docrev 0.9.5 → 0.9.7

package/CHANGELOG.md

@@ -5,6 +5,26 @@ 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).
 
+## [0.9.7] - 2026-04-29
+
+### Added
+- `rev sync --comments-only` — import only Word comments at fuzzy-matched anchors, leaving prose byte-identical. Use when the markdown was revised between sending the docx out for review and receiving it back; applying track changes from a stale draft would clobber newer edits.
+- `rev verify-anchors <docx>` — drift report classifying every comment as `clean` / `drift` / `context-only` / `ambiguous` / `unmatched` against the current section markdown. Pair with `--comments-only` to plan placement before sync. Supports `--json` for scripting.
+- `extractHeadings()` in `word-extraction.ts` — read heading paragraphs directly from `<w:pStyle>` styles, returning text + level + position in the same coordinate system as comment anchors.
+- Shared `lib/commands/section-boundaries.ts` — single source of truth that maps `sections.yaml` to docx text positions, used by both sync and verify-anchors.
+- Shared `lib/anchor-match.ts` — pure anchor-matching primitives (`findAnchorInText`, `stripCriticMarkup`, `classifyStrategy`) so sync (insertion) and verify-anchors (drift reporting) use the same fallback strategies.
+- New tests: `test/anchor-match.test.js` (11 cases covering each fallback strategy and the quality classifier).
+
+### Fixed
+- **Section detection mistook prose for headings.** The old keyword finder scanned the concatenated body text and would match "results across countries" as the Results heading or skip the real Methods heading because the structured-abstract label `Methods:` lost its colon during text-run concatenation. Replaced with paragraph-style-based heading extraction, so boundaries now reflect actual heading paragraphs. Affects the new commands; the existing sync flow already used pandoc-derived headings and was unaffected.
+- `stripCriticMarkup` regex used `[^<]*` and silently failed on comments containing `<` characters (e.g. `pre-industrial trade (<1825)`). Switched to non-greedy `[\s\S]*?`.
+- `insertCommentsIntoMarkdown` always prepended a leading space when there was no anchor, accumulating multiple spaces when several comments shared a position 0 anchor. Removed the heuristic; comments insert at exact position so prose stays byte-identical except for the inserted blocks.
+- `verify-anchors` crashed with a stack trace when given a non-docx file (e.g. an `.md` path). Now reports a friendly error.
+
+### Changed
+- New flag is `--comments-only` (positive form). The originally proposed `--no-overwrite` was dropped because Commander assigns `--no-X` to `options.x === false` rather than `options.noX === true`, which made the flag silently ignored.
+- `insertCommentsIntoMarkdown` now accepts `wrapAnchor?: boolean` (default `true`). When `false`, comment blocks are inserted next to the anchor without `[anchor]{.mark}` wrapping. `--comments-only` uses this so multiple comments sharing an anchor (e.g. 6 reviewers commenting on the same word) no longer produce nested broken CriticMarkup.
+
 ## [0.7.1] - 2025-01-02
 
 ### Added

package/dev_notes/bug_repro_comment_parser.md

@@ -0,0 +1,71 @@
+# Bug repro — comment parser drops valid comments
+
+## Symptom
+
+A markdown file with 24 valid `{>>Author: text<<}` comments is shown by `rev comments file.md` as containing only 21. Three comments are silently dropped.
+
+## Reproducer
+
+`test.md`:
+```markdown
+# Test
+
+**Para 1.** Sentence one{>>Jonathan Lenoir: short comment<<}.
+
+**Para 2.** Sentence two{>>Jens-Christian Svenning: I'm quite skeptical about these listings of all the bad things alien species do, with any kind of proper benchmarking - you could arguably make similar lists of all the annoying or dangerous things native species do<<}.
+
+**Para 3.** Sentence three{>>Jens-Christian Svenning: see https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2745.14307<<}.
+```
+
+```bash
+rev comments test.md
+```
+
+**Expected:** 3 comments listed.
+**Actual:** 1 comment listed (Lenoir's short comment). Both Svenning comments are dropped.
+
+## Root cause — `lib/annotations.ts`
+
+### Bug A: hyphenated reviewer names (line 102)
+
+```ts
+const hasAuthorPrefix = /^[A-Za-z][A-Za-z\s]{0,20}:\s/.test(commentContent.trim());
+```
+
+The character class `[A-Za-z\s]` forbids hyphens, apostrophes, and accented characters. So:
+
+- `Jens-Christian Svenning:` — fails (hyphen at position 4)
+- `Camilla T Colding-Jørgensen:` — fails (hyphen + diacritic)
+- `Renata Ćušterevska:` — fails (diacritic at position 7)
+- Any name with `-`, `'`, or non-ASCII letters fails
+
+When `hasAuthorPrefix === false` AND content > `MAX_COMMENT_CONTENT_LENGTH = 200`, line 104 discards the comment. Any long comment from a hyphenated reviewer is silently dropped.
+
+### Bug B: any comment containing a URL <150 chars (line 95)
+
+```ts
+if (/https?:\/\/|www\./i.test(commentContent) && commentContent.length < 150) return true;
+```
+
+This filter assumes URLs in CriticMarkup blocks are markdown links wrapped in CriticMarkup syntax (a real false positive). But reviewers legitimately cite URLs/DOIs inside comments — that gets dropped too.
+
+`{>>Lenoir: see https://www.pnas.org/doi/10.1073/pnas.1608980113<<}` — 60 chars, contains URL → dropped, even though `Lenoir:` is a valid author prefix.
+
+## Suggested fix
+
+1. **Line 102 — broaden author-prefix regex:**
+   ```ts
+   const hasAuthorPrefix = /^[\p{L}][\p{L}\s\-'.]{0,30}:\s/u.test(commentContent.trim());
+   ```
+   Allows hyphens, apostrophes, periods, and Unicode letters. Length bumped to 30 (Camilla T Colding-Jørgensen is 27 chars).
+
+2. **Line 95 — only filter URLs when there's no author prefix:**
+   ```ts
+   const looksLikeAuthor = /^[\p{L}][\p{L}\s\-'.]{0,30}:\s/u.test(commentContent.trim());
+   if (!looksLikeAuthor && /https?:\/\/|www\./i.test(commentContent) && commentContent.length < 150) return true;
+   ```
+   A comment with a real `Author:` prefix should not be dropped just because it cites a URL.
+
+## Impact
+
+In `paper_hexgrids_2026/abstract.md`, three reviewer comments from Jens-Christian Svenning (one tone-related, two with cited URLs/DOIs) were silently dropped from `rev comments`, `rev next`, and presumably `rev build docx --dual` output. Other affected reviewers in this manuscript: Camilla T Colding-Jørgensen (long comments would drop), Renata Ćušterevska, Jean-Christian Svenning across all sections.

package/dist/lib/anchor-match.d.ts

@@ -0,0 +1,41 @@
+/**
+ * Anchor matching primitives shared between sync (insertion) and
+ * verify-anchors (drift reporting). The functions are pure: given an
+ * anchor string and surrounding context, locate candidate positions in
+ * a target text using progressively looser strategies.
+ */
+export type AnchorStrategy = 'direct' | 'normalized' | 'stripped' | 'partial-start' | 'partial-start-stripped' | 'context-both' | 'context-before' | 'context-after' | 'split-match' | 'empty-anchor' | 'failed';
+export interface AnchorSearchResult {
+    occurrences: number[];
+    matchedAnchor: string | null;
+    strategy: AnchorStrategy;
+    stripped?: boolean;
+}
+/**
+ * Strip CriticMarkup so the matcher sees plain prose instead of
+ * `{++inserted++}`/`{--deleted--}`/etc. Used when an anchor lives
+ * underneath previously imported track changes.
+ */
+export declare function stripCriticMarkup(text: string): string;
+/**
+ * Return every starting index where `needle` occurs in `haystack`.
+ * Empty needles return no occurrences (empty matches are not useful
+ * for anchor placement).
+ */
+export declare function findAllOccurrences(haystack: string, needle: string): number[];
+/**
+ * Find candidate positions for `anchor` in `text`, falling back through
+ * progressively looser strategies (whitespace normalization, stripped
+ * CriticMarkup, partial-prefix, surrounding context, word splitting).
+ *
+ * The returned `strategy` lets callers distinguish a clean direct hit
+ * from a fuzzy approximation — useful for drift reporting.
+ */
+export declare function findAnchorInText(anchor: string, text: string, before?: string, after?: string): AnchorSearchResult;
+/**
+ * Classify a strategy as a clean hit, a fuzzy/drifted hit, or no hit.
+ * Used by `verify-anchors` to summarize per-comment match quality.
+ */
+export type AnchorMatchQuality = 'clean' | 'drift' | 'context-only' | 'unmatched';
+export declare function classifyStrategy(strategy: AnchorStrategy, occurrences: number): AnchorMatchQuality;
+//# sourceMappingURL=anchor-match.d.ts.map

package/dist/lib/anchor-match.d.ts.map

@@ -0,0 +1 @@
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package/dist/lib/anchor-match.js

@@ -0,0 +1,192 @@
+/**
+ * Anchor matching primitives shared between sync (insertion) and
+ * verify-anchors (drift reporting). The functions are pure: given an
+ * anchor string and surrounding context, locate candidate positions in
+ * a target text using progressively looser strategies.
+ */
+/**
+ * Strip CriticMarkup so the matcher sees plain prose instead of
+ * `{++inserted++}`/`{--deleted--}`/etc. Used when an anchor lives
+ * underneath previously imported track changes.
+ */
+export function stripCriticMarkup(text) {
+    return text
+        .replace(/\{\+\+([^+]*)\+\+\}/g, '$1') // insertions: keep new text
+        .replace(/\{--([^-]*)--\}/g, '') // deletions: remove old text
+        .replace(/\{~~([^~]*)~>([^~]*)~~\}/g, '$2') // substitutions: keep new text
+        .replace(/\{>>[\s\S]*?<<\}/g, '') // comments: remove (non-greedy; comment text may contain '<')
+        .replace(/\[([^\]]*)\]\{\.mark\}/g, '$1'); // marked text: keep text
+}
+/**
+ * Return every starting index where `needle` occurs in `haystack`.
+ * Empty needles return no occurrences (empty matches are not useful
+ * for anchor placement).
+ */
+export function findAllOccurrences(haystack, needle) {
+    if (!needle || needle.length === 0)
+        return [];
+    const occurrences = [];
+    let idx = 0;
+    while ((idx = haystack.indexOf(needle, idx)) !== -1) {
+        occurrences.push(idx);
+        idx += 1;
+    }
+    return occurrences;
+}
+/**
+ * Find candidate positions for `anchor` in `text`, falling back through
+ * progressively looser strategies (whitespace normalization, stripped
+ * CriticMarkup, partial-prefix, surrounding context, word splitting).
+ *
+ * The returned `strategy` lets callers distinguish a clean direct hit
+ * from a fuzzy approximation — useful for drift reporting.
+ */
+export function findAnchorInText(anchor, text, before = '', after = '') {
+    // Empty anchor: skip directly to context-based matching
+    if (!anchor || anchor.trim().length === 0) {
+        if (before || after) {
+            const beforeLower = (before || '').toLowerCase();
+            const afterLower = (after || '').toLowerCase();
+            const textLower = text.toLowerCase();
+            if (before && after) {
+                const beforeIdx = textLower.indexOf(beforeLower.slice(-50));
+                if (beforeIdx !== -1) {
+                    const searchStart = beforeIdx + beforeLower.slice(-50).length;
+                    const afterIdx = textLower.indexOf(afterLower.slice(0, 50), searchStart);
+                    if (afterIdx !== -1 && afterIdx - searchStart < 500) {
+                        return { occurrences: [searchStart], matchedAnchor: null, strategy: 'context-both' };
+                    }
+                }
+            }
+            if (before) {
+                const beforeIdx = textLower.lastIndexOf(beforeLower.slice(-30));
+                if (beforeIdx !== -1) {
+                    return {
+                        occurrences: [beforeIdx + beforeLower.slice(-30).length],
+                        matchedAnchor: null,
+                        strategy: 'context-before',
+                    };
+                }
+            }
+            if (after) {
+                const afterIdx = textLower.indexOf(afterLower.slice(0, 30));
+                if (afterIdx !== -1) {
+                    return { occurrences: [afterIdx], matchedAnchor: null, strategy: 'context-after' };
+                }
+            }
+        }
+        return { occurrences: [], matchedAnchor: null, strategy: 'empty-anchor' };
+    }
+    const anchorLower = anchor.toLowerCase();
+    const textLower = text.toLowerCase();
+    // Strategy 1: direct match
+    let occurrences = findAllOccurrences(textLower, anchorLower);
+    if (occurrences.length > 0) {
+        return { occurrences, matchedAnchor: anchor, strategy: 'direct' };
+    }
+    // Strategy 2: normalized whitespace
+    const normalizedAnchor = anchor.replace(/\s+/g, ' ').toLowerCase();
+    const normalizedText = text.replace(/\s+/g, ' ').toLowerCase();
+    const idx = normalizedText.indexOf(normalizedAnchor);
+    if (idx !== -1) {
+        return { occurrences: [idx], matchedAnchor: anchor, strategy: 'normalized' };
+    }
+    // Strategy 3: match in stripped CriticMarkup version
+    const strippedText = stripCriticMarkup(text);
+    const strippedLower = strippedText.toLowerCase();
+    occurrences = findAllOccurrences(strippedLower, anchorLower);
+    if (occurrences.length > 0) {
+        return { occurrences, matchedAnchor: anchor, strategy: 'stripped', stripped: true };
+    }
+    // Strategy 4: first N words of anchor (long anchors)
+    const words = anchor.split(/\s+/);
+    if (words.length > 3) {
+        for (let n = Math.min(6, words.length); n >= 3; n--) {
+            const partialAnchor = words.slice(0, n).join(' ').toLowerCase();
+            if (partialAnchor.length >= 15) {
+                occurrences = findAllOccurrences(textLower, partialAnchor);
+                if (occurrences.length > 0) {
+                    return { occurrences, matchedAnchor: words.slice(0, n).join(' '), strategy: 'partial-start' };
+                }
+                occurrences = findAllOccurrences(strippedLower, partialAnchor);
+                if (occurrences.length > 0) {
+                    return {
+                        occurrences,
+                        matchedAnchor: words.slice(0, n).join(' '),
+                        strategy: 'partial-start-stripped',
+                        stripped: true,
+                    };
+                }
+            }
+        }
+    }
+    // Strategy 5: context (before/after) only
+    if (before || after) {
+        const beforeLower = before.toLowerCase();
+        const afterLower = after.toLowerCase();
+        if (before && after) {
+            const beforeIdx = textLower.indexOf(beforeLower.slice(-50));
+            if (beforeIdx !== -1) {
+                const searchStart = beforeIdx + beforeLower.slice(-50).length;
+                const afterIdx = textLower.indexOf(afterLower.slice(0, 50), searchStart);
+                if (afterIdx !== -1 && afterIdx - searchStart < 500) {
+                    return { occurrences: [searchStart], matchedAnchor: null, strategy: 'context-both' };
+                }
+            }
+        }
+        if (before) {
+            const beforeIdx = textLower.lastIndexOf(beforeLower.slice(-30));
+            if (beforeIdx !== -1) {
+                return {
+                    occurrences: [beforeIdx + beforeLower.slice(-30).length],
+                    matchedAnchor: null,
+                    strategy: 'context-before',
+                };
+            }
+        }
+        if (after) {
+            const afterIdx = textLower.indexOf(afterLower.slice(0, 30));
+            if (afterIdx !== -1) {
+                return { occurrences: [afterIdx], matchedAnchor: null, strategy: 'context-after' };
+            }
+        }
+    }
+    // Strategy 6: split anchor on transition characters
+    const splitPatterns = [' ', ', ', '. ', ' - ', ' – '];
+    for (const sep of splitPatterns) {
+        if (anchor.includes(sep)) {
+            const parts = anchor.split(sep).filter(p => p.length >= 4);
+            for (const part of parts) {
+                const partLower = part.toLowerCase();
+                occurrences = findAllOccurrences(textLower, partLower);
+                if (occurrences.length > 0 && occurrences.length < 5) {
+                    return { occurrences, matchedAnchor: part, strategy: 'split-match' };
+                }
+            }
+        }
+    }
+    return { occurrences: [], matchedAnchor: null, strategy: 'failed' };
+}
+export function classifyStrategy(strategy, occurrences) {
+    if (occurrences === 0)
+        return 'unmatched';
+    switch (strategy) {
+        case 'direct':
+        case 'normalized':
+            return 'clean';
+        case 'stripped':
+        case 'partial-start':
+        case 'partial-start-stripped':
+        case 'split-match':
+            return 'drift';
+        case 'context-both':
+        case 'context-before':
+        case 'context-after':
+            return 'context-only';
+        case 'empty-anchor':
+        case 'failed':
+        default:
+            return 'unmatched';
+    }
+}
+//# sourceMappingURL=anchor-match.js.map

package/dist/lib/anchor-match.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"anchor-match.js","sourceRoot":"","sources":["../../lib/anchor-match.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAsBH;;;;GAIG;AACH,MAAM,UAAU,iBAAiB,CAAC,IAAY;IAC5C,OAAO,IAAI;SACR,OAAO,CAAC,sBAAsB,EAAE,IAAI,CAAC,CAAQ,4BAA4B;SACzE,OAAO,CAAC,kBAAkB,EAAE,EAAE,CAAC,CAAc,6BAA6B;SAC1E,OAAO,CAAC,2BAA2B,EAAE,IAAI,CAAC,CAAG,+BAA+B;SAC5E,OAAO,CAAC,mBAAmB,EAAE,EAAE,CAAC,CAAa,8DAA8D;SAC3G,OAAO,CAAC,yBAAyB,EAAE,IAAI,CAAC,CAAC,CAAI,yBAAyB;AAC3E,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,kBAAkB,CAAC,QAAgB,EAAE,MAAc;IACjE,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IAC9C,MAAM,WAAW,GAAa,EAAE,CAAC;IACjC,IAAI,GAAG,GAAG,CAAC,CAAC;IACZ,OAAO,CAAC,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC;QACpD,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QACtB,GAAG,IAAI,CAAC,CAAC;IACX,CAAC;IACD,OAAO,WAAW,CAAC;AACrB,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,gBAAgB,CAC9B,MAAc,EACd,IAAY,EACZ,SAAiB,EAAE,EACnB,QAAgB,EAAE;IAElB,wDAAwD;IACxD,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC1C,IAAI,MAAM,IAAI,KAAK,EAAE,CAAC;YACpB,MAAM,WAAW,GAAG,CAAC,MAAM,IAAI,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC;YACjD,MAAM,UAAU,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC;YAC/C,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;YAErC,IAAI,MAAM,IAAI,KAAK,EAAE,CAAC;gBACpB,MAAM,SAAS,GAAG,SAAS,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBAC5D,IAAI,SAAS,KAAK,CAAC,CAAC,EAAE,CAAC;oBACrB,MAAM,WAAW,GAAG,SAAS,GAAG,WAAW,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,MAAM,CAAC;oBAC9D,MAAM,QAAQ,GAAG,SAAS,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,WAAW,CAAC,CAAC;oBACzE,IAAI,QAAQ,KAAK,CAAC,CAAC,IAAI,QAAQ,GAAG,WAAW,GAAG,GAAG,EAAE,CAAC;wBACpD,OAAO,EAAE,WAAW,EAAE,CAAC,WAAW,CAAC,EAAE,aAAa,EAAE,IAAI,EAAE,QAAQ,EAAE,cAAc,EAAE,CAAC;oBACvF,CAAC;gBACH,CAAC;YACH,CAAC;YAED,IAAI,MAAM,EAAE,CAAC;gBACX,MAAM,SAAS,GAAG,SAAS,CAAC,WAAW,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBAChE,IAAI,SAAS,KAAK,CAAC,CAAC,EAAE,CAAC;oBACrB,OAAO;wBACL,WAAW,EAAE,CAAC,SAAS,GAAG,WAAW,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,MAAM,CAAC;wBACxD,aAAa,EAAE,IAAI;wBACnB,QAAQ,EAAE,gBAAgB;qBAC3B,CAAC;gBACJ,CAAC;YACH,CAAC;YAED,IAAI,KAAK,EAAE,CAAC;gBACV,MAAM,QAAQ,GAAG,SAAS,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;gBAC5D,IAAI,QAAQ,KAAK,CAAC,CAAC,EAAE,CAAC;oBACpB,OAAO,EAAE,WAAW,EAAE,CAAC,QAAQ,CAAC,EAAE,aAAa,EAAE,IAAI,EAAE,QAAQ,EAAE,eAAe,EAAE,CAAC;gBACrF,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,EAAE,WAAW,EAAE,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,QAAQ,EAAE,cAAc,EAAE,CAAC;IAC5E,CAAC;IAED,MAAM,WAAW,GAAG,MAAM,CAAC,WAAW,EAAE,CAAC;IACzC,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;IAErC,2BAA2B;IAC3B,IAAI,WAAW,GAAG,kBAAkB,CAAC,SAAS,EAAE,WAAW,CAAC,CAAC;IAC7D,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC3B,OAAO,EAAE,WAAW,EAAE,aAAa,EAAE,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,CAAC;IACpE,CAAC;IAED,oCAAoC;IACpC,MAAM,gBAAgB,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,WAAW,EAAE,CAAC;IACnE,MAAM,cAAc,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,WAAW,EAAE,CAAC;IAC/D,MAAM,GAAG,GAAG,cAAc,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAC;IACrD,IAAI,GAAG,KAAK,CAAC,CAAC,EAAE,CAAC;QACf,OAAO,EAAE,WAAW,EAAE,CAAC,GAAG,CAAC,EAAE,aAAa,EAAE,MAAM,EAAE,QAAQ,EAAE,YAAY,EAAE,CAAC;IAC/E,CAAC;IAED,qDAAqD;IACrD,MAAM,YAAY,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC;IAC7C,MAAM,aAAa,GAAG,YAAY,CAAC,WAAW,EAAE,CAAC;IACjD,WAAW,GAAG,kBAAkB,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC;IAC7D,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC3B,OAAO,EAAE,WAAW,EAAE,aAAa,EAAE,MAAM,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,IAAI,EAAE,CAAC;IACtF,CAAC;IAED,qDAAqD;IACrD,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC;IAClC,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACrB,KAAK,IAAI,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YACpD,MAAM,aAAa,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAC;YAChE,IAAI,aAAa,CAAC,MAAM,IAAI,EAAE,EAAE,CAAC;gBAC/B,WAAW,GAAG,kBAAkB,CAAC,SAAS,EAAE,aAAa,CAAC,CAAC;gBAC3D,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;oBAC3B,OAAO,EAAE,WAAW,EAAE,aAAa,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,QAAQ,EAAE,eAAe,EAAE,CAAC;gBAChG,CAAC;gBACD,WAAW,GAAG,kBAAkB,CAAC,aAAa,EAAE,aAAa,CAAC,CAAC;gBAC/D,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;oBAC3B,OAAO;wBACL,WAAW;wBACX,aAAa,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;wBAC1C,QAAQ,EAAE,wBAAwB;wBAClC,QAAQ,EAAE,IAAI;qBACf,CAAC;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,0CAA0C;IAC1C,IAAI,MAAM,IAAI,KAAK,EAAE,CAAC;QACpB,MAAM,WAAW,GAAG,MAAM,CAAC,WAAW,EAAE,CAAC;QACzC,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,EAAE,CAAC;QAEvC,IAAI,MAAM,IAAI,KAAK,EAAE,CAAC;YACpB,MAAM,SAAS,GAAG,SAAS,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;YAC5D,IAAI,SAAS,KAAK,CAAC,CAAC,EAAE,CAAC;gBACrB,MAAM,WAAW,GAAG,SAAS,GAAG,WAAW,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,MAAM,CAAC;gBAC9D,MAAM,QAAQ,GAAG,SAAS,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,WAAW,CAAC,CAAC;gBACzE,IAAI,QAAQ,KAAK,CAAC,CAAC,IAAI,QAAQ,GAAG,WAAW,GAAG,GAAG,EAAE,CAAC;oBACpD,OAAO,EAAE,WAAW,EAAE,CAAC,WAAW,CAAC,EA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package/dist/lib/annotations.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"annotations.d.ts","sourceRoot":"","sources":["../../lib/annotations.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAE,gBAAgB,EAAE,YAAY,EAAE,oBAAoB,EAAE,MAAM,YAAY,CAAC;AAmHnG;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,UAAU,EAAE,CA6G3D;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,GAAE,YAAiB,GAAG,MAAM,CA+EjF;AAED;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAqDvD;AAED;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAUpD;AAED;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,MAAM,EAAE,OAAO,GAAG,MAAM,CAiD3F;AAED;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,UAAU,EAAE,CAG1D;AAED;;;;;;GAMG;AACH,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,GAAE,oBAAyB,GAAG,UAAU,EAAE,CAyB1F;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,GAAG,MAAM,CAmB7F;AAED;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,gBAAgB,CAwB/D;AAED;;;;;;GAMG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CA6C3D"}
+{"version":3,"file":"annotations.d.ts","sourceRoot":"","sources":["../../lib/annotations.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAE,gBAAgB,EAAE,YAAY,EAAE,oBAAoB,EAAE,MAAM,YAAY,CAAC;AAuHnG;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,UAAU,EAAE,CA6G3D;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,GAAE,YAAiB,GAAG,MAAM,CA+EjF;AAED;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAqDvD;AAED;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAUpD;AAED;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,MAAM,EAAE,OAAO,GAAG,MAAM,CAiD3F;AAED;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,UAAU,EAAE,CAG1D;AAED;;;;;;GAMG;AACH,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,GAAE,oBAAyB,GAAG,UAAU,EAAE,CAyB1F;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,GAAG,MAAM,CAmB7F;AAED;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,gBAAgB,CAwB/D;AAED;;;;;;GAMG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CA6C3D"}

package/dist/lib/annotations.js

@@ -77,16 +77,19 @@ function isCommentFalsePositive(commentContent, fullText, position) {
     // Contains markdown figure reference syntax
     if (/\{#fig:|!\[/.test(commentContent))
         return true;
-    // Contains URL patterns (likely a link, not a comment)
-    if (/https?:\/\/|www\./i.test(commentContent) && commentContent.length < 150)
+    // Real comments typically have "Author:" at start. Accept hyphens, apostrophes,
+    // periods, and Unicode letters so names like "Jens-Christian Svenning" or
+    // "Camilla T Colding-Jørgensen" don't get rejected. See gcol33/docrev#1.
+    const hasAuthorPrefix = /^[\p{L}][\p{L}\s\-'.]{0,30}:\s/u.test(commentContent.trim());
+    const hasResolvedMark = /^[✓✔]\s/.test(commentContent.trim());
+    // Contains URL patterns (likely a link, not a comment) — only filter when
+    // there is no real author prefix, since reviewers legitimately cite URLs/DOIs.
+    if (!hasAuthorPrefix && /https?:\/\/|www\./i.test(commentContent) && commentContent.length < 150)
         return true;
     // Looks like code (contains programming patterns)
     if (/function\s*\(|=>|import\s+|export\s+|const\s+|let\s+|var\s+/.test(commentContent))
         return true;
     // Very long without clear author pattern (likely caption, not comment)
-    // Real comments typically have "Author:" at start and are shorter
-    const hasAuthorPrefix = /^[A-Za-z][A-Za-z\s]{0,20}:\s/.test(commentContent.trim());
-    const hasResolvedMark = /^[✓✔]\s/.test(commentContent.trim());
     if (!hasAuthorPrefix && !hasResolvedMark && commentContent.length > MAX_COMMENT_CONTENT_LENGTH)
         return true;
     // Looks like a figure caption (starts with "Fig" or contains typical caption words)

package/dist/lib/annotations.js.map

@@ -1 +1 @@
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package/dist/lib/commands/file-ops.d.ts

@@ -0,0 +1,11 @@
+/**
+ * File operation commands: backup, archive, export, clean
+ *
+ * Commands that create, move, or delete project files.
+ */
+import type { Command } from 'commander';
+/**
+ * Register file-ops commands with the program
+ */
+export declare function register(program: Command): void;
+//# sourceMappingURL=file-ops.d.ts.map

package/dist/lib/commands/file-ops.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"file-ops.d.ts","sourceRoot":"","sources":["../../../lib/commands/file-ops.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAgEzC;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CA0S/C"}