paperlint 7.2.0 → 8.0.0

package/hooks/paper-edit-guard.test.ts

@@ -15,7 +15,7 @@ const dir = hookConsumer(useTempDir("paper-edit-guard-"), {
 });
 /** `>` built rather than typed: a literal one here would be a redirection to the guard's own scan. */
 const GT = String.fromCharCode(62);
-const P = "papers/alpha/paper.md";
+const P = "papers/alpha/paper.tex";
 
 /** The guard's exit code for one Bash command: 2 denies, 0 lets it through. */
 const guard = (command: string): number =>
@@ -35,8 +35,8 @@ test("a `>` inside quotes, after an escaped quote, or escaped itself is not a re
 test("a redirection target is read through backslashes, quoted or not, and ends at a delimiter", () => {
   assert.deepEqual(
     [
-      guard(`echo x ${GT} "papers/alpha/pa\\per.md"`),
-      guard(`echo x ${GT} papers/alpha/pa\\per.md`),
+      guard(`echo x ${GT} "papers/alpha/pa\\per.tex"`),
+      guard(`echo x ${GT} papers/alpha/pa\\per.tex`),
       guard(`echo x ${GT}${P}; true`),
     ],
     [2, 2, 2],
@@ -55,3 +55,12 @@ test("a command cut off right after a backslash still names its target, quoted o
     [2, 2],
   );
 });
+
+test("only paper.tex is a paper source: copying over another file of the paper is let through", () => {
+  // Guards: the extension filter of the argv leg. (A redirection is refused for ANY file under the
+  // papers root, so the argv leg is the one that says which files are sources.)
+  assert.deepEqual(
+    [guard("cp /tmp/x papers/alpha/notes.txt"), guard(`cp /tmp/x ${P}`)],
+    [0, 2],
+  );
+});

package/hooks/paper-skills-nudge.hook.mjs

@@ -96,9 +96,8 @@ const papersRoot = (rawConfig) => {
   return root;
 };
 
-/** A paper SOURCE — a `.tex`, or a markdown-drafted `paper.md` / `draft.md`. Not every note or README. */
-const isPaperSource = (p) =>
-  p.endsWith(".tex") || /\/(paper|draft)\.md$/.test(p);
+/** A paper SOURCE — a `.tex`. Not every note or README. */
+const isPaperSource = (p) => p.endsWith(".tex");
 
 const CHECKLIST = `📄 Editing a paper — drive it with the \`paper-pipeline\` skill, don't wing the review.
   → Update <paper-dir>/PIPELINE-STATUS.md: mark the row for any stage you (re)ran, and read its

package/hooks/paper-skills-nudge.test.ts

@@ -10,11 +10,11 @@ import { useTempDir } from "../test/support.ts";
 
 const root = useTempDir("paper-skills-nudge-");
 
-test("no paperlint.json: an edit to papers/<p>/paper.md gets the checklist", () => {
+test("no paperlint.json: an edit to papers/<p>/paper.tex gets the checklist", () => {
   const dir = hookConsumer(join(root, "default"));
   const r = runShippedHook(
     "paper-skills-nudge",
-    onEdit("papers/alpha/paper.md"),
+    onEdit("papers/alpha/paper.tex"),
     dir,
   );
   assert.equal(r.exitCode, 0);
@@ -27,7 +27,17 @@ test("a paperlint.json that does not parse: silent, exit 0", () => {
   });
   const r = runShippedHook(
     "paper-skills-nudge",
-    onEdit("papers/alpha/paper.md"),
+    onEdit("papers/alpha/paper.tex"),
+    dir,
+  );
+  assert.deepEqual([r.exitCode, r.stdout, r.stderr], [0, "", ""]);
+});
+
+test("an edit to a file of the paper other than its source: silent", () => {
+  const dir = hookConsumer(join(root, "not-a-source"));
+  const r = runShippedHook(
+    "paper-skills-nudge",
+    onEdit("papers/alpha/notes.txt"),
     dir,
   );
   assert.deepEqual([r.exitCode, r.stdout, r.stderr], [0, "", ""]);

package/hooks/paper-status-gates.hook.mjs

@@ -31,7 +31,7 @@
  * harness's own edit helper builds a RELATIVE path. The live harness sends an ABSOLUTE one.
  * Measured against the real runtime:
  *
- *   file_path "<root>/<paper>/paper.md"                → fires
+ *   file_path "<root>/<paper>/paper.tex"               → fires
  *   file_path "/abs/path/to/repo/<root>/<paper>/…"      → SILENT
  *
  * So the hook would have been dead in production and green in the tests: precisely the
@@ -120,7 +120,7 @@ const papersRoot = (rawConfig) => {
  */
 const paperSourceRe = (root) =>
   new RegExp(
-    `(?:^|/)${root.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}/([A-Za-z0-9._-]+)/(?:[^/]*\\.tex|(?:.*/)?(?:paper|draft)\\.md)$`,
+    `(?:^|/)${root.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}/([A-Za-z0-9._-]+)/[^/]*\\.tex$`,
   );
 
 /**

package/hooks/paper-status-gates.test.ts

@@ -17,7 +17,7 @@ test("no paperlint.json: an edit under papers/ runs the gates for that paper", (
   });
   const r = runShippedHook(
     "paper-status-gates",
-    onEdit("papers/alpha/paper.md"),
+    onEdit("papers/alpha/paper.tex"),
     dir,
   );
   assert.equal(r.exitCode, 0);
@@ -31,7 +31,19 @@ test("a paperlint.json that does not parse: silent, exit 0", () => {
   });
   const r = runShippedHook(
     "paper-status-gates",
-    onEdit("papers/alpha/paper.md"),
+    onEdit("papers/alpha/paper.tex"),
+    dir,
+  );
+  assert.deepEqual([r.exitCode, r.stdout, r.stderr], [0, "", ""]);
+});
+
+test("an edit to a file of the paper other than its source: no gates run", () => {
+  const dir = hookConsumer(join(root, "not-a-source"), {
+    "papers/alpha/PIPELINE-STATUS.md": STATUS,
+  });
+  const r = runShippedHook(
+    "paper-status-gates",
+    onEdit("papers/alpha/notes.txt"),
     dir,
   );
   assert.deepEqual([r.exitCode, r.stdout, r.stderr], [0, "", ""]);

package/lib/markdown.test.mjs

@@ -1,7 +1,7 @@
 /**
  * markdown.mjs — the markup readers every script shares, on the shapes their callers rely on:
  * frontmatter blanked (offsets kept) or cut, headings from the parser (not from a `#` inside a
- * fence), sections by level, fences, paragraphs and tables. And the one thing a test run never
+ * fence), and fences. And the one thing a test run never
  * sees by accident: markdown-it failing to resolve, where every reader must degrade to its
  * documented empty value and `requireMarkdown` must refuse with exit 2.
  */
@@ -17,11 +17,8 @@ import {
   frontmatterBlock,
   headings,
   requireMarkdown,
-  paragraphs,
-  splitSections,
   stripFences,
   stripFrontmatter,
-  tables,
 } from "./markdown.ts";
 
 const DOC = [
@@ -93,27 +90,6 @@ test("an empty ATX heading has empty text", () => {
   );
 });
 
-test("splitSections: a preamble always first, then each heading of the level range", () => {
-  assert.deepEqual(
-    splitSections(DOC, { min: 2, max: 2 }).map((s) => [
-      s.heading?.text ?? null,
-      s.body.split("\n")[0],
-    ]),
-    [
-      [null, "---"],
-      ["One", "Body one."],
-      ["Two", "last"],
-    ],
-  );
-  assert.deepEqual(
-    splitSections("## A").map((s) => [s.heading?.text ?? null, s.body]),
-    [
-      [null, ""],
-      ["A", ""],
-    ],
-  );
-});
-
 test("fences and indented code, as content; stripped as lines, or blanked in place", () => {
   const src = "a\n```\nx\n```\n\n    y\nb";
   assert.deepEqual(
@@ -126,30 +102,6 @@ test("fences and indented code, as content; stripped as lines, or blanked in pla
   );
 });
 
-test("paragraphs are line ranges; tables are rows of cells, the alignment row skipped", () => {
-  assert.deepEqual(
-    { paragraphs: paragraphs(DOC), tables: tables(DOC) },
-    {
-      paragraphs: [
-        { line: 6, endLine: 7 },
-        { line: 9, endLine: 10 },
-        { line: 13, endLine: 14 },
-        { line: 27, endLine: 28 },
-      ],
-      tables: [
-        {
-          line: 22,
-          endLine: 25,
-          rows: [
-            ["a", "b"],
-            ["1", "2"],
-          ],
-        },
-      ],
-    },
-  );
-});
-
 const root = useTempDir("markdown-no-parser-");
 writeTree(root, {
   // Registered with --import: resolving `markdown-it` fails, as it does with no node_modules.
@@ -159,7 +111,7 @@ writeTree(root, {
   "probe.mjs":
     `const m = await import(${JSON.stringify(join(dirname(fileURLToPath(import.meta.url)), "markdown.ts"))});\n` +
     "const t = '# H\\n\\n```\\nx\\n```\\n';\n" +
-    "console.log(JSON.stringify([m.MD_AVAILABLE(), m.headings(t), m.fences(t), m.stripFences(t), m.paragraphs(t), m.tables(t)]));\n" +
+    "console.log(JSON.stringify([m.MD_AVAILABLE(), m.headings(t), m.fences(t), m.stripFences(t)]));\n" +
     "m.requireMarkdown();\n" +
     "console.log('not reached');\n",
   "probe-plugin.mjs":
@@ -188,22 +140,15 @@ test("with no markdown-it, every reader degrades to its empty value and requireM
   });
   assert.deepEqual(r, {
     status: 2,
-    stdout:
-      JSON.stringify([false, [], [], "# H\n\n```\nx\n```\n", [], []]) + "\n",
+    stdout: JSON.stringify([false, [], [], "# H\n\n```\nx\n```\n"]) + "\n",
     stderr:
       "markdown-it does not resolve — this script parses markup with a parser and without it would produce a confident zero instead of an error.\n" +
       "  Cured by `npm i` at the repo root.\n",
   });
 });
 
-test("splitSections of a document with no heading is the preamble alone; requireMarkdown is silent with a parser", () => {
-  assert.deepEqual(
-    [
-      splitSections("just text").map((s) => [s.heading, s.body]),
-      requireMarkdown(),
-    ],
-    [[[null, "just text"]], undefined],
-  );
+test("requireMarkdown is silent with a parser", () => {
+  assert.equal(requireMarkdown(), undefined);
 });
 
 test("headings read a token stream that breaks markdown-it's shape as empty text and offset 0", () => {

package/lib/markdown.ts

@@ -1,11 +1,10 @@
 /**
  * markdown.mjs — markup parsing for EVERYTHING in this repo that reads markdown.
  *
- * Three kinds of consumer: two advisory linters (`kb-lint`, `paper-lint` — through the
- * re-export from `lint-core.mjs`) and skill scripts (`tighten-paper/structure.mjs`,
- * `grade-paper-writing/prose-lint.mjs`, `paper-pipeline/scripts/*`). Hence the home is
- * here and not in the linter core: importing "the linter core" from a skill script
- * would be a lie about the direction of the dependency.
+ * Its consumers read the package's own markdown — skills' `SKILL.md` frontmatter
+ * (`skill-corpus.mjs`), fenced commands — and a consumer's linters of its own files.
+ * Hence the home is here and not in a linter core: importing "the linter core" from a
+ * skill script would be a lie about the direction of the dependency.
  *
  * CHECKS NOTHING AND PRINTS NOTHING: text in, data out. What to do with a missing
  * parser is the caller's decision, and the decisions DIFFER:
@@ -43,13 +42,6 @@ export interface Heading {
   readonly offset: number;
 }
 
-/** A chunk of the document: the heading it starts with (`null` for the preamble), with and without it. */
-export interface Section {
-  readonly heading: Heading | null;
-  readonly raw: string;
-  readonly body: string;
-}
-
 /** A block tokenizer with markdown-it's shape — the default, or one a test passes. */
 export type Parse = (text: string) => readonly Token[];
 
@@ -169,56 +161,6 @@ export function headings(
   return out;
 }
 
-/**
- * Slicing the document into chunks "a heading + everything up to the next heading FROM
- * THE SAME RANGE of levels". → `[{ heading, raw, body }]`.
- *
- * This is exactly what four scripts did as `split(/^(?=## )/m)` and
- * `split(/^(?=#{2,3} )/m)`. The shape of the expression lied about the intent: "two or
- * three hashes" is about CHARACTERS, while what is needed is the LEVEL, and `#{2,3}`
- * also caught a hash inside a ```-block, that is, it cut a quotation from someone
- * else's paper as a section of its own.
- *
- * `heading` — `null` on the zeroth element (the preamble before the first heading). It
- * is ALWAYS there, including empty: the former `split` also always returned the chunk
- * before the first separator as its zeroth element, and callers rely on that
- * (`sub === chunk` in `artifact-coverage` meant "there are no subsections").
- *
- * `raw` — WITH the heading line (it is used to count `§` references and bold numbers,
- * which occur in the heading itself too), `body` — without it (it is used to count words).
- *
- * 2026-08-11: moved here rather than copied into every script, because the chunk
- * boundary is the one place where an off-by-one is easy, and such a mistake has already
- * happened (`recordBlock` in `skill-corpus.mjs` returned a single "#" character for all
- * 21 skills).
- */
-export function splitSections(
-  text: string,
-  { min = 2, max = 6 }: { min?: number; max?: number } = {},
-): Section[] {
-  const hs = headings(text).filter((h) => h.depth >= min && h.depth <= max);
-  const out: Section[] = [];
-  const [first] = hs;
-  const preEnd = first ? first.offset : text.length;
-  out.push({
-    heading: null,
-    raw: text.slice(0, preEnd),
-    body: text.slice(0, preEnd),
-  });
-  for (const [i, h] of hs.entries()) {
-    const next = hs[i + 1];
-    const end = next ? next.offset : text.length;
-    const nl = text.indexOf("\n", h.offset);
-    const bodyStart = nl === -1 || nl + 1 > end ? end : nl + 1;
-    out.push({
-      heading: h,
-      raw: text.slice(h.offset, end),
-      body: text.slice(bodyStart, end),
-    });
-  }
-  return out;
-}
-
 /**
  * The text without the contents of ```-blocks (the fence lines themselves go too).
  *
@@ -229,14 +171,11 @@ export function splitSections(
  * `blank: true` — the block's lines are NOT deleted but REPLACED with empty ones. The
  * difference is not cosmetic: deleting the lines GLUES the paragraph before the block to
  * the paragraph after it, and a code block is a block boundary — on the other side a
- * different paragraph starts. Measured 2026-08-11 on `<papers-root>/<paper>/README.md`:
- * `prose-lint` counted 82 sentences there, and after the lines were deleted it counted
- * 81 — the lead paragraph "**Reproduction commands:**" merged with the text AFTER the
- * block into one sentence. That is exactly the failure against which `prose-lint` itself
- * says "Paragraph and heading boundaries END a sentence", and it inflates the
- * claims-per-sentence counter — the threshold at which the file emits findings. The
- * former regex preserved the boundary (it left one newline on each side), so `blank` is
- * also a preservation of the former behaviour where that behaviour was right.
+ * different paragraph starts. Measured 2026-08-11 on a README: a sentence counter counted
+ * 82 sentences there, and after the lines were deleted it counted 81 — the lead paragraph
+ * "**Reproduction commands:**" merged with the text AFTER the block into one sentence.
+ * The former regex preserved the boundary (it left one newline on each side), so `blank`
+ * is also a preservation of the former behaviour where that behaviour was right.
  */
 /**
  * The CONTENTS of fenced blocks — the other side of `stripFences`.
@@ -304,69 +243,3 @@ export function requireMarkdown({
   );
   process.exit(2);
 }
-
-/**
- * GFM tables — rows, cells and the line range, WITH THE PARSER.
- *
- * The only consumer as of 2026-08-20 is `crosspost-article`, which needs to re-lay a
- * table into a monospace block for a platform without tables (Medium). It lives here
- * and not in the skill, by the rule "markup is parsed with a parser, and in one place":
- * with a regex a table is told apart from a line of text with pipes only by its
- * neighbours, and that is exactly the class that has already cost this repo 27 places.
- *
- * Returns `{ line, endLine, rows }`, where `rows[0]` is the header; the alignment row
- * (`| --- |`) is thrown away, because in monospace output it has nothing to express.
- */
-/**
- * The document's paragraphs — `paragraph_open` line ranges, WITH THE PARSER.
- * `[{ line, endLine }]`.
- *
- * The only consumer as of 2026-08-21 is `crosspost-article`: the blog's sources are
- * hard-wrapped at a column (an editorial habit, not markdown), and the platforms render
- * a single `\n` inside a paragraph DIFFERENTLY — dev.to (Redcarpet) keeps it as a
- * literal line break, and the paragraph arrives torn into short lines exactly at the
- * source file's boundaries. Medium has no such defect not because the platform is more
- * honest, but because the paste goes through "Import a story" — the importer takes the
- * ALREADY RENDERED page of the site (where the breaks were collapsed by the browser long
- * ago), not the raw markdown.
- *
- * The range is EXACTLY the one `t.map` gives on `paragraph_open` — that is, a code
- * fence, a heading, a table, a list (in a TIGHT list the item is not wrapped in a
- * `paragraph_open` at all, it has no paragraph of its own) fall outside this function
- * automatically, by the construction of the parser, and not by a separate line-type
- * check.
- */
-export function paragraphs(text: string): { line: number; endLine: number }[] {
-  if (md === null) return [];
-  return md
-    .parse(blankFrontmatter(text), {})
-    .flatMap((t) =>
-      t.type === "paragraph_open" && t.map
-        ? [{ line: t.map[0], endLine: t.map[1] }]
-        : [],
-    );
-}
-
-export function tables(
-  text: string,
-): { line: number; endLine: number; rows: string[][] }[] {
-  if (md === null) return [];
-  const lines = blankFrontmatter(text).split("\n");
-  const out: { line: number; endLine: number; rows: string[][] }[] = [];
-  for (const t of md.parse(blankFrontmatter(text), {})) {
-    if (t.type !== "table_open" || !t.map) continue;
-    const rows: string[][] = [];
-    for (const raw of lines.slice(t.map[0], t.map[1])) {
-      if (/^\s*\|?[\s:|-]+\|?\s*$/.test(raw) && raw.includes("-")) continue; // alignment
-      rows.push(
-        raw
-          .replace(/^\s*\|/, "")
-          .replace(/\|\s*$/, "")
-          .split("|")
-          .map((c) => c.trim()),
-      );
-    }
-    out.push({ line: t.map[0], endLine: t.map[1], rows });
-  }
-  return out;
-}

package/lib/paper-config.ts

@@ -49,8 +49,6 @@ export const CONFIG_FILE: string = "paperlint.json";
  */
 export const PAPER_MARKERS: readonly string[] = Object.freeze([
   "paper.tex",
-  "paper.md",
-  "draft.md",
   "PIPELINE-STATUS.md",
 ]);
 

package/lib/skill-checks.test.mjs

@@ -236,7 +236,10 @@ test("a Bash entry narrowed to the instructed script permits it, and one narrowe
     await brokenBy("verify-citations", narrowTo("extract-ref-facts.mjs")),
     null,
   );
-  const lines = await brokenBy("verify-citations", narrowTo("round-diff.mjs"));
+  const lines = await brokenBy(
+    "verify-citations",
+    narrowTo("generated-code.mjs"),
+  );
   assert.equal(
     lines?.[0],
     '2 assertion(s) failed for skill "verify-citations":',

package/lib/skill-eval-fixture.ts

@@ -10,54 +10,61 @@
  * and the zero was an artifact of the empty directory, not a fact about the skill.
  *
  * Extracted from `paper-pipeline/pipeline-firing.eval.mjs`, which had it right
- * from the start, so the two runners cannot drift apart on what the model sees.
+ * from the start; the `paper-pipeline/*.eval.mjs` experiments carry the same
+ * block, byte for byte.
  *
  * ⚠️ AND THE PRICE, so this file is not a one-sided story (measured 2026-08-12).
  * With a fixture present the model OPENS THE PAPER and looks around, so the number
  * stops being "did the DESCRIPTION fire" and becomes "did the model go investigate
  * and then fire". A different quantity, and a costlier one: ~590k → ~780k tokens
- * per skill (+190k) and 67s → 84s, while this whole fixture is 1,537 characters
- * ≈ 384 tokens. The growth is reading, not input size (`cache` 470k → 652k).
+ * per skill (+190k) and 67s → 84s, while the fixture measured then was 1,537
+ * characters ≈ 384 tokens. The growth is reading, not input size (`cache`
+ * 470k → 652k).
  * Cite the trigger numbers with that caveat attached — it is written out in
  * `vigiles/repro/skill-trigger-2026-08-11/README.md` under "How to read".
  */
 export const FIXTURE = {
-  "paper/paper.md": [
-    "# Prose Isn't Policy: Measuring Whether Agent-Config Rules Are Enforceable",
+  "paper/paper.tex": [
+    "\\documentclass{article}",
+    "\\title{Prose Isn't Policy: Measuring Whether Agent-Config Rules Are Enforceable}",
+    "\\begin{document}",
+    "\\maketitle",
     "",
-    "## Abstract",
+    "\\begin{abstract}",
     "Agent configuration files state rules in prose and assume the model obeys them. We compile a",
-    "corpus of real rules and measure what fraction can be mechanically enforced. We find that 84%",
+    "corpus of real rules and measure what fraction can be mechanically enforced. We find that 84\\%",
     "of rules in our corpus are enforceable, and that LLM-authored checkers for the remainder leak",
-    "silently in 84-96% of adversarial cases \\cite{greshake2023}.",
+    "silently in 84--96\\% of adversarial cases~\\cite{greshake2023}.",
+    "\\end{abstract}",
     "",
-    "## 1 Introduction",
+    "\\section{Introduction}",
     "Every agent harness ships a natural-language rulebook. Nothing checks it. This is the same",
-    "mistake as a code comment that claims an invariant no test enforces \\cite{thompson1984}.",
+    "mistake as a code comment that claims an invariant no test enforces~\\cite{thompson1984}.",
     "",
-    "## 2 Method",
+    "\\section{Method}",
     "We gather rules from public repositories, classify each by enforceability, and build a",
     "two-stage adversarial gate that validates a synthesized rule against a blind gold set.",
     "",
-    "## 3 Results",
-    "See Table 1. The headline number is 84%.",
+    "\\section{Results}",
+    "See Table~1. The headline number is 84\\%.",
     "",
-    "## 4 Discussion",
+    "\\section{Discussion}",
     "The result generalizes beyond our corpus in the sense that the mechanism is not corpus-specific,",
     "though of course the specific percentages are, and it is important to note in this context that",
     "the framing itself may be what carries, rather than the measurement.",
     "",
-    "## 5 Threats to Validity",
+    "\\section{Threats to Validity}",
     "Our corpus is drawn from public repositories and may not represent private configurations.",
     "",
-    "## 6 Related Work",
+    "\\section{Related Work}",
     "TODO",
     "",
-    "## 7 Conclusion",
+    "\\section{Conclusion}",
     "Prose is not policy.",
+    "\\end{document}",
   ].join("\n"),
   "paper/repro/README.md":
-    "# Reproduction artifact\n\n`python3 paper_numbers.py` recomputes every bolded figure in paper.md.\n",
+    "# Reproduction artifact\n\n`python3 paper_numbers.py` recomputes every bolded figure in paper.tex.\n",
   "paper/PIPELINE-STATUS.md":
     "# Pipeline status\n\n| gate | state |\n|---|---|\n| numbers | pass |\n| structure | not run |\n| citations | not run |\n",
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "paperlint",
-  "version": "7.2.0",
+  "version": "8.0.0",
   "description": "A linter for scientific papers written in LaTeX: catches mistakes before you submit to a conference or journal.",
   "type": "module",
   "license": "MIT",
@@ -114,8 +114,6 @@
     "eslint.config.mjs",
     "fixtures",
     "!fixtures/accepted-papers",
-    "!fixtures/real-markdown-paper",
-    "fixtures/real-markdown-paper/baseline.*",
     "hooks",
     "lib",
     "presets",

package/presets/realm.jsonc

@@ -72,7 +72,7 @@
     //
     // A gate on banal's number would give 13 against a limit of 8 and would redden on a paper that
     // is within the limit. For an `error`-level rule that is the worst outcome. The limit stays
-    // owned by the counter inside `build-submission.sh`: it reads the markdown source and therefore
+    // owned by the counter inside `build-submission.sh`: it reads the paper's source and therefore
     // KNOWS where the body ends, which the PDF does not.
     //
     // The numbers below are DATA for that counter and for humans, not an input to the rule. Source:

package/scripts/harness-api.frozen.json

@@ -10,7 +10,6 @@
     "eslint-rules/pdf-last-page-balance.harness.mjs",
     "eslint-rules/temp-root-realpath.harness.mjs",
     "eslint-rules/tex-build.harness.mjs",
-    "fixtures/real-markdown-paper/real-markdown-paper.harness.ts",
     "lib/agent-cli-version.harness.mjs",
     "lib/paper-config.harness.mjs",
     "lib/skill-trigger-cases.harness.mjs",
@@ -30,13 +29,9 @@
     "skills/osf-artifact-upload/osf-artifact-upload.harness.ts",
     "skills/paper-adversarial-review/paper-adversarial-review.harness.mjs",
     "skills/paper-pipeline/paper-pipeline.harness.mjs",
-    "skills/paper-pipeline/scripts/artifact-coverage.harness.mjs",
     "skills/paper-pipeline/scripts/consumer.harness.mjs",
     "skills/paper-pipeline/scripts/extract-ref-facts.harness.mjs",
     "skills/paper-pipeline/scripts/generated-code.harness.mjs",
-    "skills/paper-pipeline/scripts/population-map.harness.mjs",
-    "skills/paper-pipeline/scripts/provenance.harness.mjs",
-    "skills/paper-pipeline/scripts/round-diff.harness.ts",
     "skills/paper-status/paper-status.harness.mjs",
     "skills/pc-panel-review/pc-panel-review.harness.mjs",
     "skills/plan-paper-timeline/plan-paper-timeline.harness.mjs",

package/skills/cold-read-diff/SKILL.md

@@ -5,7 +5,7 @@ context: fork
 allowed-tools: [Bash, Read, Agent]
 ---
 
-<!-- vigiles:sha256:293f0627e6873774 compiled from skills/cold-read-diff/SKILL.md.spec.ts -->
+<!-- vigiles:sha256:c3a1f2644781eb6f compiled from skills/cold-read-diff/SKILL.md.spec.ts -->
 
 # cold-read-diff — the reader who cannot fake understanding
 
@@ -55,7 +55,7 @@ one, and its confusion is the finding.
 
 ## How to run it
 
-1. **Take the diff.** `git diff -U0 -- <paper.md>` since the last commit, or the `new_string` of the
+1. **Take the diff.** `git diff -U0 -- <paper.tex>` since the last commit, or the `new_string` of the
    edits just applied. Prose only — skip comments, tables, bibliography.
 2. **Spawn TWO agents with no repository context, one per persona, in parallel.** Give each the
    changed paragraphs **as text in the prompt**, not as a file path. A path is an invitation to read
@@ -105,7 +105,7 @@ Two more things the same run proved:
 - **Expand build-time macros first.** The reader saw seven raw `{{placeholders}}` and correctly
   reported that every headline number was missing. That is a true statement about the extract and a
   false one about the paper.
-- **Strip working comments.** He graded `<!-- JUSTIFY … -->` notes as prose because he could not tell
+- **Strip working comments.** He graded `% JUSTIFY …` comment notes as prose because he could not tell
   them apart — and said so, which is itself a finding about the extract.
 
 **So:** take the changed lines, then widen each to its enclosing paragraph, expand macros, drop

package/skills/cold-read-diff/SKILL.md.spec.ts

@@ -60,7 +60,7 @@ one, and its confusion is the finding.
 
 ## How to run it
 
-1. **Take the diff.** \`git diff -U0 -- <paper.md>\` since the last commit, or the \`new_string\` of the
+1. **Take the diff.** \`git diff -U0 -- <paper.tex>\` since the last commit, or the \`new_string\` of the
    edits just applied. Prose only — skip comments, tables, bibliography.
 2. **Spawn TWO agents with no repository context, one per persona, in parallel.** Give each the
    changed paragraphs **as text in the prompt**, not as a file path. A path is an invitation to read
@@ -110,7 +110,7 @@ Two more things the same run proved:
 - **Expand build-time macros first.** The reader saw seven raw \`{{placeholders}}\` and correctly
   reported that every headline number was missing. That is a true statement about the extract and a
   false one about the paper.
-- **Strip working comments.** He graded \`<!-- JUSTIFY … -->\` notes as prose because he could not tell
+- **Strip working comments.** He graded \`% JUSTIFY …\` comment notes as prose because he could not tell
   them apart — and said so, which is itself a finding about the extract.
 
 **So:** take the changed lines, then widen each to its enclosing paragraph, expand macros, drop