docrev 0.10.1 → 0.10.2

package/completions/rev.zsh

@@ -1,207 +1,207 @@
-#compdef rev
-
-# Zsh completion for rev (docrev)
-# Install: add to fpath or run:
-#   eval "$(rev completions zsh)"
-
-_rev() {
-    local -a commands build_formats doi_actions eq_actions help_topics journals preview_formats
-
-    commands=(
-        'build:Build PDF/DOCX/TEX from sections'
-        'new:Create new project from template'
-        'import:Import Word document'
-        'sections:Import to section files'
-        'extract:Extract text from Word'
-        'review:Interactive review TUI'
-        'status:Show annotation counts'
-        'comments:List comments'
-        'resolve:Mark comment as resolved'
-        'reply:Reply to comments'
-        'strip:Output clean markdown'
-        'refs:Show reference status'
-        'migrate:Convert hardcoded refs'
-        'config:Configure settings'
-        'install:Check dependencies'
-        'doi:DOI validation'
-        'citations:Validate citations'
-        'equations:Extract equations'
-        'figures:List figures'
-        'response:Generate response letter'
-        'anonymize:Prepare for blind review'
-        'validate:Check journal requirements'
-        'merge:Merge reviewer feedback'
-        'diff:Compare against git history'
-        'history:Show revision history'
-        'help:Show help'
-        'init:Initialize project'
-        'split:Split paper.md to sections'
-        'word-count:Show word counts per section'
-        'wc:Show word counts (alias)'
-        'stats:Show project statistics'
-        'search:Search across files'
-        'backup:Create timestamped backup'
-        'export:Export project as zip'
-        'preview:Build and open document'
-        'watch:Watch and auto-rebuild'
-        'lint:Check for issues'
-        'grammar:Check grammar and style'
-        'annotate:Add comments to DOCX'
-        'apply:Apply annotations as track changes'
-        'comment:Interactive comment mode'
-        'completions:Generate shell completions'
-    )
-
-    preview_formats=(
-        'pdf:Preview PDF'
-        'docx:Preview Word document'
-    )
-
-    build_formats=(
-        'pdf:Build PDF'
-        'docx:Build Word document'
-        'tex:Build LaTeX'
-        'all:Build all formats'
-    )
-
-    doi_actions=(
-        'check:Validate DOIs'
-        'lookup:Find missing DOIs'
-        'fetch:Get BibTeX from DOI'
-        'add:Add citation by DOI'
-    )
-
-    eq_actions=(
-        'list:List equations'
-        'extract:Extract to file'
-        'convert:Convert to Word'
-        'from-word:Extract from Word'
-    )
-
-    help_topics=(
-        'workflow:Review workflow'
-        'syntax:CriticMarkup syntax'
-        'commands:All commands'
-    )
-
-    journals=(
-        'nature:Nature journal'
-        'science:Science journal'
-        'plos:PLOS ONE'
-        'cell:Cell journal'
-        'ecology:Ecology journals'
-        'custom:Custom profile'
-    )
-
-    case "$words[2]" in
-        build)
-            _describe -t formats 'format' build_formats
-            _arguments \
-                '--toc[Include table of contents]' \
-                '--show-changes[Show track changes in DOCX]' \
-                '--clean[Clean build files]'
-            ;;
-        new)
-            _arguments \
-                '--list[List templates]' \
-                '--template[Template name]:template:(paper minimal thesis proposal)'
-            ;;
-        doi)
-            _describe -t actions 'action' doi_actions
-            ;;
-        equations|eq)
-            _describe -t actions 'action' eq_actions
-            ;;
-        validate)
-            _arguments \
-                '--list[List journals]' \
-                '--journal[Journal name]:journal:($journals)'
-            ;;
-        help)
-            _describe -t topics 'topic' help_topics
-            ;;
-        config)
-            _values 'setting' 'user[Set user name]'
-            ;;
-        word-count|wc)
-            _arguments \
-                '--limit[Word limit]:number:' \
-                '--journal[Use journal word limit]:journal:'
-            ;;
-        preview)
-            _describe -t formats 'format' preview_formats
-            ;;
-        watch)
-            _arguments \
-                '--no-open[Do not open after build]'
-            _values 'format' 'pdf' 'docx' 'all'
-            ;;
-        lint)
-            _arguments \
-                '--fix[Auto-fix issues]'
-            ;;
-        grammar)
-            _arguments \
-                '--learn[Add word to dictionary]:word:' \
-                '--forget[Remove from dictionary]:word:' \
-                '--list[List dictionary words]' \
-                '--rules[List grammar rules]' \
-                '--no-scientific[Disable science rules]' \
-                '--severity[Minimum severity]:level:(error warning info)'
-            _files -g '*.md'
-            ;;
-        annotate)
-            _arguments \
-                '-m[Comment message]:text:' \
-                '-s[Search text]:text:' \
-                '-a[Author name]:name:'
-            _files -g '*.docx'
-            ;;
-        apply)
-            _arguments \
-                '-a[Author name]:name:'
-            _files -g '*.md'
-            ;;
-        comment)
-            _arguments \
-                '-a[Author name]:name:'
-            _files -g '*.docx'
-            ;;
-        completions)
-            _values 'shell' 'bash' 'zsh'
-            ;;
-        import|sections|extract|review|status|comments|strip|refs|migrate|figures|response|anonymize|split|search|stats)
-            _files -g '*.md' -g '*.docx'
-            ;;
-        resolve|reply)
-            _arguments \
-                '-n[Comment number]:number:' \
-                '-m[Reply message]:message:'
-            _files -g '*.md'
-            ;;
-        check|lookup|add|citations)
-            _files -g '*.bib'
-            ;;
-        merge)
-            _files -g '*.md' -g '*.docx'
-            ;;
-        backup)
-            _arguments \
-                '--name[Custom backup name]:name:' \
-                '--output[Output directory]:dir:_files -/'
-            ;;
-        export)
-            _arguments \
-                '--output[Output filename]:file:' \
-                '--include-output[Include built files]'
-            ;;
-        *)
-            _describe -t commands 'command' commands
-            _arguments \
-                '--help[Show help]' \
-                '--version[Show version]'
-            ;;
-    esac
-}
-
-_rev "$@"
+#compdef rev
+
+# Zsh completion for rev (docrev)
+# Install: add to fpath or run:
+#   eval "$(rev completions zsh)"
+
+_rev() {
+    local -a commands build_formats doi_actions eq_actions help_topics journals preview_formats
+
+    commands=(
+        'build:Build PDF/DOCX/TEX from sections'
+        'new:Create new project from template'
+        'import:Import Word document'
+        'sections:Import to section files'
+        'extract:Extract text from Word'
+        'review:Interactive review TUI'
+        'status:Show annotation counts'
+        'comments:List comments'
+        'resolve:Mark comment as resolved'
+        'reply:Reply to comments'
+        'strip:Output clean markdown'
+        'refs:Show reference status'
+        'migrate:Convert hardcoded refs'
+        'config:Configure settings'
+        'install:Check dependencies'
+        'doi:DOI validation'
+        'citations:Validate citations'
+        'equations:Extract equations'
+        'figures:List figures'
+        'response:Generate response letter'
+        'anonymize:Prepare for blind review'
+        'validate:Check journal requirements'
+        'merge:Merge reviewer feedback'
+        'diff:Compare against git history'
+        'history:Show revision history'
+        'help:Show help'
+        'init:Initialize project'
+        'split:Split paper.md to sections'
+        'word-count:Show word counts per section'
+        'wc:Show word counts (alias)'
+        'stats:Show project statistics'
+        'search:Search across files'
+        'backup:Create timestamped backup'
+        'export:Export project as zip'
+        'preview:Build and open document'
+        'watch:Watch and auto-rebuild'
+        'lint:Check for issues'
+        'grammar:Check grammar and style'
+        'annotate:Add comments to DOCX'
+        'apply:Apply annotations as track changes'
+        'comment:Interactive comment mode'
+        'completions:Generate shell completions'
+    )
+
+    preview_formats=(
+        'pdf:Preview PDF'
+        'docx:Preview Word document'
+    )
+
+    build_formats=(
+        'pdf:Build PDF'
+        'docx:Build Word document'
+        'tex:Build LaTeX'
+        'all:Build all formats'
+    )
+
+    doi_actions=(
+        'check:Validate DOIs'
+        'lookup:Find missing DOIs'
+        'fetch:Get BibTeX from DOI'
+        'add:Add citation by DOI'
+    )
+
+    eq_actions=(
+        'list:List equations'
+        'extract:Extract to file'
+        'convert:Convert to Word'
+        'from-word:Extract from Word'
+    )
+
+    help_topics=(
+        'workflow:Review workflow'
+        'syntax:CriticMarkup syntax'
+        'commands:All commands'
+    )
+
+    journals=(
+        'nature:Nature journal'
+        'science:Science journal'
+        'plos:PLOS ONE'
+        'cell:Cell journal'
+        'ecology:Ecology journals'
+        'custom:Custom profile'
+    )
+
+    case "$words[2]" in
+        build)
+            _describe -t formats 'format' build_formats
+            _arguments \
+                '--toc[Include table of contents]' \
+                '--show-changes[Show track changes in DOCX]' \
+                '--clean[Clean build files]'
+            ;;
+        new)
+            _arguments \
+                '--list[List templates]' \
+                '--template[Template name]:template:(paper minimal thesis proposal)'
+            ;;
+        doi)
+            _describe -t actions 'action' doi_actions
+            ;;
+        equations|eq)
+            _describe -t actions 'action' eq_actions
+            ;;
+        validate)
+            _arguments \
+                '--list[List journals]' \
+                '--journal[Journal name]:journal:($journals)'
+            ;;
+        help)
+            _describe -t topics 'topic' help_topics
+            ;;
+        config)
+            _values 'setting' 'user[Set user name]'
+            ;;
+        word-count|wc)
+            _arguments \
+                '--limit[Word limit]:number:' \
+                '--journal[Use journal word limit]:journal:'
+            ;;
+        preview)
+            _describe -t formats 'format' preview_formats
+            ;;
+        watch)
+            _arguments \
+                '--no-open[Do not open after build]'
+            _values 'format' 'pdf' 'docx' 'all'
+            ;;
+        lint)
+            _arguments \
+                '--fix[Auto-fix issues]'
+            ;;
+        grammar)
+            _arguments \
+                '--learn[Add word to dictionary]:word:' \
+                '--forget[Remove from dictionary]:word:' \
+                '--list[List dictionary words]' \
+                '--rules[List grammar rules]' \
+                '--no-scientific[Disable science rules]' \
+                '--severity[Minimum severity]:level:(error warning info)'
+            _files -g '*.md'
+            ;;
+        annotate)
+            _arguments \
+                '-m[Comment message]:text:' \
+                '-s[Search text]:text:' \
+                '-a[Author name]:name:'
+            _files -g '*.docx'
+            ;;
+        apply)
+            _arguments \
+                '-a[Author name]:name:'
+            _files -g '*.md'
+            ;;
+        comment)
+            _arguments \
+                '-a[Author name]:name:'
+            _files -g '*.docx'
+            ;;
+        completions)
+            _values 'shell' 'bash' 'zsh'
+            ;;
+        import|sections|extract|review|status|comments|strip|refs|migrate|figures|response|anonymize|split|search|stats)
+            _files -g '*.md' -g '*.docx'
+            ;;
+        resolve|reply)
+            _arguments \
+                '-n[Comment number]:number:' \
+                '-m[Reply message]:message:'
+            _files -g '*.md'
+            ;;
+        check|lookup|add|citations)
+            _files -g '*.bib'
+            ;;
+        merge)
+            _files -g '*.md' -g '*.docx'
+            ;;
+        backup)
+            _arguments \
+                '--name[Custom backup name]:name:' \
+                '--output[Output directory]:dir:_files -/'
+            ;;
+        export)
+            _arguments \
+                '--output[Output filename]:file:' \
+                '--include-output[Include built files]'
+            ;;
+        *)
+            _describe -t commands 'command' commands
+            _arguments \
+                '--help[Show help]' \
+                '--version[Show version]'
+            ;;
+    esac
+}
+
+_rev "$@"

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

@@ -4,7 +4,7 @@
  * 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 type AnchorStrategy = 'direct' | 'normalized' | 'stripped' | 'partial-start' | 'partial-start-stripped' | 'partial-window' | 'partial-window-stripped' | 'context-both' | 'context-before' | 'context-after' | 'split-match' | 'empty-anchor' | 'failed';
 export interface AnchorSearchResult {
     occurrences: number[];
     matchedAnchor: string | null;

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

@@ -1 +1 @@
-{"version":3,"file":"anchor-match.d.ts","sourceRoot":"","sources":["../../lib/anchor-match.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,MAAM,MAAM,cAAc,GACtB,QAAQ,GACR,YAAY,GACZ,UAAU,GACV,eAAe,GACf,wBAAwB,GACxB,cAAc,GACd,gBAAgB,GAChB,eAAe,GACf,aAAa,GACb,cAAc,GACd,QAAQ,CAAC;AAEb,MAAM,WAAW,kBAAkB;IACjC,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,QAAQ,EAAE,cAAc,CAAC;IACzB,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAOtD;AAED;;;;GAIG;AACH;;;;;;;;GAQG;AACH,wBAAgB,cAAc,CAC5B,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,GAChB,MAAM,CAqBR;AAED,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,EAAE,CAS7E;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAC9B,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,MAAM,EACZ,MAAM,GAAE,MAAW,EACnB,KAAK,GAAE,MAAW,GACjB,kBAAkB,CA2IpB;AAED;;;GAGG;AACH,MAAM,MAAM,kBAAkB,GAAG,OAAO,GAAG,OAAO,GAAG,cAAc,GAAG,WAAW,CAAC;AAElF,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,GAAG,kBAAkB,CAoBlG"}
+{"version":3,"file":"anchor-match.d.ts","sourceRoot":"","sources":["../../lib/anchor-match.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,MAAM,MAAM,cAAc,GACtB,QAAQ,GACR,YAAY,GACZ,UAAU,GACV,eAAe,GACf,wBAAwB,GACxB,gBAAgB,GAChB,yBAAyB,GACzB,cAAc,GACd,gBAAgB,GAChB,eAAe,GACf,aAAa,GACb,cAAc,GACd,QAAQ,CAAC;AAEb,MAAM,WAAW,kBAAkB;IACjC,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,QAAQ,EAAE,cAAc,CAAC;IACzB,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAOtD;AAED;;;;GAIG;AACH;;;;;;;;GAQG;AACH,wBAAgB,cAAc,CAC5B,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,GAChB,MAAM,CAqBR;AAED,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,EAAE,CAS7E;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAC9B,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,MAAM,EACZ,MAAM,GAAE,MAAW,EACnB,KAAK,GAAE,MAAW,GACjB,kBAAkB,CAuKpB;AAED;;;GAGG;AACH,MAAM,MAAM,kBAAkB,GAAG,OAAO,GAAG,OAAO,GAAG,cAAc,GAAG,WAAW,CAAC;AAElF,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,GAAG,kBAAkB,CAsBlG"}

package/dist/lib/anchor-match.js

@@ -133,39 +133,67 @@ export function findAnchorInText(anchor, text, before = '', after = '') {
     if (occurrences.length > 0) {
         return { occurrences, matchedAnchor: anchor, strategy: 'stripped', stripped: true };
     }
-    // Strategy 4: first N words of anchor (long anchors)
+    // Strategy 4: word window from anchor (prefix or interior).
+    // Sliding the window across the anchor catches the case where the
+    // anchor's prefix has been edited but a chunk in the middle/end
+    // survived intact (e.g. "Sensitivity analyses were performed by
+    // perturbing the prior variance" → drifted "Sensitivity analyses
+    // perturbed the prior variance" still contains "the prior variance").
     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' };
+            for (let start = 0; start + n <= words.length; start++) {
+                const window = words.slice(start, start + n).join(' ');
+                const windowLower = window.toLowerCase();
+                if (windowLower.length < 15)
+                    continue;
+                let occ = findAllOccurrences(textLower, windowLower);
+                if (occ.length > 0) {
+                    const strategy = start === 0 ? 'partial-start' : 'partial-window';
+                    return { occurrences: occ, matchedAnchor: window, strategy };
                 }
-                occurrences = findAllOccurrences(strippedLower, partialAnchor);
-                if (occurrences.length > 0) {
-                    return {
-                        occurrences,
-                        matchedAnchor: words.slice(0, n).join(' '),
-                        strategy: 'partial-start-stripped',
-                        stripped: true,
-                    };
+                occ = findAllOccurrences(strippedLower, windowLower);
+                if (occ.length > 0) {
+                    const strategy = start === 0 ? 'partial-start-stripped' : 'partial-window-stripped';
+                    return { occurrences: occ, matchedAnchor: window, strategy, stripped: true };
                 }
             }
         }
     }
-    // Strategy 5: context (before/after) only
+    // Strategy 5: context (before/after) only.
+    //
+    // For a non-empty anchor that already failed every text-based strategy
+    // above, we treat context as a degraded placement: classify it
+    // 'context-only' so callers can warn the user. We also reject
+    // implausible brackets — if both contexts match but the gap between
+    // them is far too small to contain the anchor (e.g. the anchored
+    // sentence was deleted), do not silently land the comment between
+    // the surviving sentences. Return 'failed' so the user is told to
+    // place it manually.
     if (before || after) {
         const beforeLower = before.toLowerCase();
         const afterLower = after.toLowerCase();
+        const anchorLen = anchor.length;
         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 (afterIdx !== -1) {
+                    const gap = afterIdx - searchStart;
+                    // Require the bracket to plausibly contain a remnant of the anchor.
+                    // Below 30% of anchor length: anchor was deleted — refuse to place.
+                    // Above 2× anchor length + slack: brackets are too far apart, the
+                    // matcher has latched onto unrelated repeats of common context.
+                    const minGap = Math.floor(anchorLen * 0.3);
+                    const maxGap = Math.min(500, anchorLen * 2 + 50);
+                    if (gap >= minGap && gap <= maxGap) {
+                        return { occurrences: [searchStart], matchedAnchor: null, strategy: 'context-both' };
+                    }
+                    // Both brackets found but gap implausible: anchor likely deleted.
+                    // Don't fall back to single-side context — that would silently
+                    // place the comment in the wrong location.
+                    return { occurrences: [], matchedAnchor: null, strategy: 'failed' };
                 }
             }
         }
@@ -212,6 +240,8 @@ export function classifyStrategy(strategy, occurrences) {
         case 'stripped':
         case 'partial-start':
         case 'partial-start-stripped':
+        case 'partial-window':
+        case 'partial-window-stripped':
         case 'split-match':
             return 'drift';
         case 'context-both':

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

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

@@ -968,10 +968,10 @@ export function buildPandocArgs(format, config, outputPath) {
         }
         // Fit images within slide bounds (default: true)
         if (beamer.fit_images !== false) {
-            const fitImagesHeader = `\\makeatletter
-\\def\\maxwidth{\\ifdim\\Gin@nat@width>\\linewidth\\linewidth\\else\\Gin@nat@width\\fi}
-\\def\\maxheight{\\ifdim\\Gin@nat@height>0.75\\textheight 0.75\\textheight\\else\\Gin@nat@height\\fi}
-\\makeatother
+            const fitImagesHeader = `\\makeatletter
+\\def\\maxwidth{\\ifdim\\Gin@nat@width>\\linewidth\\linewidth\\else\\Gin@nat@width\\fi}
+\\def\\maxheight{\\ifdim\\Gin@nat@height>0.75\\textheight 0.75\\textheight\\else\\Gin@nat@height\\fi}
+\\makeatother
 \\setkeys{Gin}{width=\\maxwidth,height=\\maxheight,keepaspectratio}`;
             args.push('-V', `header-includes=${fitImagesHeader}`);
         }

package/dist/lib/commands/sync.d.ts.map

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