paperlint 11.1.2 → 12.0.0

package/docs/layout.md

@@ -136,28 +136,28 @@ A check runs at one of four moments:
   The lint-only job skips what needs a build (pages, fonts, references).
 - **On demand** — a skill, when you ask for what it does. A skill stops nothing; it writes.
 
-| what                                                                                        | kind    | when it runs                                                | what it stops                                                                                                                                             |
-| ------------------------------------------------------------------------------------------- | ------- | ----------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `paper-folder-layout`                                                                       | hook    | before an agent creates a file (Edit, Write)                | a new entry the layout does not allow, at a paper's root or the top of its `repro/`; never an existing file                                               |
-| `paper-edit-guard`                                                                          | hook    | before an agent's shell command                             | a shell command that writes or moves a paper's source, which would skip the hooks that run after an edit                                                  |
-| `submission-confirm`                                                                        | hook    | before an agent's shell command                             | nothing by itself: Claude Code asks the person before a submission is sent (`--save`, `--submit`, or straight to HotCRP)                                  |
-| `paper-skills-nudge`                                                                        | hook    | after an agent edits a paper's source                       | nothing: it shows the agent the pre-submit checklist                                                                                                      |
-| `paper-status-gates`                                                                        | hook    | after an agent edits a paper's source                       | nothing: it prints the paper's readiness and its unrun gates, for a person reading the transcript                                                         |
-| [`paper/allowed-files-only`](rules/paper/allowed-files-only.md)                             | rule    | every `paperlint lint`, and CI                              | a stray file or folder at a paper's root (error)                                                                                                          |
-| [`repro/allowed-files-only`](rules/repro/allowed-files-only.md)                             | rule    | every `paperlint lint`, and CI                              | a loose entry at the top of `repro/`, a folder that is not a study's, a study folder without `README.md` (error)                                          |
-| [`repro/study-registered`](rules/repro/study-registered.md)                                 | rule    | every `paperlint lint`, and CI                              | a study folder without its row in `repro/studies.json`, a row that does not match, a measurement or plan that does not hold, an index out of sync (error) |
-| [`repro/study-plan-name`](rules/repro/study-plan-name.md)                                   | rule    | every `paperlint lint`, and CI                              | nothing: it warns when a study's plan is still named `prereg.json`                                                                                        |
-| [`repro/outputs-before-decision`](rules/repro/outputs-before-decision.md)                   | rule    | every `paperlint lint`, and CI (with the whole history)     | an output of a study decided before its run that git shows was not made after the decision                                                                |
-| `paperlint studies gate`                                                                    | command | before a decide-first study's run                           | the run, until the decision is committed                                                                                                                  |
-| [`study/declare-sample`](rules/study/declare-sample.md)                                     | rule    | every `paperlint lint`, and CI, once a paper turns it on    | a study's `prereg.json` without its population, strata, screens, coverage or the author's check (experimental, off by default)                            |
-| [`paper/folder-venue-leftover`](rules/paper/folder-venue-leftover.md)                       | rule    | every `paperlint lint`, and CI                              | nothing: it warns when the folder is named after another venue                                                                                            |
-| `review/frontmatter`, `sibling/frontmatter`                                                 | rule    | every `paperlint lint`, and CI                              | a review whose findings break the schema (error); a sibling card that does not say how much was read (warning)                                            |
-| `paper/stages`, `paper/source`                                                              | rule    | every `paperlint lint`, and CI                              | a stage whose frozen PDF or source is missing or changed (error)                                                                                          |
-| the rules on the source (`tex/*`, `paper/*`, `bib/*`)                                       | rule    | every `paperlint lint`, and CI                              | what each one's [row](rules.md) says                                                                                                                      |
-| the rules on what `paperlint build` measured (`pdf/*`, `format/page-limit`, the references) | rule    | every `paperlint lint` after a build; CI's full job         | a PDF over the page limit, in the wrong font or format, or with a bad reference                                                                           |
-| `study-accepted-papers`                                                                     | skill   | when you ask; stage 2 (modes A, B) and stage 5 (modes C, D) | nothing: it fills the venue's corpus, and writes the strong-accept scorecard in `PIPELINE-STATUS.md`                                                      |
-| `build-benchmark`                                                                           | skill   | when you ask; stage 3                                       | nothing: it registers the study with `paperlint studies new`, writes its design, fills its `plan.json`, and updates its row when it ends                  |
-| `build-label-page`                                                                          | skill   | when you ask; stage 3                                       | nothing: it builds the labelling page, and exports the answers into the study's `data/`                                                                   |
+| what                                                                                        | kind    | when it runs                                                | what it stops                                                                                                                                                                          |
+| ------------------------------------------------------------------------------------------- | ------- | ----------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `paper-folder-layout`                                                                       | hook    | before an agent creates a file (Edit, Write)                | a new entry the layout does not allow, at a paper's root or the top of its `repro/`; never an existing file                                                                            |
+| `paper-edit-guard`                                                                          | hook    | before an agent's shell command                             | a shell command that writes or moves a paper's source, which would skip the hooks that run after an edit                                                                               |
+| `submission-confirm`                                                                        | hook    | before an agent's shell command                             | a submission send (`--save`, `--submit`), or a command naming a portal's host, that the person has not said yes to in a question naming its PDF's sha256 (or the host and the command) |
+| `paper-skills-nudge`                                                                        | hook    | after an agent edits a paper's source                       | nothing: it shows the agent the pre-submit checklist                                                                                                                                   |
+| `paper-status-gates`                                                                        | hook    | after an agent edits a paper's source                       | nothing: it prints the paper's readiness and its unrun gates, for a person reading the transcript                                                                                      |
+| [`paper/allowed-files-only`](rules/paper/allowed-files-only.md)                             | rule    | every `paperlint lint`, and CI                              | a stray file or folder at a paper's root (error)                                                                                                                                       |
+| [`repro/allowed-files-only`](rules/repro/allowed-files-only.md)                             | rule    | every `paperlint lint`, and CI                              | a loose entry at the top of `repro/`, a folder that is not a study's, a study folder without `README.md` (error)                                                                       |
+| [`repro/study-registered`](rules/repro/study-registered.md)                                 | rule    | every `paperlint lint`, and CI                              | a study folder without its row in `repro/studies.json`, a row that does not match, a measurement or plan that does not hold, an index out of sync (error)                              |
+| [`repro/study-plan-name`](rules/repro/study-plan-name.md)                                   | rule    | every `paperlint lint`, and CI                              | nothing: it warns when a study's plan is still named `prereg.json`                                                                                                                     |
+| [`repro/outputs-before-decision`](rules/repro/outputs-before-decision.md)                   | rule    | every `paperlint lint`, and CI (with the whole history)     | an output of a study decided before its run that git shows was not made after the decision                                                                                             |
+| `paperlint studies gate`                                                                    | command | before a decide-first study's run                           | the run, until the decision is committed                                                                                                                                               |
+| [`study/declare-sample`](rules/study/declare-sample.md)                                     | rule    | every `paperlint lint`, and CI, once a paper turns it on    | a study's `prereg.json` without its population, strata, screens, coverage or the author's check (experimental, off by default)                                                         |
+| [`paper/folder-venue-leftover`](rules/paper/folder-venue-leftover.md)                       | rule    | every `paperlint lint`, and CI                              | nothing: it warns when the folder is named after another venue                                                                                                                         |
+| `review/frontmatter`, `sibling/frontmatter`                                                 | rule    | every `paperlint lint`, and CI                              | a review whose findings break the schema (error); a sibling card that does not say how much was read (warning)                                                                         |
+| `paper/stages`, `paper/source`                                                              | rule    | every `paperlint lint`, and CI                              | a stage whose frozen PDF or source is missing or changed (error)                                                                                                                       |
+| the rules on the source (`tex/*`, `paper/*`, `bib/*`)                                       | rule    | every `paperlint lint`, and CI                              | what each one's [row](rules.md) says                                                                                                                                                   |
+| the rules on what `paperlint build` measured (`pdf/*`, `format/page-limit`, the references) | rule    | every `paperlint lint` after a build; CI's full job         | a PDF over the page limit, in the wrong font or format, or with a bad reference                                                                                                        |
+| `study-accepted-papers`                                                                     | skill   | when you ask; stage 2 (modes A, B) and stage 5 (modes C, D) | nothing: it fills the venue's corpus, and writes the strong-accept scorecard in `PIPELINE-STATUS.md`                                                                                   |
+| `build-benchmark`                                                                           | skill   | when you ask; stage 3                                       | nothing: it registers the study with `paperlint studies new`, writes its design, fills its `plan.json`, and updates its row when it ends                                               |
+| `build-label-page`                                                                          | skill   | when you ask; stage 3                                       | nothing: it builds the labelling page, and exports the answers into the study's `data/`                                                                                                |
 
 The hooks are wired by `paperlint init` ([`install.md`](install.md)). A rule's level and options:
 [`rules.md`](rules.md).

package/docs/submission.md

@@ -111,14 +111,38 @@ The command refuses one thing by itself: `--save` when no build facts describe t
 of other bytes) exits 2 and sends nothing. Rebuild (`paperlint build`) and run the dry run again.
 Everything else, including over the limit, is the person's call.
 
-**The `submission-confirm` hook** (installed by `paperlint init`) makes Claude Code ask the person
-before any `submission new|update` with `--save` or `--submit`, and before any command that names a
-portal's host (a HotCRP-hosted site, or a host a venue preset declares), whatever program it runs.
-The question names, for each send in the command, the paper, the PDF and its sha256, and the body
-pages of the last build. No flag turns it off; it asks even in auto mode. It does not see an upload
-from a script file that names the host only inside the file. The hook catches an agent that runs a
-send without asking; it is not a security boundary against an agent that deliberately disguises a
-send.
+**The `submission-confirm` hook** (installed by `paperlint init`) stops any `submission new|update`
+with `--save` or `--submit` until the person has said yes to that exact PDF in that exact folder. The flow:
+
+1. Run the dry run (the same command without `--save`) and read its venue check.
+2. Ask the person with Claude Code's question tool (`AskUserQuestion`), with the options "Yes, send
+   it" and "No". The question names the paper folder (its full path, as the hook prints it), the PDF and the
+   first 12 characters of its sha256, the body pages, and quotes the dry run's venue check.
+3. On a yes, run the send.
+
+Without a yes, the hook stops the send and tells the agent what to ask, with the folder and the sha256 filled in.
+It reads the answer from the session's transcript. The question must contain the folder's full path
+and the PDF's sha256, so a yes to an older build, another PDF, or the same bytes in another folder
+(the same manuscript for another venue) does not count. One yes lets one send through; the next send
+needs a new question. That holds inside one command too: each send in a chain (`… --save && … --save`)
+takes a yes of its own, so one yes naming two shas, or two sends of the same PDF, covers only one. A send whose PDF cannot be found or told for certain is stopped, and so is
+any send when the transcript cannot be read.
+
+A command that names a portal's host (a HotCRP-hosted site, or a host a venue preset declares),
+whatever program it runs, may send around the venue check. It runs only after a yes to a question
+that contains that host and the command's first 60 characters; the hook prints both when it stops
+the command, the start compared as written (the host in any case). One yes lets one such command through, and a command that also sends a paper needs a separate yes for each. If the venue presets cannot be read, only
+HotCRP-hosted sites and paperlint sends are recognised, and the hook says so when it stops one;
+other commands run as usual. The hook does not see an upload from a script file that names the
+host only inside the file.
+
+The agent writes the question, so a deliberately misleading question still passes. The hook
+catches an agent that sends without asking, or asks about the wrong PDF; it is not a security
+boundary against an agent that deliberately disguises a send.
+
+Why a question and not Claude Code's own permission prompt: in the Claude mobile app that prompt
+shows only the command line, not which paper or PDF it sends. The question shows everything, on
+every client.
 
 ## What it does not do
 

package/fixtures/build-e2e/lost-character/PIPELINE-STATUS.md

@@ -0,0 +1,3 @@
+# Fixture
+
+Stage: draft

package/fixtures/build-e2e/lost-character/expect.json

@@ -0,0 +1,15 @@
+{
+  "$comment": "pdflatex exits 0 and writes a PDF without a character the font has no glyph for; the build fails on the log line (FAILING_WARNINGS in src/latex-log.ts).",
+  "build": {
+    "outcome": "failed"
+  },
+  "says": [
+    "✗ compile: pdflatex exited 0, but its final log carries a warning that fails the build",
+    "lost-character — the font has no glyph for this character, so pdflatex left it out of the PDF:",
+    "Missing character: There is no",
+    "in font cmr10!"
+  ],
+  "saysNot": [
+    "✓"
+  ]
+}

package/fixtures/build-e2e/lost-character/paper.tex

@@ -0,0 +1,8 @@
+% A paper whose font has no glyph for one character. pdflatex prints "Missing character: There is no
+% ... in font cmr10!" to the log (LaTeX sets \tracinglostchars=2), exits 0 and writes a PDF without
+% it -- the way an abstract once printed 7 x 10^13 for 7 x 10^-13. `paperlint build` must fail, quote
+% the log line, and leave no paper.pdf.
+\documentclass{article}
+\begin{document}
+A rate of $7\times 10^{13}$ and a character cmr10 cannot draw: \char"FF.
+\end{document}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "paperlint",
-  "version": "11.1.2",
+  "version": "12.0.0",
   "description": "A linter for scientific papers written in LaTeX: catches mistakes before you submit to a conference or journal.",
   "type": "module",
   "license": "MIT",

package/skills/submission-portal/SKILL.md

@@ -4,7 +4,7 @@ description: "Create, read or change a paper's submission on the venue's HotCRP
 allowed-tools: [Read, Grep, Glob, Bash, Edit, AskUserQuestion]
 ---
 
-<!-- vigiles:sha256:3fa4bf1d06de4d7a compiled from skills/submission-portal/SKILL.md.spec.ts -->
+<!-- vigiles:sha256:8b1352dd55af2d2b compiled from skills/submission-portal/SKILL.md.spec.ts -->
 
 # submission-portal — create, read and update the submission on the portal, then prove it landed
 
@@ -62,25 +62,31 @@ A missing key or token stops the command with exit 2 and a line naming what to s
    `\begin{abstract}`) and each `field` it sends. Read them with the author; an abstract the
    command cannot read, or one that reads wrong, is given as a plain-text file with
    `--abstract <file>`.
-2. **Send it.** Show the author the dry run's venue check (its lint findings, or "venue rules: no
-   errors") and what goes (title, authors, abstract, each field), then run
-   `npx paperlint submission new papers/my-paper --save` — the `submission-confirm` hook makes
-   Claude Code ask the author before it runs. Then the printed "still to do" list with the author.
+2. **Ask, then send.** Ask the author with `AskUserQuestion` — options "Yes, send it" and "No" —
+   naming the paper folder (its full path, as the hook prints it), the PDF and its sha256, the body
+   pages, and quoting the dry run's venue
+   check (its lint findings, or "venue rules at their default options: no errors"), plus what goes
+   (title, authors, abstract, each field). On a yes, run
+   `npx paperlint submission new papers/my-paper --save`. Then the printed "still to do" list
+   with the author.
 3. **Read it.** `npx paperlint submission show papers/my-paper` — status, the PDF the portal holds,
    and `match`: whether it is the local build. Rebuild first if the local PDF is stale.
 4. **Dry run the change.** `npx paperlint submission update papers/my-paper` (`--abstract <file>`,
    `--submit` to mark it submitted); it sends the paper's `"fields"` too. Exit 1 means the portal
    would refuse it, or did not take a topic — report why, stop.
-5. **Send it.** Show the author the dry run's venue check and what changes, then run the same
-   command with `--save`; the `submission-confirm` hook makes Claude Code ask the author before
-   any send. A refusal (exit 2) means the last build is not of this PDF: rebuild, dry run again.
+5. **Ask, then send.** Ask the author with `AskUserQuestion` as in step 2: the question names the
+   paper folder (full path), the PDF's sha256 and quotes the dry run's venue check, and says what changes. On a yes, run the same
+   command with `--save`. Where the `submission-confirm` hook is installed, a send without that
+   yes is stopped, and the hook says what to ask, with the folder and the sha256 filled in; ask exactly that. One
+   yes covers one send: to send again, or to send a second paper in the same command, ask again. A refusal by the command itself (exit 2) means
+   the last build is not of this PDF: rebuild, dry run again.
 6. **Prove it landed.** `show` again: `match` must read `yes — the portal holds this build`, and
    the status must be what was intended. Anything else is not done — say so.
 
 🔴 `--save` creates or changes a real submission that reviewers will see: never without the
 author's own yes, never "to test", never because a dry run passed. Before every `--save`, ask the
-author with `AskUserQuestion`, showing the dry run's venue check; where the `submission-confirm`
-hook is installed, Claude Code also asks before the command runs.
+author with `AskUserQuestion`, naming the paper folder, the PDF's sha256 and quoting the dry run's venue check; where
+the `submission-confirm` hook is installed, it stops any send without that yes.
 
 ```bash
 npx paperlint build papers/my-paper
@@ -88,11 +94,11 @@ npx paperlint submission topics papers/my-paper
 # … AskUserQuestion: which topics; the chosen ones into "fields" …
 # only while the paper has no submission id:
 npx paperlint submission new papers/my-paper
-# … the author reads the dry run and says yes …
+# … AskUserQuestion naming the folder, the PDF's sha256 and the venue check; the author says yes …
 npx paperlint submission new papers/my-paper --save
 npx paperlint submission show papers/my-paper
 npx paperlint submission update papers/my-paper --submit
-# … the author reads the dry run and says yes …
+# … AskUserQuestion naming the folder, the PDF's sha256 and the venue check; the author says yes …
 npx paperlint submission update papers/my-paper --submit --save
 npx paperlint submission show papers/my-paper
 ```

package/skills/submission-portal/SKILL.md.spec.ts

@@ -66,25 +66,31 @@ A missing key or token stops the command with exit 2 and a line naming what to s
    \`\\begin{abstract}\`) and each \`field\` it sends. Read them with the author; an abstract the
    command cannot read, or one that reads wrong, is given as a plain-text file with
    \`--abstract <file>\`.
-2. **Send it.** Show the author the dry run's venue check (its lint findings, or "venue rules: no
-   errors") and what goes (title, authors, abstract, each field), then run
-   \`npx paperlint submission new papers/my-paper --save\` — the \`submission-confirm\` hook makes
-   Claude Code ask the author before it runs. Then the printed "still to do" list with the author.
+2. **Ask, then send.** Ask the author with \`AskUserQuestion\` — options "Yes, send it" and "No" —
+   naming the paper folder (its full path, as the hook prints it), the PDF and its sha256, the body
+   pages, and quoting the dry run's venue
+   check (its lint findings, or "venue rules at their default options: no errors"), plus what goes
+   (title, authors, abstract, each field). On a yes, run
+   \`npx paperlint submission new papers/my-paper --save\`. Then the printed "still to do" list
+   with the author.
 3. **Read it.** \`npx paperlint submission show papers/my-paper\` — status, the PDF the portal holds,
    and \`match\`: whether it is the local build. Rebuild first if the local PDF is stale.
 4. **Dry run the change.** \`npx paperlint submission update papers/my-paper\` (\`--abstract <file>\`,
    \`--submit\` to mark it submitted); it sends the paper's \`"fields"\` too. Exit 1 means the portal
    would refuse it, or did not take a topic — report why, stop.
-5. **Send it.** Show the author the dry run's venue check and what changes, then run the same
-   command with \`--save\`; the \`submission-confirm\` hook makes Claude Code ask the author before
-   any send. A refusal (exit 2) means the last build is not of this PDF: rebuild, dry run again.
+5. **Ask, then send.** Ask the author with \`AskUserQuestion\` as in step 2: the question names the
+   paper folder (full path), the PDF's sha256 and quotes the dry run's venue check, and says what changes. On a yes, run the same
+   command with \`--save\`. Where the \`submission-confirm\` hook is installed, a send without that
+   yes is stopped, and the hook says what to ask, with the folder and the sha256 filled in; ask exactly that. One
+   yes covers one send: to send again, or to send a second paper in the same command, ask again. A refusal by the command itself (exit 2) means
+   the last build is not of this PDF: rebuild, dry run again.
 6. **Prove it landed.** \`show\` again: \`match\` must read \`yes — the portal holds this build\`, and
    the status must be what was intended. Anything else is not done — say so.
 
 🔴 \`--save\` creates or changes a real submission that reviewers will see: never without the
 author's own yes, never "to test", never because a dry run passed. Before every \`--save\`, ask the
-author with \`AskUserQuestion\`, showing the dry run's venue check; where the \`submission-confirm\`
-hook is installed, Claude Code also asks before the command runs.
+author with \`AskUserQuestion\`, naming the paper folder, the PDF's sha256 and quoting the dry run's venue check; where
+the \`submission-confirm\` hook is installed, it stops any send without that yes.
 
 \`\`\`bash
 npx paperlint build papers/my-paper
@@ -92,11 +98,11 @@ npx paperlint submission topics papers/my-paper
 # … AskUserQuestion: which topics; the chosen ones into "fields" …
 # only while the paper has no submission id:
 npx paperlint submission new papers/my-paper
-# … the author reads the dry run and says yes …
+# … AskUserQuestion naming the folder, the PDF's sha256 and the venue check; the author says yes …
 npx paperlint submission new papers/my-paper --save
 npx paperlint submission show papers/my-paper
 npx paperlint submission update papers/my-paper --submit
-# … the author reads the dry run and says yes …
+# … AskUserQuestion naming the folder, the PDF's sha256 and the venue check; the author says yes …
 npx paperlint submission update papers/my-paper --submit --save
 npx paperlint submission show papers/my-paper
 \`\`\`

package/src/build.test.ts

@@ -265,12 +265,55 @@ test("compile: a document whose .aux never settles did not converge", async () =
   assert.match(line, /^ {2}✗ compile: pdflatex did not converge\n/);
 });
 
-test("compile: warnings the final log still reports are named in the note", async () => {
-  const { r } = await build(paper(), {
+test("🔴 compile: pdflatex exits 0 but its log says a character was dropped — the build fails, quoting the line, and the PDF goes", async () => {
+  const dir = paper();
+  // The log as pdflatex writes it: raw UTF-8 bytes, which the build reads as latin1 and shows as UTF-8.
+  const { r, line } = await build(dir, {
+    log: [
+      "(./paper.aux)",
+      "Missing character: There is no ⁻ in font cmr10!",
+      "Overfull \\hbox (1.2pt too wide) in paragraph at lines 4--5",
+      "Missing character: There is no ⁻ in font cmr10!",
+      "",
+    ].join("\n"),
+  });
+  assert.equal(r.status, "failed");
+  assert.equal(
+    line,
+    [
+      "  ✗ compile: pdflatex exited 0, but its final log carries a warning that fails the build",
+      "      lost-character — the font has no glyph for this character, so pdflatex left it out of the PDF:",
+      "        Missing character: There is no ⁻ in font cmr10! (2 times)",
+      `      full log: ${join(dir, "paper.log").replace(root, "<root>")}`,
+      "      paper.pdf removed — a stale PDF must not pass for this build",
+    ].join("\n"),
+  );
+  assert.equal(existsSync(join(dir, "paper.pdf")), false);
+});
+
+test("compile: undefined references in the final log fail the build — no longer a note on a green one", async () => {
+  const { r, line } = await build(paper(), {
     log: "LaTeX Warning: There were undefined references.\n",
   });
+  assert.equal(r.status, "failed");
+  assert.match(
+    line,
+    /\n {6}undefined-references — .*:\n {8}LaTeX Warning: There were undefined references\.\n/,
+  );
+});
+
+test("compile: warnings off the failing list — overfull boxes, a font substitution, one undefined reference — leave the build green", async () => {
+  const { r } = await build(paper(), {
+    log: [
+      "Overfull \\hbox (1.2pt too wide) in paragraph at lines 4--5",
+      "LaTeX Font Warning: Font shape `OT1/cmr/bx/sc' undefined",
+      "(Font)              using `OT1/cmr/bx/n' instead on input line 3.",
+      "LaTeX Warning: Reference `sec:x' on page 1 undefined on input line 4.",
+      "",
+    ].join("\n"),
+  });
   assert.equal(r.status, "built");
-  assert.match(r.notes?.[0] ?? "", /— ⚠️ the final log still reports /);
+  assert.doesNotMatch(r.notes?.[0] ?? "", /⚠️/);
 });
 
 test("references: without a reader the step says it was not wired; with one and no checker, the record says not checked", async () => {

package/src/build.ts

@@ -83,6 +83,7 @@ import {
   auxBib,
   bibtexExcerpt,
   errorExcerpt,
+  failingWarnings,
   logMarkers,
   unwrapLog,
 } from "./latex-log.ts";
@@ -90,6 +91,7 @@ import {
   nextStep,
   summarize,
   type BibInput,
+  type FailCause,
   type Hashes,
   type Observation,
   type Step,
@@ -401,6 +403,10 @@ function latexPass(
     markers: logMarkers(log),
     bib: bibInput(ctx.paperDir),
     fls: readOr(join(ctx.paperDir, `${JOB}.fls`), "utf8"),
+    failing: failingWarnings(log).map((h) => ({
+      ...h,
+      quotes: h.quotes.map((q) => ({ ...q, text: fromLatin1(q.text) })),
+    })),
     errorLines:
       exitCode === 0
         ? []
@@ -494,6 +500,18 @@ export function compile(ctx: BuildContext): {
 
 const NO_PDF = `pdflatex exited 0 but wrote no ${JOB}.pdf — does the document have any pages?`;
 
+/** The head of a failed compile: which program, and how it ended. */
+function whereFailed(bin: string, cause: FailCause): string {
+  switch (cause.kind) {
+    case "exit":
+      return `${bin} exited with ${String(cause.code)}`;
+    case "no-convergence":
+      return `${bin} did not converge`;
+    case "log-warnings":
+      return `${bin} exited 0, but its final log carries a warning that fails the build`;
+  }
+}
+
 const plural = (n: number, one: string, many: string): string =>
   `${String(n)} ${n === 1 ? one : many}`;
 
@@ -517,10 +535,7 @@ export const compileStep: BuildStep = {
     const { end, latex, bibtex, run } = compile(ctx);
     if (end.kind === "fail") {
       const bin = end.step === "latex" ? "pdflatex" : "bibtex";
-      const where =
-        end.cause.kind === "exit"
-          ? `${bin} exited with ${String(end.cause.code)}`
-          : `${bin} did not converge`;
+      const where = whereFailed(bin, end.cause);
       const log = join(
         ctx.paperDir,
         `${JOB}.${end.step === "latex" ? "log" : "blg"}`,
@@ -545,12 +560,9 @@ export const compileStep: BuildStep = {
         ok: false,
         lines: [NO_PDF, `full log: ${join(ctx.paperDir, `${JOB}.log`)}`],
       };
-    const warn = end.warnings.length
-      ? ` — ⚠️ the final log still reports ${end.warnings.join(", ")}`
-      : "";
     return {
       ok: true,
-      note: `${plural(latex, "pdflatex pass", "pdflatex passes")}, ${plural(bibtex, "bibtex run", "bibtex runs")}${warn}; ${recordingNote(ctx.recordSources(ctx.paperDir, run))}`,
+      note: `${plural(latex, "pdflatex pass", "pdflatex passes")}, ${plural(bibtex, "bibtex run", "bibtex runs")}; ${recordingNote(ctx.recordSources(ctx.paperDir, run))}`,
     };
   },
 };

package/src/cli.test.ts

@@ -242,7 +242,7 @@ test("runHook paper-folder-layout: in-process, on the real disk — a refusal on
   );
 });
 
-test("runHook submission-confirm: in-process — an ask on stdout for a send, nothing for anything else, and an ask when its input cannot be read", () => {
+test("runHook submission-confirm: in-process — a refusal on stdout for a send with no yes, nothing for anything else, and a refusal when its input cannot be read", () => {
   const hook = (stdin: () => string) => {
     const out: string[] = [];
     const code = runHook("submission-confirm", {
@@ -260,7 +260,7 @@ test("runHook submission-confirm: in-process — an ask on stdout for a send, no
   assert.equal(send.code, 0);
   assert.match(
     send.out.join(""),
-    /^\{"hookSpecificOutput":\{"hookEventName":"PreToolUse","permissionDecision":"ask","permissionDecisionReason":"This sends the paper to the venue's portal/,
+    /^\{"hookSpecificOutput":\{"hookEventName":"PreToolUse","permissionDecision":"deny","permissionDecisionReason":"Not run: this sends the paper to the venue's portal/,
   );
   assert.deepEqual(hook(command("npx paperlint submission show nope")), {
     code: 0,
@@ -272,7 +272,7 @@ test("runHook submission-confirm: in-process — an ask on stdout for a send, no
   assert.equal(unreadable.code, 0);
   assert.match(
     unreadable.out.join(""),
-    /"permissionDecision":"ask","permissionDecisionReason":"paperlint could not read this command/,
+    /"permissionDecision":"deny","permissionDecisionReason":"Not run: paperlint could not read this command/,
   );
 });
 

package/src/cli.ts

@@ -1247,7 +1247,7 @@ const IN_PROCESS_HOOKS: Readonly<Record<string, (io: HookIo) => number>> = {
     }
     return 0;
   },
-  // Never advisory-silent: an input it cannot read is asked about, not let through.
+  // Never advisory-silent: an input it cannot read is refused, not let through.
   "submission-confirm": ({ stdin, out }) => {
     const said = ((): ReturnType<typeof submissionConfirm> => {
       try {
@@ -1717,7 +1717,7 @@ function projectPresets(cwd: string): readonly Preset[] {
 
 /**
  * The host of every venue portal paperlint knows of from `cwd` — the shipped presets', and those the
- * project's papers extend: what `submission-confirm` asks about when a request goes straight there.
+ * project's papers extend: what `submission-confirm` refuses when a request goes straight there.
  */
 export function portalHosts(cwd: string): readonly string[] {
   return [...resolveShipped(PRESET_DEPS), ...projectPresets(cwd)].flatMap(