
+
+- `.gitignore` covers `models/hf-cache/`, `.ce/` and `.ccm/` — relocated model
+  cache and machine-local tool state, never repository content.
+- Suite: 394 tests across 20 files; `validate_plugin.py` 9/9.
+
+## v0.35.0 — 2026-08-27
+
+The axis that counts numbers could not see numbers written as macros, a public
+repository was carrying an unpublished manuscript's method summary, and the
+worked example that demonstrates any of this now runs on a synthetic paper
+instead of a real one.
+
+### Numbers held in macros were invisible, in both directions
+
+A manuscript that writes `\newcommand{\Nsamples}{12}` in its preamble and
+`\Nsamples{}` in its results put a measured quantity where neither named text
+projection could read it. `RE_TEX_SIMPLE_CMD` reduces a command to its
+argument, so the use site contributed nothing while the definition site
+contributed the digits once, in the preamble, attributed to no reported
+section. Two errors running in opposite directions, which is why the net stayed
+small enough to go unnoticed: on the manuscript that surfaced it, expanding the
+uses adds 650 digits and dropping the definitions removes 493.
+
+Found by running the tools on a real manuscript, not by a test. The salience
+axis had been reporting recital percentiles for that paper computed on 91% of
+its digits, and correcting it moved that paper from 16 recital findings to 26.
+
+`tools/tex_macros.py` expands numeric-literal macros once, on the assembled
+document root, because that is the only scope holding both a preamble
+definition and a body use — the same reason `read_tex_document` folds
+`\include` in the first place. Only a bare numeric literal expands, so
+`\newcommand{\Msun}{M_\odot}` and every macro taking an argument are untouched.
+
+Both salience baselines were rebuilt rather than left to score expanded
+manuscripts against an unexpanded reference. They move by **zero to four
+decimals** at the p90 and p95 gates, across all three features and all seven
+buckets, in both `wgl` and `wgl-letter`: 88.2% of 390 corpus documents never
+use the construction. That is what separates a correction from a rescaling, and
+it means no published salience figure in `EVALUATION.md` changes (§22).
+
+### An unpublished manuscript's method summary was in a public repository
+
+This repository is public. Content from the author's unpublished manuscripts
+had accumulated in the evaluation record since 2026-07-12, in increments that
+each looked locally harmless — a codename in a test fixture, a macro and its
+value in a docstring, one fidelity-preserving rewrite quoted in full.
+
+The aggregate was a complete method summary: enough of the method for a competitor to reconstruct the contribution. Public for 46 days.
+
+The quoted rewrite was the largest single exposure, and it was labelled a
+proposal rather than a quotation, which is exactly why it survived review: the
+rewrite gate protects numbers, citations, macros, entities and claim/evidence
+relations, so a fidelity-preserving rewrite discloses what the original
+discloses. Being a rewrite is not a defence.
+
+Removed: the quoted block, the method-component list, manuscript codenames
+throughout, one real measured value, and manuscript-derived test fixtures,
+which now use invented macros. Kept: every measurement. Finding counts,
+percentiles, rule names, before/after tables and the panel results describe how
+the tools behave, not what the paper found, and they are why the record exists.
+
+Git history was rewritten to remove the same content from every earlier commit.
+That does not undo publication — the content may persist in existing clones,
+forks and upstream caches.
+
+### A worked example that is safe to ship
+
+`examples/` now carries a synthetic manuscript and the same paper after acting
+on the findings. The topic is a textbook one and every value is invented, so
+the demonstration no longer depends on anyone's unpublished work.
+
+It is also a more honest demonstration than a clean sweep would be. L0 targets
+go to zero and `discourse-cohesion` from 3 findings to 1, while
+`salience-recital` **rises** from 4 to 6 — because carrying a noun forward to
+link two sentences pulls the subject into sentences that also carry a numeral.
+In a number-dense passage cohesion and recital want opposite things and no
+rewrite satisfies both. Both findings are true, and which to act on is the
+author's judgement, which is why neither is a blocker and there is no score.
+
+### Also
+
+- The re-export contract test named its excluded module imports one at a time
+  (`re`, `defaultdict`, `Path`), so it failed the moment a new import appeared.
+  It now excludes module objects by type.
+- Suite: 393 tests across 20 files; `validate_plugin.py` 9/9.

CHANGELOG-ARCHIVE.md

@@ -6,6 +6,7 @@ the repository's 750-line budget. Nothing here is edited; the history is
 verbatim.
 
 - Current releases: [CHANGELOG.md](CHANGELOG.md)
+- **v0.35.0 through v0.35.1**: [CHANGELOG-ARCHIVE-v0.35.md](CHANGELOG-ARCHIVE-v0.35.md)
 - **v0.33.0 through v0.34.0**: [CHANGELOG-ARCHIVE-v0.33-v0.34.md](CHANGELOG-ARCHIVE-v0.33-v0.34.md)
 - **v0.27.1 through v0.32.0**: [CHANGELOG-ARCHIVE-RECENT.md](CHANGELOG-ARCHIVE-RECENT.md)
 - **v0.21.0 and earlier**: [CHANGELOG-ARCHIVE-EARLY.md](CHANGELOG-ARCHIVE-EARLY.md)
@@ -395,7 +396,7 @@ repeats nothing — what it lacks is rank.
   subfields.
 - **The same bank must not become the register reference.** 254 documents
   cannot express a rate below 1/254 = 3.9e-3, 39.4× coarser than the 1e-4
-  threshold, so `saddle`, `classifier`, `recall`, and `ablation` flip to
+  threshold, so `classifier`, `recall`, and `ablation` flip to
   foreign on zero counts. A register reference needs of order 10,000
   documents. The bank is stored and wired to nothing.
 
@@ -462,8 +463,8 @@ the pre-2022 date filter turns out to bound less than it appears to.
 - **The same bank must NOT become the register reference.** `deai_register`
   calls a term foreign below a document-frequency rate of 1e-4, but 254
   documents cannot express a non-zero rate below 1/254 = 3.9e-3, 39x
-  coarser than the threshold. Under that reference `saddle` — the central
-  concept of one of this suite's manuscripts — flips from native to
+  coarser than the threshold. Under that reference the central concept
+  of one of this suite's manuscripts flips from native to
   foreign purely on zero counts, as do `classifier`, `recall`, and
   `ablation`. A register reference needs of order 10,000 documents for a
   single occurrence to land at the threshold, so the broad bank stays.