docrev 0.11.3 → 0.12.0

package/CHANGELOG.md

@@ -5,6 +5,28 @@ All notable changes to docrev will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.12.0] - 2026-07-08
+
+### Fixed
+- **Images restored by caption match keep their `{#fig:label}` crossref anchor.** An add-then-check ordering bug in `restoreImagesFromRegistry` guaranteed the anchor was always dropped, so every `@fig:` reference to a caption-matched figure broke on the next build.
+- **Markdown tables in CRLF files are protected through the import diff.** The table-protection pattern required `|\n` line endings, so on Windows-authored files no table was ever protected and the diff engine could mangle rows. Math protection also no longer captures escaped `\$` (currency amounts) as math spans.
+- **Postprocess script failures now surface without `--verbose`.** A failing `postprocess.pdf`/`.docx` script used to be invisible unless verbose was on, with the build still reporting success; the failure is now returned through the build warnings and printed.
+- **Reply comments whose anchor contains nested brackets no longer vanish.** The reply-places-parent-markers path re-parsed the anchor with a regex that bailed at the first inner `]`, silently dropping both the parent and the reply from the rebuilt docx; it now uses the anchor already extracted by the nested-bracket parser.
+- **`rev orcid` and CSL style downloads can no longer hang forever.** Both now route through the shared rate limiter (per-request timeout via AbortController, bounded retries) that the DOI commands already used.
+- **Unexpected errors inside commands print a clean message instead of a raw Node stack.** The CLI now runs `parseAsync` inside a try/catch and installs `unhandledRejection`/`uncaughtException` handlers (`DEBUG=1` shows the stack). A corrupt `package.json` or `.rev/conflicts.json` degrades gracefully instead of crashing.
+- **Table cell text decodes XML entities correctly.** Table extraction had a private decoder that double-unescaped `<` and corrupted emoji/astral characters; it now shares the ooxml layer's decoder.
+- **`rev completions` and `rev install-cli-skill` work from the published package.** Both resolved package assets with a fixed number of `..` segments that only matched the source layout, not `dist/`; assets now resolve via the nearest `package.json`. A CI pack-smoke-test job installs the tarball and exercises the CLI to keep this class of regression out.
+- Temp files (`.paper-marked.*`, `.paper-annotated.*`, equation-sheet `.tmp.md`) are cleaned up in `finally` blocks, so a failed pandoc run no longer leaks them into the project directory.
+
+### Changed
+- **Table extraction is parser-backed.** Word tables are now read through the structural OOXML layer (namespace by URI, `gridSpan`/`vMerge` from cell properties), so documents binding WordprocessingML to a prefix other than `w:` yield their tables.
+- **Visible-comment conversion is stricter.** `[Author: text]` conversion now requires a name-like author (no digits), skips documentary lead-ins (`[Note: …]`), markdown links, and image alt text, so bracketed prose is no longer rewritten into reviewer comments during import.
+- Dual-mode orchestration (`_comments.docx` / `_comments.pdf`) moved from the command layer into `build.ts` (`buildCommentsDocx` / `buildCommentsPdf`) with a single output-suffix helper.
+- Dead pre-parser extractors were removed from `word.ts`; its public comment/anchor entry points now delegate to the shipping implementations, so tests exercise the real code path. `isWordDocument` is content-based (ZIP + `word/document.xml`) rather than extension-based.
+- crossref section discovery, config-key typo detection, and command suggestions now share single implementations (`resolveSectionsConfig`, `utils.levenshtein`).
+- Packaging: `files` allowlist replaces `.npmignore` (tarball drops from 3.7 MB/412 files to 2.1 MB/312 files — no more TS source, mkdocs site, or planning docs), `tsx` moved to devDependencies, legacy hand-written `types/index.d.ts` removed, MIT `LICENSE` file added.
+- CI: the test glob now includes `.test.ts` files (the pptx-template suite was silently excluded everywhere), ESLint actually lints the TypeScript source (it previously linted only compiled `dist/` output), and a pack-smoke-test job was added.
+
 ## [0.11.3] - 2026-07-08
 
 ### Fixed

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025-2026 Gilles Colling
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/dist/bin/rev.js

@@ -10,24 +10,19 @@ import chalk from 'chalk';
 import * as fs from 'fs';
 // Import refactored command modules
 import { registerAllCommands, setQuietMode, setJsonMode, } from '../lib/commands/index.js';
-// Global flags
-let quietMode = false;
-let jsonMode = false;
-// Levenshtein distance for command suggestions
-function levenshtein(a, b) {
-    const matrix = Array(b.length + 1).fill(null).map(() => Array(a.length + 1).fill(0));
-    for (let i = 0; i <= a.length; i++)
-        matrix[0][i] = i;
-    for (let j = 0; j <= b.length; j++)
-        matrix[j][0] = j;
-    for (let j = 1; j <= b.length; j++) {
-        for (let i = 1; i <= a.length; i++) {
-            const cost = a[i - 1] === b[j - 1] ? 0 : 1;
-            matrix[j][i] = Math.min(matrix[j][i - 1] + 1, matrix[j - 1][i] + 1, matrix[j - 1][i - 1] + cost);
-        }
+import { levenshtein } from '../lib/utils.js';
+// Any rejection that escapes a command action must fail cleanly, not dump a
+// raw Node stack (or crash with ERR_UNHANDLED_REJECTION on newer Node).
+function fail(err) {
+    const message = err instanceof Error ? err.message : String(err);
+    console.error(chalk.red(`Error: ${message}`));
+    if (process.env.DEBUG && err instanceof Error && err.stack) {
+        console.error(chalk.dim(err.stack));
     }
-    return matrix[b.length][a.length];
+    process.exit(1);
 }
+process.on('unhandledRejection', fail);
+process.on('uncaughtException', fail);
 // Find similar commands for typo suggestions
 function suggestCommand(input, commands) {
     const suggestions = commands
@@ -38,9 +33,16 @@ function suggestCommand(input, commands) {
         .map(({ cmd }) => cmd);
     return suggestions;
 }
-// Read version from package.json
+// Read version from package.json. A corrupt or missing file must not take
+// down the whole CLI before any command runs.
 const pkgPath = new URL('../../package.json', import.meta.url);
-const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf-8'));
+let pkg = { version: 'unknown' };
+try {
+    pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf-8'));
+}
+catch {
+    // Keep the fallback version; every command still works.
+}
 program
     .name('rev')
     .description('Revision workflow for Word ↔ Markdown round-trips')
@@ -58,11 +60,9 @@ program
         chalk.level = 0;
     }
     if (opts.quiet) {
-        quietMode = true;
         setQuietMode(true);
     }
     if (opts.json) {
-        jsonMode = true;
         setJsonMode(true);
         chalk.level = 0; // Disable colors in JSON mode
     }
@@ -114,5 +114,13 @@ if (args.length === 0 || (hasOnlyGlobalOpts && !hasCommand && !args.includes('-h
         process.argv.push('status');
     }
 }
-program.parse();
+// parseAsync so errors thrown inside async command actions reject here and
+// hit the catch, instead of becoming unhandled rejections after parse()
+// returns synchronously.
+try {
+    await program.parseAsync();
+}
+catch (err) {
+    fail(err);
+}
 //# sourceMappingURL=rev.js.map

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+{"version":3,"file":"rev.js","sourceRoot":"","sources":["../../bin/rev.ts"],"names":[],"mappings":";AAEA;;;;;GAKG;AAEH,OAAO,EAAE,OAAO,EAAW,MAAM,WAAW,CAAC;AAC7C,OAAO,KAAK,MAAM,OAAO,CAAC;AAC1B,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AAEzB,oCAAoC;AACpC,OAAO,EACL,mBAAmB,EACnB,YAAY,EACZ,WAAW,GACZ,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAE9C,4EAA4E;AAC5E,wEAAwE;AACxE,SAAS,IAAI,CAAC,GAAY;IACxB,MAAM,OAAO,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;IACjE,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,UAAU,OAAO,EAAE,CAAC,CAAC,CAAC;IAC9C,IAAI,OAAO,CAAC,GAAG,CAAC,KAAK,IAAI,GAAG,YAAY,KAAK,IAAI,GAAG,CAAC,KAAK,EAAE,CAAC;QAC3D,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;IACtC,CAAC;IACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC;AAED,OAAO,CAAC,EAAE,CAAC,oBAAoB,EAAE,IAAI,CAAC,CAAC;AACvC,OAAO,CAAC,EAAE,CAAC,mBAAmB,EAAE,IAAI,CAAC,CAAC;AAEtC,6CAA6C;AAC7C,SAAS,cAAc,CAAC,KAAa,EAAE,QAAkB;IACvD,MAAM,WAAW,GAAG,QAAQ;SACzB,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,EAAE,WAAW,CAAC,KAAK,CAAC,WAAW,EAAE,EAAE,GAAG,CAAC,WAAW,EAAE,CAAC,EAAE,CAAC,CAAC;SAChF,MAAM,CAAC,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,IAAI,IAAI,CAAC,CAAC;SAC/B,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC;SAC/B,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC;SACX,GAAG,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC;IACzB,OAAO,WAAW,CAAC;AACrB,CAAC;AASD,0EAA0E;AAC1E,8CAA8C;AAC9C,MAAM,OAAO,GAAG,IAAI,GAAG,CAAC,iBAAiB,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AAC5D,IAAI,GAAG,GAAgB,EAAE,OAAO,EAAE,SAAS,EAAE,CAAC;AAC9C,IAAI,CAAC;IACH,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,YAAY,CAAC,OAAO,EAAE,OAAO,CAAC,CAAgB,CAAC;AACrE,CAAC;AAAC,MAAM,CAAC;IACP,wDAAwD;AAC1D,CAAC;AAED,OAAO;KACJ,IAAI,CAAC,KAAK,CAAC;KACX,WAAW,CAAC,mDAAmD,CAAC;KAChE,OAAO,CAAC,GAAG,GAAG,CAAC,OAAO,UAAU,OAAO,CAAC,OAAO,MAAM,OAAO,CAAC,QAAQ,IAAI,OAAO,CAAC,IAAI,EAAE,EAAE,eAAe,EAAE,4BAA4B,CAAC;KACvI,eAAe,CAAC;IACf,WAAW,EAAE,CAAC,GAAW,EAAE,KAA4B,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;CAClF,CAAC;KACD,kBAAkB,CAAC,KAAK,CAAC,GAAG,CAAC,oCAAoC,CAAC,CAAC;KACnE,MAAM,CAAC,YAAY,EAAE,wBAAwB,CAAC;KAC9C,MAAM,CAAC,aAAa,EAAE,+BAA+B,CAAC;KACtD,MAAM,CAAC,QAAQ,EAAE,uCAAuC,CAAC;KACzD,IAAI,CAAC,WAAW,EAAE,CAAC,WAAoB,EAAE,EAAE;IAC1C,MAAM,IAAI,GAAG,WAAW,CAAC,IAAI,EAAwD,CAAC;IACtF,IAAI,IAAI,CAAC,KAAK,KAAK,KAAK,EAAE,CAAC;QACzB,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC;IAClB,CAAC;IACD,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC;QACf,YAAY,CAAC,IAAI,CAAC,CAAC;IACrB,CAAC;IACD,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,WAAW,CAAC,IAAI,CAAC,CAAC;QAClB,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,8BAA8B;IACjD,CAAC;AACH,CAAC,CAAC,CAAC;AAEL,+BAA+B;AAC/B,gCAAgC;AAChC,mCAAmC;AACnC,yFAAyF;AACzF,+BAA+B;AAC/B,qDAAqD;AACrD,oDAAoD;AACpD,yDAAyD;AACzD,8DAA8D;AAC9D,uBAAuB;AACvB,4CAA4C;AAC5C,iFAAiF;AACjF,mFAAmF;AACnF,kFAAkF;AAClF,mBAAmB,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;AAElC,6CAA6C;AAC7C,MAAM,WAAW,GAAG,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,CAAC;AAC5D,MAAM,UAAU,GAAG,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC,CAAC;AAClE,MAAM,eAAe,GAAG,CAAC,GAAG,WAAW,EAAE,GAAG,UAAU,CAAC,CAAC;AAExD,2CAA2C;AAC3C,OAAO,CAAC,EAAE,CAAC,WAAW,EAAE,CAAC,QAAkB,EAAE,EAAE;IAC7C,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;IAC5B,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,oBAAoB,OAAO,EAAE,CAAC,CAAC,CAAC;IAExD,MAAM,WAAW,GAAG,cAAc,CAAC,OAAQ,EAAE,eAAe,CAAC,CAAC;IAC9D,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC3B,OAAO,CAAC,KAAK,EAAE,CAAC;QAChB,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC,CAAC;QAC7C,KAAK,MAAM,CAAC,IAAI,WAAW,EAAE,CAAC;YAC5B,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC;QAC1C,CAAC;IACH,CAAC;IACD,OAAO,CAAC,KAAK,EAAE,CAAC;IAChB,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,wCAAwC,CAAC,CAAC,CAAC;IACnE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC,CAAC,CAAC;AAEH,0CAA0C;AAC1C,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;AACnC,MAAM,UAAU,GAAG,CAAC,YAAY,EAAE,IAAI,EAAE,SAAS,EAAE,QAAQ,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,QAAQ,CAAC,CAAC;AAChG,MAAM,iBAAiB,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,IAAI,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC;AACxH,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC;AAEvF,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,iBAAiB,IAAI,CAAC,UAAU,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,EAAE,CAAC;IACvK,2CAA2C;IAC3C,MAAM,SAAS,GAAG,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC;IACrF,IAAI,SAAS,KAAK,CAAC,CAAC,EAAE,CAAC;QACrB,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;IAC9B,CAAC;AACH,CAAC;AAED,2EAA2E;AAC3E,wEAAwE;AACxE,yBAAyB;AACzB,IAAI,CAAC;IACH,MAAM,OAAO,CAAC,UAAU,EAAE,CAAC;AAC7B,CAAC;AAAC,OAAO,GAAG,EAAE,CAAC;IACb,IAAI,CAAC,GAAG,CAAC,CAAC;AACZ,CAA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package/dist/lib/build.d.ts

@@ -155,6 +155,7 @@ export interface BuildResult {
     success: boolean;
     outputPath?: string;
     error?: string;
+    warnings?: string[];
 }
 interface BuildOptions {
     verbose?: boolean;
@@ -183,6 +184,7 @@ interface PandocResult {
     outputPath: string;
     success: boolean;
     error?: string;
+    warnings?: string[];
 }
 interface FullBuildResult {
     results: BuildResult[];
@@ -310,6 +312,47 @@ export interface ReviewedDocxResult {
  * @param options - Output path, author, comment handling
  */
 export declare function buildReviewedDocx(directory: string, paperPath: string, config: BuildConfig, options: ReviewedDocxOptions): Promise<ReviewedDocxResult>;
+/**
+ * Insert a suffix before the file extension: `paper.docx` + `_comments`
+ * → `paper_comments.docx`. Single source for the dual-output naming that
+ * used to be hand-rolled per format in the command layer.
+ */
+export declare function withOutputSuffix(filePath: string, suffix: string): string;
+export interface DualCommentsResult {
+    success: boolean;
+    /** True when there were no comments to thread — nothing was built. */
+    skipped?: boolean;
+    outputPath?: string;
+    commentCount?: number;
+    skippedComments?: number;
+    realigned?: number;
+    warnings: string[];
+    error?: string;
+}
+interface DualCommentsOptions {
+    referencePath?: string | null;
+    pandocArgs?: string[];
+    verbose?: boolean;
+}
+/**
+ * Build the `_comments.docx` half of dual mode: the clean DOCX plus a twin
+ * carrying the CriticMarkup comments as threaded Word comments.
+ *
+ * Pipeline: realign anchors from a reference docx (optional) → strip
+ * annotations keeping comments → shared DOCX transforms → marker
+ * placement → pandoc → comment injection. Temp files are cleaned in a
+ * finally so a pandoc failure cannot leak `.paper-marked.*` into the
+ * project directory.
+ */
+export declare function buildCommentsDocx(directory: string, paperPath: string, config: BuildConfig, cleanDocxPath: string, options?: DualCommentsOptions): Promise<DualCommentsResult>;
+/**
+ * Build the `_comments.pdf` half of dual mode: the clean PDF plus a twin
+ * carrying the CriticMarkup comments as todonotes margin notes.
+ *
+ * Temp files (`.paper-annotated.md`, the preamble sidecar) are cleaned in a
+ * finally so a pandoc failure cannot leak them into the project directory.
+ */
+export declare function buildCommentsPdf(directory: string, paperPath: string, config: BuildConfig, cleanPdfPath: string, options?: DualCommentsOptions): Promise<DualCommentsResult>;
 /**
  * A raw LaTeX `\begin{figure}...\end{figure}` block found in source markdown.
  * `exotic` blocks contain features we don't auto-translate (multiple

package/dist/lib/build.d.ts.map

@@ -1 +1 @@
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package/dist/lib/build.js

@@ -779,6 +779,170 @@ export async function buildReviewedDocx(directory, paperPath, config, options) {
         }
     }
 }
+/**
+ * Insert a suffix before the file extension: `paper.docx` + `_comments`
+ * → `paper_comments.docx`. Single source for the dual-output naming that
+ * used to be hand-rolled per format in the command layer.
+ */
+export function withOutputSuffix(filePath, suffix) {
+    const ext = path.extname(filePath);
+    return filePath.slice(0, filePath.length - ext.length) + suffix + ext;
+}
+/**
+ * Build the `_comments.docx` half of dual mode: the clean DOCX plus a twin
+ * carrying the CriticMarkup comments as threaded Word comments.
+ *
+ * Pipeline: realign anchors from a reference docx (optional) → strip
+ * annotations keeping comments → shared DOCX transforms → marker
+ * placement → pandoc → comment injection. Temp files are cleaned in a
+ * finally so a pandoc failure cannot leak `.paper-marked.*` into the
+ * project directory.
+ */
+export async function buildCommentsDocx(directory, paperPath, config, cleanDocxPath, options = {}) {
+    const warnings = [];
+    let realigned;
+    let markdown = fs.readFileSync(paperPath, 'utf-8');
+    if (options.referencePath) {
+        if (fs.existsSync(options.referencePath)) {
+            try {
+                const { realignMarkdown } = await import('./comment-realign.js');
+                const realignResult = await realignMarkdown(options.referencePath, markdown);
+                if (realignResult.success) {
+                    markdown = realignResult.markdown;
+                    realigned = realignResult.insertions;
+                }
+                else {
+                    warnings.push(`Could not realign comments: ${realignResult.error}`);
+                }
+            }
+            catch (err) {
+                warnings.push(`Could not realign comments: ${err.message}`);
+            }
+        }
+        else {
+            warnings.push(`Reference not found: ${options.referencePath}`);
+        }
+    }
+    markdown = stripAnnotations(markdown, { keepComments: true });
+    // Apply DOCX transforms (author affiliations, @fig: → "Figure 1") before
+    // injecting markers, so the comments DOCX matches the clean DOCX in
+    // everything but the comments themselves.
+    const registry = buildRegistry(directory, config.sections);
+    markdown = applyFormatTransforms(markdown, 'docx', config, registry);
+    const { markedMarkdown, comments } = prepareMarkdownWithMarkers(markdown);
+    if (comments.length === 0) {
+        return { success: true, skipped: true, warnings };
+    }
+    const markedPath = path.join(directory, '.paper-marked.md');
+    const markedDocxPath = path.join(directory, '.paper-marked.docx');
+    try {
+        fs.writeFileSync(markedPath, markedMarkdown, 'utf-8');
+        const pandocResult = await runPandoc(markedPath, 'docx', config, {
+            outputPath: markedDocxPath,
+            pandocArgs: options.pandocArgs,
+            verbose: options.verbose,
+        });
+        if (!pandocResult.success) {
+            return { success: false, error: pandocResult.error, warnings };
+        }
+        const commentsDocxPath = withOutputSuffix(cleanDocxPath, '_comments');
+        const injection = await injectCommentsAtMarkers(markedDocxPath, comments, commentsDocxPath);
+        if (!injection.success) {
+            return { success: false, error: injection.error, warnings };
+        }
+        return {
+            success: true,
+            outputPath: commentsDocxPath,
+            commentCount: injection.commentCount,
+            skippedComments: injection.skippedComments,
+            realigned,
+            warnings,
+        };
+    }
+    finally {
+        if (!process.env.DEBUG) {
+            for (const tmp of [markedPath, markedDocxPath]) {
+                try {
+                    fs.unlinkSync(tmp);
+                }
+                catch { /* best-effort */ }
+            }
+        }
+    }
+}
+/**
+ * Build the `_comments.pdf` half of dual mode: the clean PDF plus a twin
+ * carrying the CriticMarkup comments as todonotes margin notes.
+ *
+ * Temp files (`.paper-annotated.md`, the preamble sidecar) are cleaned in a
+ * finally so a pandoc failure cannot leak them into the project directory.
+ */
+export async function buildCommentsPdf(directory, paperPath, config, cleanPdfPath, options = {}) {
+    const warnings = [];
+    const { prepareMarkdownForAnnotatedPdf } = await import('./pdf-comments.js');
+    let markdown = fs.readFileSync(paperPath, 'utf-8');
+    markdown = stripAnnotations(markdown, { keepComments: true });
+    // Apply PDF transforms (table normalization, authblk header injection)
+    // before todonotes preamble work, so the comments PDF matches the clean
+    // PDF in everything but the margin notes.
+    const registry = buildRegistry(directory, config.sections);
+    markdown = applyFormatTransforms(markdown, 'pdf', config, registry);
+    const { markdown: annotatedMd, preamble, commentCount } = prepareMarkdownForAnnotatedPdf(markdown, {
+        useTodonotes: true,
+        stripResolved: true,
+    });
+    if (commentCount === 0) {
+        return { success: true, skipped: true, warnings };
+    }
+    const annotatedPath = path.join(directory, '.paper-annotated.md');
+    const preamblePath = path.join(directory, '.paper-annotated.preamble.tex');
+    try {
+        fs.writeFileSync(annotatedPath, annotatedMd, 'utf-8');
+        const annotatedConfig = JSON.parse(JSON.stringify(config));
+        annotatedConfig.pdf = annotatedConfig.pdf || {};
+        // Pandoc consumes header-includes via -H <file>. Write preamble (plus any
+        // existing user header file) to a temp .tex and point headerIncludes at it.
+        const preambleParts = [];
+        const existingHeader = annotatedConfig.pdf.headerIncludes;
+        if (existingHeader) {
+            const existingPath = path.isAbsolute(existingHeader)
+                ? existingHeader
+                : path.join(directory, existingHeader);
+            if (fs.existsSync(existingPath)) {
+                preambleParts.push(fs.readFileSync(existingPath, 'utf-8'));
+            }
+        }
+        preambleParts.push(preamble);
+        fs.writeFileSync(preamblePath, preambleParts.join('\n'), 'utf-8');
+        annotatedConfig.pdf.headerIncludes = preamblePath;
+        annotatedConfig.pdf.geometry = 'left=2.5cm,right=4.5cm,top=2.5cm,bottom=2.5cm,marginparwidth=3.5cm';
+        const annotatedPdfPath = withOutputSuffix(cleanPdfPath, '_comments');
+        const pandocResult = await runPandoc(annotatedPath, 'pdf', annotatedConfig, {
+            outputPath: annotatedPdfPath,
+            pandocArgs: options.pandocArgs,
+            verbose: options.verbose,
+        });
+        if (!pandocResult.success) {
+            return { success: false, error: pandocResult.error, warnings };
+        }
+        return {
+            success: true,
+            outputPath: annotatedPdfPath,
+            commentCount,
+            warnings,
+        };
+    }
+    finally {
+        if (!process.env.DEBUG) {
+            for (const tmp of [annotatedPath, preamblePath]) {
+                try {
+                    fs.unlinkSync(tmp);
+                }
+                catch { /* best-effort */ }
+            }
+        }
+    }
+}
 /**
  * Convert @fig:label references to display format (Figure 1)
  */
@@ -1496,12 +1660,15 @@ export async function runPandoc(inputPath, format, config, options = {}) {
                         }
                     }
                 }
-                // Run user postprocess scripts
+                // Run user postprocess scripts. The pandoc output exists, so the
+                // build itself succeeded — but a failing script must be surfaced,
+                // not hidden behind --verbose: the user would otherwise ship an
+                // un-postprocessed file believing everything ran.
                 const postResult = await runPostprocess(outputPath, format, config, options);
-                if (!postResult.success && options.verbose) {
-                    console.error(`Postprocess warning: ${postResult.error}`);
-                }
-                resolve({ outputPath, success: true });
+                const postWarnings = postResult.success
+                    ? undefined
+                    : [`Postprocess failed for ${format}: ${postResult.error}`];
+                resolve({ outputPath, success: true, warnings: postWarnings });
             }
             else {
                 resolve({ outputPath, success: false, error: stderr || `Exit code ${code}` });
@@ -1565,6 +1732,9 @@ export async function build(directory, formats = ['pdf', 'docx'], options = {})
         const preparedPath = prepareForFormat(paperPath, format, config, options);
         // Run pandoc
         const result = await runPandoc(preparedPath, format, config, options);
+        if (result.warnings) {
+            warnings.push(...result.warnings);
+        }
         results.push({ format, ...result });
         // Clean up temp file
         try {