docrev 0.11.1 → 0.11.3

package/lib/commands/citations.ts

@@ -1,515 +1,515 @@
-/**
- * Citation commands: citations, figures, equations, pdf-comments
- *
- * Commands for validating citations, managing figures/tables, and equation handling.
- */
-
-import {
-  chalk,
-  fs,
-  path,
-  fmt,
-} from './context.js';
-import type { Command } from 'commander';
-
-interface CitationsOptions {
-  bib: string;
-}
-
-interface EquationsOptions {
-  output?: string;
-}
-
-interface PdfCommentsOptions {
-  append?: string;
-  json?: boolean;
-  byPage?: boolean;
-  byAuthor?: boolean;
-  withText?: boolean;
-}
-
-/**
- * Register citation commands with the program
- */
-export function register(program: Command): void {
-  // ==========================================================================
-  // CITATIONS command - Validate citations against .bib file
-  // ==========================================================================
-
-  program
-    .command('citations')
-    .alias('cite')
-    .description('Validate citations against bibliography')
-    .argument('[files...]', 'Markdown files to check (default: all section files)')
-    .option('-b, --bib <file>', 'Bibliography file', 'references.bib')
-    .action(async (files: string[], options: CitationsOptions) => {
-      const { getCitationStats } = await import('../citations.js');
-
-      // If no files specified, find all .md files
-      let mdFiles = files;
-      if (!mdFiles || mdFiles.length === 0) {
-        mdFiles = fs.readdirSync('.').filter(f =>
-          f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f)
-        );
-      }
-
-      if (!fs.existsSync(options.bib)) {
-        console.error(fmt.status('error', `Bibliography not found: ${options.bib}`));
-        process.exit(1);
-      }
-
-      const stats = getCitationStats(mdFiles, options.bib);
-
-      console.log(fmt.header('Citation Check'));
-      console.log();
-
-      // Summary table
-      const rows: string[][] = [
-        ['Total citations', stats.totalCitations.toString()],
-        ['Unique keys cited', stats.uniqueCited.toString()],
-        ['Bib entries', stats.bibEntries.toString()],
-        [chalk.green('Valid'), chalk.green(stats.valid.toString())],
-        [stats.missing > 0 ? chalk.red('Missing') : 'Missing', stats.missing > 0 ? chalk.red(stats.missing.toString()) : '0'],
-        [chalk.dim('Unused in bib'), chalk.dim(stats.unused.toString())],
-      ];
-      console.log(fmt.table(['Metric', 'Count'], rows));
-
-      // Show missing keys
-      if (stats.missingKeys.length > 0) {
-        console.log();
-        console.log(fmt.status('error', 'Missing citations:'));
-        for (const key of stats.missingKeys) {
-          console.log(chalk.red(`  - ${key}`));
-        }
-      }
-
-      // Show unused (if verbose)
-      if (stats.unusedKeys.length > 0 && stats.unusedKeys.length <= 10) {
-        console.log();
-        console.log(chalk.dim('Unused bib entries:'));
-        for (const key of stats.unusedKeys.slice(0, 10)) {
-          console.log(chalk.dim(`  - ${key}`));
-        }
-        if (stats.unusedKeys.length > 10) {
-          console.log(chalk.dim(`  ... and ${stats.unusedKeys.length - 10} more`));
-        }
-      }
-
-      console.log();
-      if (stats.missing === 0) {
-        console.log(fmt.status('success', 'All citations valid'));
-      } else {
-        console.log(fmt.status('warning', `${stats.missing} citation(s) missing from ${options.bib}`));
-        process.exit(1);
-      }
-    });
-
-  // ==========================================================================
-  // FIGURES command - Figure/table inventory
-  // ==========================================================================
-
-  program
-    .command('figures')
-    .alias('figs')
-    .description('List all figures and tables with reference counts')
-    .argument('[files...]', 'Markdown files to scan')
-    .action(async (files: string[]) => {
-      const { buildRegistry } = await import('../crossref.js');
-
-      // If no files specified, find all .md files
-      let mdFiles = files;
-      if (!mdFiles || mdFiles.length === 0) {
-        mdFiles = fs.readdirSync('.').filter(f =>
-          f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f)
-        );
-      }
-
-      // Build registry
-      const registry = buildRegistry('.');
-
-      // Count references in files
-      const refCounts = new Map<string, number>();
-      for (const file of mdFiles) {
-        if (!fs.existsSync(file)) continue;
-        const text = fs.readFileSync(file, 'utf-8');
-
-        // Count @fig: and @tbl: references
-        const figRefs = text.matchAll(/@fig:([a-zA-Z0-9_-]+)/g);
-        for (const match of figRefs) {
-          const key = `fig:${match[1]}`;
-          refCounts.set(key, (refCounts.get(key) || 0) + 1);
-        }
-
-        const tblRefs = text.matchAll(/@tbl:([a-zA-Z0-9_-]+)/g);
-        for (const match of tblRefs) {
-          const key = `tbl:${match[1]}`;
-          refCounts.set(key, (refCounts.get(key) || 0) + 1);
-        }
-      }
-
-      console.log(fmt.header('Figure & Table Inventory'));
-      console.log();
-
-      // Figures
-      if (registry.figures.size > 0) {
-        const figRows = [...registry.figures.entries()].map(([label, info]) => {
-          const key = `fig:${label}`;
-          const refs = refCounts.get(key) || 0;
-          const num = info.isSupp ? `S${info.num}` : info.num.toString();
-          return [
-            `Figure ${num}`,
-            chalk.cyan(`@fig:${label}`),
-            info.file,
-            refs > 0 ? chalk.green(refs.toString()) : chalk.yellow('0'),
-          ];
-        });
-        console.log(fmt.table(['#', 'Label', 'File', 'Refs'], figRows));
-        console.log();
-      }
-
-      // Tables
-      if (registry.tables.size > 0) {
-        const tblRows = [...registry.tables.entries()].map(([label, info]) => {
-          const key = `tbl:${label}`;
-          const refs = refCounts.get(key) || 0;
-          const num = info.isSupp ? `S${info.num}` : info.num.toString();
-          return [
-            `Table ${num}`,
-            chalk.cyan(`@tbl:${label}`),
-            info.file,
-            refs > 0 ? chalk.green(refs.toString()) : chalk.yellow('0'),
-          ];
-        });
-        console.log(fmt.table(['#', 'Label', 'File', 'Refs'], tblRows));
-        console.log();
-      }
-
-      if (registry.figures.size === 0 && registry.tables.size === 0) {
-        console.log(chalk.dim('No figures or tables found.'));
-        console.log(chalk.dim('Add anchors like {#fig:label} to your figures.'));
-      }
-
-      // Warn about unreferenced
-      const unreferenced: string[] = [];
-      for (const [label] of registry.figures) {
-        if (!refCounts.get(`fig:${label}`)) unreferenced.push(`@fig:${label}`);
-      }
-      for (const [label] of registry.tables) {
-        if (!refCounts.get(`tbl:${label}`)) unreferenced.push(`@tbl:${label}`);
-      }
-
-      if (unreferenced.length > 0) {
-        console.log(fmt.status('warning', `${unreferenced.length} unreferenced figure(s)/table(s)`));
-      }
-    });
-
-  // ==========================================================================
-  // EQUATIONS command - Extract and convert equations
-  // ==========================================================================
-
-  program
-    .command('equations')
-    .alias('eq')
-    .description('Extract equations or convert to Word')
-    .argument('<action>', 'Action: list, extract, convert, from-word')
-    .argument('[input]', 'Input file (.md for extract/convert, .docx for from-word)')
-    .option('-o, --output <file>', 'Output file')
-    .action(async (action: string, input: string | undefined, options: EquationsOptions) => {
-      const { extractEquations, getEquationStats, createEquationsDoc, extractEquationsFromWord, getWordEquationStats } = await import('../equations.js');
-
-      if (action === 'from-word') {
-        // Extract equations from Word document
-        if (!input) {
-          console.error(fmt.status('error', 'Word document required'));
-          process.exit(1);
-        }
-
-        if (!input.endsWith('.docx')) {
-          console.error(fmt.status('error', 'Input must be a .docx file'));
-          process.exit(1);
-        }
-
-        const spin = fmt.spinner(`Extracting equations from ${path.basename(input)}...`).start();
-
-        const result = await extractEquationsFromWord(input);
-
-        if (!result.success) {
-          spin.error(result.error!);
-          process.exit(1);
-        }
-
-        spin.stop();
-        console.log(fmt.header('Equations from Word'));
-        console.log();
-
-        if (result.equations.length === 0) {
-          console.log(chalk.dim('No equations found in document.'));
-          return;
-        }
-
-        const display = result.equations.filter(e => e.type === 'display');
-        const inline = result.equations.filter(e => e.type === 'inline');
-
-        console.log(chalk.dim(`Found ${result.equations.length} equations (${display.length} display, ${inline.length} inline)`));
-        console.log();
-
-        // Show equations
-        for (let i = 0; i < result.equations.length; i++) {
-          const eq = result.equations[i];
-          const typeLabel = eq.type === 'display' ? chalk.cyan('[display]') : chalk.yellow('[inline]');
-
-          if (eq.latex) {
-            console.log(`${chalk.bold((i + 1).toString())}. ${typeLabel}`);
-            console.log(chalk.dim('   LaTeX:'), eq.latex.length > 80 ? eq.latex.substring(0, 77) + '...' : eq.latex);
-          } else {
-            console.log(`${chalk.bold((i + 1).toString())}. ${typeLabel} ${chalk.red('[conversion failed]')}`);
-          }
-        }
-
-        // Optionally save to file
-        if (options.output) {
-          const latex = result.equations
-            .filter(e => e.latex)
-            .map((e, i) => `%% Equation ${i + 1} (${e.type})\n${e.type === 'display' ? '$$' : '$'}${e.latex}${e.type === 'display' ? '$$' : '$'}`)
-            .join('\n\n');
-
-          fs.writeFileSync(options.output, latex, 'utf-8');
-          console.log();
-          console.log(fmt.status('success', `Saved ${result.equations.filter(e => e.latex).length} equations to ${options.output}`));
-        }
-
-      } else if (action === 'list') {
-        // List equations in all section files
-        const mdFiles = fs.readdirSync('.').filter(f =>
-          f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f)
-        );
-
-        const stats = getEquationStats(mdFiles);
-
-        console.log(fmt.header('Equations'));
-        console.log();
-
-        if (stats.byFile.length === 0) {
-          console.log(chalk.dim('No equations found.'));
-          return;
-        }
-
-        const rows = stats.byFile.map(f => [
-          f.file,
-          f.display > 0 ? chalk.cyan(f.display.toString()) : chalk.dim('-'),
-          f.inline > 0 ? chalk.yellow(f.inline.toString()) : chalk.dim('-'),
-        ]);
-        rows.push([
-          chalk.bold('Total'),
-          chalk.bold.cyan(stats.display.toString()),
-          chalk.bold.yellow(stats.inline.toString()),
-        ]);
-
-        console.log(fmt.table(['File', 'Display', 'Inline'], rows));
-
-      } else if (action === 'extract') {
-        if (!input) {
-          console.error(fmt.status('error', 'Input file required'));
-          process.exit(1);
-        }
-
-        const output = options.output || input.replace('.md', '-equations.md');
-        const result = await createEquationsDoc(input, output);
-
-        if (result.success) {
-          console.log(fmt.status('success', result.message));
-          console.log(chalk.dim(`  ${result.stats!.display} display, ${result.stats!.inline} inline equations`));
-        } else {
-          console.error(fmt.status('error', result.message));
-          process.exit(1);
-        }
-
-      } else if (action === 'convert') {
-        if (!input) {
-          console.error(fmt.status('error', 'Input file required'));
-          process.exit(1);
-        }
-
-        const output = options.output || input.replace('.md', '.docx');
-
-        const spin = fmt.spinner(`Converting ${path.basename(input)} to Word...`).start();
-
-        try {
-          const { exec } = await import('child_process');
-          const { promisify } = await import('util');
-          const execAsync = promisify(exec);
-
-          await execAsync(`pandoc "${input}" -o "${output}" --mathml`);
-          spin.success(`Created ${output}`);
-        } catch (err) {
-          const error = err as Error;
-          spin.error(error.message);
-          process.exit(1);
-        }
-      } else {
-        console.error(fmt.status('error', `Unknown action: ${action}`));
-        console.log(chalk.dim('Actions: list, extract, convert, from-word'));
-        process.exit(1);
-      }
-    });
-
-  // ==========================================================================
-  // PDF-COMMENTS command - Extract comments from PDF
-  // ==========================================================================
-
-  program
-    .command('pdf-comments')
-    .alias('pdf')
-    .description('Extract and manage comments from annotated PDFs')
-    .argument('<pdf>', 'PDF file with annotations')
-    .option('-a, --append <file>', 'Append comments to markdown file')
-    .option('--json', 'Output as JSON')
-    .option('--by-page', 'Group comments by page')
-    .option('--by-author', 'Group comments by author')
-    .option('--with-text', 'Extract highlighted text (slower but shows what was highlighted)')
-    .action(async (pdf: string, options: PdfCommentsOptions) => {
-      if (!fs.existsSync(pdf)) {
-        console.error(fmt.status('error', `File not found: ${pdf}`));
-        process.exit(1);
-      }
-
-      if (!pdf.toLowerCase().endsWith('.pdf')) {
-        console.error(fmt.status('error', 'File must be a PDF'));
-        process.exit(1);
-      }
-
-      const {
-        extractPdfComments,
-        extractPdfAnnotationsWithText,
-        formatPdfComments,
-        getPdfCommentStats,
-        insertPdfCommentsIntoMarkdown,
-        formatAnnotationWithText,
-      } = await import('../pdf-import.js');
-
-      const spin = fmt.spinner(`Extracting comments from ${path.basename(pdf)}...`).start();
-
-      try {
-        let comments: any[];
-
-        if (options.withText) {
-          // Use the new text extraction feature
-          const annotations = await extractPdfAnnotationsWithText(pdf);
-          spin.stop();
-
-          if (annotations.length === 0) {
-            console.log(fmt.status('info', 'No annotations found in PDF.'));
-            return;
-          }
-
-          // Convert to comment format with highlighted text
-          comments = annotations.map(a => ({
-            author: a.author || 'Reviewer',
-            text: a.highlightedText
-              ? `"${a.highlightedText}"${a.contents ? ' → ' + a.contents : ''}`
-              : a.contents,
-            page: a.page,
-            type: a.type,
-            date: a.date,
-            highlightedText: a.highlightedText,
-          })).filter(c => c.text);
-        } else {
-          comments = await extractPdfComments(pdf);
-          spin.stop();
-        }
-
-        if (comments.length === 0) {
-          console.log(fmt.status('info', 'No comments found in PDF.'));
-          return;
-        }
-
-        const stats = getPdfCommentStats(comments);
-
-        // JSON output
-        if (options.json) {
-          console.log(JSON.stringify({ comments, stats }, null, 2));
-          return;
-        }
-
-        // Append to markdown file
-        if (options.append) {
-          if (!fs.existsSync(options.append)) {
-            console.error(fmt.status('error', `Markdown file not found: ${options.append}`));
-            process.exit(1);
-          }
-
-          const markdown = fs.readFileSync(options.append, 'utf-8');
-          const updated = insertPdfCommentsIntoMarkdown(markdown, comments);
-          fs.writeFileSync(options.append, updated, 'utf-8');
-
-          console.log(fmt.status('success', `Added ${comments.length} comments to ${options.append}`));
-          return;
-        }
-
-        // Display comments
-        console.log(fmt.header(`PDF Comments: ${path.basename(pdf)}`));
-        console.log();
-
-        if (options.byAuthor) {
-          // Group by author
-          const byAuthor: Record<string, any[]> = {};
-          for (const c of comments) {
-            const author = c.author || 'Unknown';
-            if (!byAuthor[author]) byAuthor[author] = [];
-            byAuthor[author].push(c);
-          }
-
-          for (const [author, authorComments] of Object.entries(byAuthor)) {
-            console.log(chalk.bold(`${author} (${authorComments.length}):`));
-            for (const c of authorComments) {
-              if (c.highlightedText) {
-                console.log(`  [p.${c.page}] ${chalk.yellow(`"${c.highlightedText}"`)}${c.text !== c.highlightedText ? ` → ${c.text.replace(`"${c.highlightedText}" → `, '')}` : ''}`);
-              } else {
-                console.log(`  [p.${c.page}] ${c.text}`);
-              }
-            }
-            console.log();
-          }
-        } else {
-          // Default: by page
-          if (options.withText) {
-            let currentPage = 0;
-            for (const c of comments) {
-              if (c.page !== currentPage) {
-                if (currentPage > 0) console.log();
-                console.log(`Page ${c.page}:`);
-                currentPage = c.page;
-              }
-              if (c.highlightedText) {
-                console.log(`  ${chalk.yellow(`"${c.highlightedText}"`)} → ${c.text.replace(`"${c.highlightedText}" → `, '')}`);
-              } else {
-                console.log(`  ${c.text}`);
-              }
-            }
-            console.log();
-          } else {
-            console.log(formatPdfComments(comments));
-            console.log();
-          }
-        }
-
-        // Summary
-        const authorList = Object.entries(stats.byAuthor)
-          .map(([author, count]) => `${author} (${count})`)
-          .join(', ');
-        console.log(chalk.dim(`Total: ${stats.total} comments from ${authorList}`));
-        console.log();
-        if (!options.withText) {
-          console.log(chalk.dim(`Tip: Use --with-text to extract the highlighted text content`));
-        }
-        console.log(chalk.dim(`Tip: Use --append <file.md> to add comments to your markdown`));
-
-      } catch (err) {
-        spin.stop();
-        const error = err as Error;
-        console.error(fmt.status('error', `Failed to extract PDF comments: ${error.message}`));
-        if (process.env.DEBUG) console.error(error.stack);
-        process.exit(1);
-      }
-    });
-}
+/**
+ * Citation commands: citations, figures, equations, pdf-comments
+ *
+ * Commands for validating citations, managing figures/tables, and equation handling.
+ */
+
+import {
+  chalk,
+  fs,
+  path,
+  fmt,
+} from './context.js';
+import type { Command } from 'commander';
+
+interface CitationsOptions {
+  bib: string;
+}
+
+interface EquationsOptions {
+  output?: string;
+}
+
+interface PdfCommentsOptions {
+  append?: string;
+  json?: boolean;
+  byPage?: boolean;
+  byAuthor?: boolean;
+  withText?: boolean;
+}
+
+/**
+ * Register citation commands with the program
+ */
+export function register(program: Command): void {
+  // ==========================================================================
+  // CITATIONS command - Validate citations against .bib file
+  // ==========================================================================
+
+  program
+    .command('citations')
+    .alias('cite')
+    .description('Validate citations against bibliography')
+    .argument('[files...]', 'Markdown files to check (default: all section files)')
+    .option('-b, --bib <file>', 'Bibliography file', 'references.bib')
+    .action(async (files: string[], options: CitationsOptions) => {
+      const { getCitationStats } = await import('../citations.js');
+
+      // If no files specified, find all .md files
+      let mdFiles = files;
+      if (!mdFiles || mdFiles.length === 0) {
+        mdFiles = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f)
+        );
+      }
+
+      if (!fs.existsSync(options.bib)) {
+        console.error(fmt.status('error', `Bibliography not found: ${options.bib}`));
+        process.exit(1);
+      }
+
+      const stats = getCitationStats(mdFiles, options.bib);
+
+      console.log(fmt.header('Citation Check'));
+      console.log();
+
+      // Summary table
+      const rows: string[][] = [
+        ['Total citations', stats.totalCitations.toString()],
+        ['Unique keys cited', stats.uniqueCited.toString()],
+        ['Bib entries', stats.bibEntries.toString()],
+        [chalk.green('Valid'), chalk.green(stats.valid.toString())],
+        [stats.missing > 0 ? chalk.red('Missing') : 'Missing', stats.missing > 0 ? chalk.red(stats.missing.toString()) : '0'],
+        [chalk.dim('Unused in bib'), chalk.dim(stats.unused.toString())],
+      ];
+      console.log(fmt.table(['Metric', 'Count'], rows));
+
+      // Show missing keys
+      if (stats.missingKeys.length > 0) {
+        console.log();
+        console.log(fmt.status('error', 'Missing citations:'));
+        for (const key of stats.missingKeys) {
+          console.log(chalk.red(`  - ${key}`));
+        }
+      }
+
+      // Show unused (if verbose)
+      if (stats.unusedKeys.length > 0 && stats.unusedKeys.length <= 10) {
+        console.log();
+        console.log(chalk.dim('Unused bib entries:'));
+        for (const key of stats.unusedKeys.slice(0, 10)) {
+          console.log(chalk.dim(`  - ${key}`));
+        }
+        if (stats.unusedKeys.length > 10) {
+          console.log(chalk.dim(`  ... and ${stats.unusedKeys.length - 10} more`));
+        }
+      }
+
+      console.log();
+      if (stats.missing === 0) {
+        console.log(fmt.status('success', 'All citations valid'));
+      } else {
+        console.log(fmt.status('warning', `${stats.missing} citation(s) missing from ${options.bib}`));
+        process.exit(1);
+      }
+    });
+
+  // ==========================================================================
+  // FIGURES command - Figure/table inventory
+  // ==========================================================================
+
+  program
+    .command('figures')
+    .alias('figs')
+    .description('List all figures and tables with reference counts')
+    .argument('[files...]', 'Markdown files to scan')
+    .action(async (files: string[]) => {
+      const { buildRegistry } = await import('../crossref.js');
+
+      // If no files specified, find all .md files
+      let mdFiles = files;
+      if (!mdFiles || mdFiles.length === 0) {
+        mdFiles = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f)
+        );
+      }
+
+      // Build registry
+      const registry = buildRegistry('.');
+
+      // Count references in files
+      const refCounts = new Map<string, number>();
+      for (const file of mdFiles) {
+        if (!fs.existsSync(file)) continue;
+        const text = fs.readFileSync(file, 'utf-8');
+
+        // Count @fig: and @tbl: references
+        const figRefs = text.matchAll(/@fig:([a-zA-Z0-9_-]+)/g);
+        for (const match of figRefs) {
+          const key = `fig:${match[1]}`;
+          refCounts.set(key, (refCounts.get(key) || 0) + 1);
+        }
+
+        const tblRefs = text.matchAll(/@tbl:([a-zA-Z0-9_-]+)/g);
+        for (const match of tblRefs) {
+          const key = `tbl:${match[1]}`;
+          refCounts.set(key, (refCounts.get(key) || 0) + 1);
+        }
+      }
+
+      console.log(fmt.header('Figure & Table Inventory'));
+      console.log();
+
+      // Figures
+      if (registry.figures.size > 0) {
+        const figRows = [...registry.figures.entries()].map(([label, info]) => {
+          const key = `fig:${label}`;
+          const refs = refCounts.get(key) || 0;
+          const num = info.isSupp ? `S${info.num}` : info.num.toString();
+          return [
+            `Figure ${num}`,
+            chalk.cyan(`@fig:${label}`),
+            info.file,
+            refs > 0 ? chalk.green(refs.toString()) : chalk.yellow('0'),
+          ];
+        });
+        console.log(fmt.table(['#', 'Label', 'File', 'Refs'], figRows));
+        console.log();
+      }
+
+      // Tables
+      if (registry.tables.size > 0) {
+        const tblRows = [...registry.tables.entries()].map(([label, info]) => {
+          const key = `tbl:${label}`;
+          const refs = refCounts.get(key) || 0;
+          const num = info.isSupp ? `S${info.num}` : info.num.toString();
+          return [
+            `Table ${num}`,
+            chalk.cyan(`@tbl:${label}`),
+            info.file,
+            refs > 0 ? chalk.green(refs.toString()) : chalk.yellow('0'),
+          ];
+        });
+        console.log(fmt.table(['#', 'Label', 'File', 'Refs'], tblRows));
+        console.log();
+      }
+
+      if (registry.figures.size === 0 && registry.tables.size === 0) {
+        console.log(chalk.dim('No figures or tables found.'));
+        console.log(chalk.dim('Add anchors like {#fig:label} to your figures.'));
+      }
+
+      // Warn about unreferenced
+      const unreferenced: string[] = [];
+      for (const [label] of registry.figures) {
+        if (!refCounts.get(`fig:${label}`)) unreferenced.push(`@fig:${label}`);
+      }
+      for (const [label] of registry.tables) {
+        if (!refCounts.get(`tbl:${label}`)) unreferenced.push(`@tbl:${label}`);
+      }
+
+      if (unreferenced.length > 0) {
+        console.log(fmt.status('warning', `${unreferenced.length} unreferenced figure(s)/table(s)`));
+      }
+    });
+
+  // ==========================================================================
+  // EQUATIONS command - Extract and convert equations
+  // ==========================================================================
+
+  program
+    .command('equations')
+    .alias('eq')
+    .description('Extract equations or convert to Word')
+    .argument('<action>', 'Action: list, extract, convert, from-word')
+    .argument('[input]', 'Input file (.md for extract/convert, .docx for from-word)')
+    .option('-o, --output <file>', 'Output file')
+    .action(async (action: string, input: string | undefined, options: EquationsOptions) => {
+      const { extractEquations, getEquationStats, createEquationsDoc, extractEquationsFromWord, getWordEquationStats } = await import('../equations.js');
+
+      if (action === 'from-word') {
+        // Extract equations from Word document
+        if (!input) {
+          console.error(fmt.status('error', 'Word document required'));
+          process.exit(1);
+        }
+
+        if (!input.endsWith('.docx')) {
+          console.error(fmt.status('error', 'Input must be a .docx file'));
+          process.exit(1);
+        }
+
+        const spin = fmt.spinner(`Extracting equations from ${path.basename(input)}...`).start();
+
+        const result = await extractEquationsFromWord(input);
+
+        if (!result.success) {
+          spin.error(result.error!);
+          process.exit(1);
+        }
+
+        spin.stop();
+        console.log(fmt.header('Equations from Word'));
+        console.log();
+
+        if (result.equations.length === 0) {
+          console.log(chalk.dim('No equations found in document.'));
+          return;
+        }
+
+        const display = result.equations.filter(e => e.type === 'display');
+        const inline = result.equations.filter(e => e.type === 'inline');
+
+        console.log(chalk.dim(`Found ${result.equations.length} equations (${display.length} display, ${inline.length} inline)`));
+        console.log();
+
+        // Show equations
+        for (let i = 0; i < result.equations.length; i++) {
+          const eq = result.equations[i];
+          const typeLabel = eq.type === 'display' ? chalk.cyan('[display]') : chalk.yellow('[inline]');
+
+          if (eq.latex) {
+            console.log(`${chalk.bold((i + 1).toString())}. ${typeLabel}`);
+            console.log(chalk.dim('   LaTeX:'), eq.latex.length > 80 ? eq.latex.substring(0, 77) + '...' : eq.latex);
+          } else {
+            console.log(`${chalk.bold((i + 1).toString())}. ${typeLabel} ${chalk.red('[conversion failed]')}`);
+          }
+        }
+
+        // Optionally save to file
+        if (options.output) {
+          const latex = result.equations
+            .filter(e => e.latex)
+            .map((e, i) => `%% Equation ${i + 1} (${e.type})\n${e.type === 'display' ? '$$' : '$'}${e.latex}${e.type === 'display' ? '$$' : '$'}`)
+            .join('\n\n');
+
+          fs.writeFileSync(options.output, latex, 'utf-8');
+          console.log();
+          console.log(fmt.status('success', `Saved ${result.equations.filter(e => e.latex).length} equations to ${options.output}`));
+        }
+
+      } else if (action === 'list') {
+        // List equations in all section files
+        const mdFiles = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f)
+        );
+
+        const stats = getEquationStats(mdFiles);
+
+        console.log(fmt.header('Equations'));
+        console.log();
+
+        if (stats.byFile.length === 0) {
+          console.log(chalk.dim('No equations found.'));
+          return;
+        }
+
+        const rows = stats.byFile.map(f => [
+          f.file,
+          f.display > 0 ? chalk.cyan(f.display.toString()) : chalk.dim('-'),
+          f.inline > 0 ? chalk.yellow(f.inline.toString()) : chalk.dim('-'),
+        ]);
+        rows.push([
+          chalk.bold('Total'),
+          chalk.bold.cyan(stats.display.toString()),
+          chalk.bold.yellow(stats.inline.toString()),
+        ]);
+
+        console.log(fmt.table(['File', 'Display', 'Inline'], rows));
+
+      } else if (action === 'extract') {
+        if (!input) {
+          console.error(fmt.status('error', 'Input file required'));
+          process.exit(1);
+        }
+
+        const output = options.output || input.replace('.md', '-equations.md');
+        const result = await createEquationsDoc(input, output);
+
+        if (result.success) {
+          console.log(fmt.status('success', result.message));
+          console.log(chalk.dim(`  ${result.stats!.display} display, ${result.stats!.inline} inline equations`));
+        } else {
+          console.error(fmt.status('error', result.message));
+          process.exit(1);
+        }
+
+      } else if (action === 'convert') {
+        if (!input) {
+          console.error(fmt.status('error', 'Input file required'));
+          process.exit(1);
+        }
+
+        const output = options.output || input.replace('.md', '.docx');
+
+        const spin = fmt.spinner(`Converting ${path.basename(input)} to Word...`).start();
+
+        try {
+          const { exec } = await import('child_process');
+          const { promisify } = await import('util');
+          const execAsync = promisify(exec);
+
+          await execAsync(`pandoc "${input}" -o "${output}" --mathml`);
+          spin.success(`Created ${output}`);
+        } catch (err) {
+          const error = err as Error;
+          spin.error(error.message);
+          process.exit(1);
+        }
+      } else {
+        console.error(fmt.status('error', `Unknown action: ${action}`));
+        console.log(chalk.dim('Actions: list, extract, convert, from-word'));
+        process.exit(1);
+      }
+    });
+
+  // ==========================================================================
+  // PDF-COMMENTS command - Extract comments from PDF
+  // ==========================================================================
+
+  program
+    .command('pdf-comments')
+    .alias('pdf')
+    .description('Extract and manage comments from annotated PDFs')
+    .argument('<pdf>', 'PDF file with annotations')
+    .option('-a, --append <file>', 'Append comments to markdown file')
+    .option('--json', 'Output as JSON')
+    .option('--by-page', 'Group comments by page')
+    .option('--by-author', 'Group comments by author')
+    .option('--with-text', 'Extract highlighted text (slower but shows what was highlighted)')
+    .action(async (pdf: string, options: PdfCommentsOptions) => {
+      if (!fs.existsSync(pdf)) {
+        console.error(fmt.status('error', `File not found: ${pdf}`));
+        process.exit(1);
+      }
+
+      if (!pdf.toLowerCase().endsWith('.pdf')) {
+        console.error(fmt.status('error', 'File must be a PDF'));
+        process.exit(1);
+      }
+
+      const {
+        extractPdfComments,
+        extractPdfAnnotationsWithText,
+        formatPdfComments,
+        getPdfCommentStats,
+        insertPdfCommentsIntoMarkdown,
+        formatAnnotationWithText,
+      } = await import('../pdf-import.js');
+
+      const spin = fmt.spinner(`Extracting comments from ${path.basename(pdf)}...`).start();
+
+      try {
+        let comments: any[];
+
+        if (options.withText) {
+          // Use the new text extraction feature
+          const annotations = await extractPdfAnnotationsWithText(pdf);
+          spin.stop();
+
+          if (annotations.length === 0) {
+            console.log(fmt.status('info', 'No annotations found in PDF.'));
+            return;
+          }
+
+          // Convert to comment format with highlighted text
+          comments = annotations.map(a => ({
+            author: a.author || 'Reviewer',
+            text: a.highlightedText
+              ? `"${a.highlightedText}"${a.contents ? ' → ' + a.contents : ''}`
+              : a.contents,
+            page: a.page,
+            type: a.type,
+            date: a.date,
+            highlightedText: a.highlightedText,
+          })).filter(c => c.text);
+        } else {
+          comments = await extractPdfComments(pdf);
+          spin.stop();
+        }
+
+        if (comments.length === 0) {
+          console.log(fmt.status('info', 'No comments found in PDF.'));
+          return;
+        }
+
+        const stats = getPdfCommentStats(comments);
+
+        // JSON output
+        if (options.json) {
+          console.log(JSON.stringify({ comments, stats }, null, 2));
+          return;
+        }
+
+        // Append to markdown file
+        if (options.append) {
+          if (!fs.existsSync(options.append)) {
+            console.error(fmt.status('error', `Markdown file not found: ${options.append}`));
+            process.exit(1);
+          }
+
+          const markdown = fs.readFileSync(options.append, 'utf-8');
+          const updated = insertPdfCommentsIntoMarkdown(markdown, comments);
+          fs.writeFileSync(options.append, updated, 'utf-8');
+
+          console.log(fmt.status('success', `Added ${comments.length} comments to ${options.append}`));
+          return;
+        }
+
+        // Display comments
+        console.log(fmt.header(`PDF Comments: ${path.basename(pdf)}`));
+        console.log();
+
+        if (options.byAuthor) {
+          // Group by author
+          const byAuthor: Record<string, any[]> = {};
+          for (const c of comments) {
+            const author = c.author || 'Unknown';
+            if (!byAuthor[author]) byAuthor[author] = [];
+            byAuthor[author].push(c);
+          }
+
+          for (const [author, authorComments] of Object.entries(byAuthor)) {
+            console.log(chalk.bold(`${author} (${authorComments.length}):`));
+            for (const c of authorComments) {
+              if (c.highlightedText) {
+                console.log(`  [p.${c.page}] ${chalk.yellow(`"${c.highlightedText}"`)}${c.text !== c.highlightedText ? ` → ${c.text.replace(`"${c.highlightedText}" → `, '')}` : ''}`);
+              } else {
+                console.log(`  [p.${c.page}] ${c.text}`);
+              }
+            }
+            console.log();
+          }
+        } else {
+          // Default: by page
+          if (options.withText) {
+            let currentPage = 0;
+            for (const c of comments) {
+              if (c.page !== currentPage) {
+                if (currentPage > 0) console.log();
+                console.log(`Page ${c.page}:`);
+                currentPage = c.page;
+              }
+              if (c.highlightedText) {
+                console.log(`  ${chalk.yellow(`"${c.highlightedText}"`)} → ${c.text.replace(`"${c.highlightedText}" → `, '')}`);
+              } else {
+                console.log(`  ${c.text}`);
+              }
+            }
+            console.log();
+          } else {
+            console.log(formatPdfComments(comments));
+            console.log();
+          }
+        }
+
+        // Summary
+        const authorList = Object.entries(stats.byAuthor)
+          .map(([author, count]) => `${author} (${count})`)
+          .join(', ');
+        console.log(chalk.dim(`Total: ${stats.total} comments from ${authorList}`));
+        console.log();
+        if (!options.withText) {
+          console.log(chalk.dim(`Tip: Use --with-text to extract the highlighted text content`));
+        }
+        console.log(chalk.dim(`Tip: Use --append <file.md> to add comments to your markdown`));
+
+      } catch (err) {
+        spin.stop();
+        const error = err as Error;
+        console.error(fmt.status('error', `Failed to extract PDF comments: ${error.message}`));
+        if (process.env.DEBUG) console.error(error.stack);
+        process.exit(1);
+      }
+    });
+}