docrev 0.6.13 → 0.7.6

package/lib/commands/utilities.js

@@ -0,0 +1,2272 @@
+/**
+ * Utility commands: help, completions, word-count, stats, search, backup, archive,
+ * export, preview, watch, lint, grammar, annotate, apply, comment, clean, check,
+ * open, spelling, upgrade, batch, install-cli-skill, uninstall-cli-skill
+ *
+ * Miscellaneous utility commands for project management.
+ */
+
+import {
+  chalk,
+  fs,
+  path,
+  fmt,
+  findFiles,
+  loadBuildConfig,
+  getComments,
+  setCommentStatus,
+  countAnnotations,
+  stripAnnotations,
+  parseAnnotations,
+  getUserName,
+} from './context.js';
+
+/**
+ * Register utility commands with the program
+ * @param {import('commander').Command} program
+ * @param {object} [pkg] - Package.json object for version info
+ */
+export function register(program, pkg) {
+  // ==========================================================================
+  // HELP command - Comprehensive help
+  // ==========================================================================
+
+  program
+    .command('help')
+    .description('Show detailed help and workflow guide')
+    .argument('[topic]', 'Help topic: workflow, syntax, commands')
+    .action((topic) => {
+      if (!topic || topic === 'all') {
+        showFullHelp(pkg);
+      } else if (topic === 'workflow') {
+        showWorkflowHelp();
+      } else if (topic === 'syntax') {
+        showSyntaxHelp();
+      } else if (topic === 'commands') {
+        showCommandsHelp();
+      } else {
+        console.log(chalk.yellow(`Unknown topic: ${topic}`));
+        console.log(chalk.dim('Available topics: workflow, syntax, commands'));
+      }
+    });
+
+  // ==========================================================================
+  // COMPLETIONS command - Shell completions
+  // ==========================================================================
+
+  program
+    .command('completions')
+    .description('Output shell completions')
+    .argument('<shell>', 'Shell type: bash, zsh, powershell')
+    .action((shell) => {
+      const completionsDir = path.join(import.meta.dirname, '..', '..', 'completions');
+
+      if (shell === 'bash') {
+        const bashFile = path.join(completionsDir, 'rev.bash');
+        if (fs.existsSync(bashFile)) {
+          console.log(fs.readFileSync(bashFile, 'utf-8'));
+        } else {
+          console.error(chalk.red('Bash completions not found'));
+          process.exit(1);
+        }
+      } else if (shell === 'zsh') {
+        const zshFile = path.join(completionsDir, 'rev.zsh');
+        if (fs.existsSync(zshFile)) {
+          console.log(fs.readFileSync(zshFile, 'utf-8'));
+        } else {
+          console.error(chalk.red('Zsh completions not found'));
+          process.exit(1);
+        }
+      } else if (shell === 'powershell' || shell === 'pwsh') {
+        const psFile = path.join(completionsDir, 'rev.ps1');
+        if (fs.existsSync(psFile)) {
+          console.log(fs.readFileSync(psFile, 'utf-8'));
+        } else {
+          console.error(chalk.red('PowerShell completions not found'));
+          process.exit(1);
+        }
+      } else {
+        console.error(chalk.red(`Unknown shell: ${shell}`));
+        console.log(chalk.dim('Supported shells: bash, zsh, powershell'));
+        process.exit(1);
+      }
+    });
+
+  // ==========================================================================
+  // WORD-COUNT command - Per-section word counts
+  // ==========================================================================
+
+  program
+    .command('word-count')
+    .alias('wc')
+    .description('Show word counts per section')
+    .option('-l, --limit <number>', 'Warn if total exceeds limit', parseInt)
+    .option('-j, --journal <name>', 'Use journal word limit')
+    .action(async (options) => {
+      let config = {};
+      try {
+        config = loadBuildConfig() || {};
+      } catch {
+        // Not in a rev project, that's ok
+      }
+      const sections = config.sections || [];
+
+      if (sections.length === 0) {
+        // Try to find .md files
+        const mdFiles = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f)
+        );
+        if (mdFiles.length === 0) {
+          console.error(chalk.red('No section files found. Run from a rev project directory.'));
+          process.exit(1);
+        }
+        sections.push(...mdFiles);
+      }
+
+      const countWords = (text) => {
+        return text
+          .replace(/^---[\s\S]*?---/m, '')
+          .replace(/!\[.*?\]\(.*?\)/g, '')
+          .replace(/\[([^\]]+)\]\([^)]+\)/g, '$1')
+          .replace(/#+\s*/g, '')
+          .replace(/\*\*|__|[*_`]/g, '')
+          .replace(/```[\s\S]*?```/g, '')
+          .replace(/\{[^}]+\}/g, '')
+          .replace(/@\w+:\w+/g, '')
+          .replace(/@\w+/g, '')
+          .replace(/\|[^|]+\|/g, ' ')
+          .replace(/\n+/g, ' ')
+          .trim()
+          .split(/\s+/)
+          .filter(w => w.length > 0).length;
+      };
+
+      let total = 0;
+      const rows = [];
+
+      for (const section of sections) {
+        if (!fs.existsSync(section)) continue;
+        const text = fs.readFileSync(section, 'utf-8');
+        const words = countWords(text);
+        total += words;
+        rows.push([section, words.toLocaleString()]);
+      }
+
+      rows.push(['', '']);
+      rows.push([chalk.bold('Total'), chalk.bold(total.toLocaleString())]);
+
+      console.log(fmt.header('Word Count'));
+      console.log(fmt.table(['Section', 'Words'], rows));
+
+      // Check limit
+      let limit = options.limit;
+      if (options.journal) {
+        const { getJournalProfile } = await import('../journals.js');
+        const profile = getJournalProfile(options.journal);
+        if (profile?.requirements?.wordLimit?.main) {
+          limit = profile.requirements.wordLimit.main;
+          console.log(chalk.dim(`\nUsing ${profile.name} word limit: ${limit.toLocaleString()}`));
+        }
+      }
+
+      if (limit && total > limit) {
+        console.log(chalk.red(`\n⚠ Over limit by ${(total - limit).toLocaleString()} words`));
+      } else if (limit) {
+        console.log(chalk.green(`\n✓ Within limit (${(limit - total).toLocaleString()} words remaining)`));
+      }
+    });
+
+  // ==========================================================================
+  // STATS command - Project dashboard
+  // ==========================================================================
+
+  program
+    .command('stats')
+    .description('Show project statistics dashboard')
+    .action(async () => {
+      let config = {};
+      try {
+        config = loadBuildConfig() || {};
+      } catch {
+        // Not in a rev project, that's ok
+      }
+      let sections = config.sections || [];
+
+      if (sections.length === 0) {
+        sections = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f)
+        );
+      }
+
+      const countWords = (text) => {
+        return text
+          .replace(/^---[\s\S]*?---/m, '')
+          .replace(/!\[.*?\]\(.*?\)/g, '')
+          .replace(/\[([^\]]+)\]\([^)]+\)/g, '$1')
+          .replace(/[#*_`]/g, '')
+          .replace(/\{[^}]+\}/g, '')
+          .replace(/@\w+/g, '')
+          .replace(/\n+/g, ' ')
+          .trim()
+          .split(/\s+/)
+          .filter(w => w.length > 0).length;
+      };
+
+      let totalWords = 0;
+      let totalFigures = 0;
+      let totalTables = 0;
+      let totalComments = 0;
+      let pendingComments = 0;
+      const citations = new Set();
+
+      for (const section of sections) {
+        if (!fs.existsSync(section)) continue;
+        const text = fs.readFileSync(section, 'utf-8');
+
+        totalWords += countWords(text);
+        totalFigures += (text.match(/!\[.*?\]\(.*?\)/g) || []).length;
+        totalTables += (text.match(/^\|[^|]+\|/gm) || []).length / 5; // Approximate
+
+        const comments = getComments(text);
+        totalComments += comments.length;
+        pendingComments += comments.filter(c => !c.resolved).length;
+
+        const cites = text.match(/@(\w+)(?![:\w])/g) || [];
+        cites.forEach(c => citations.add(c.slice(1)));
+      }
+
+      console.log(fmt.header('Project Statistics'));
+      console.log();
+
+      const stats = [
+        ['Sections', sections.length],
+        ['Words', totalWords.toLocaleString()],
+        ['Figures', Math.round(totalFigures)],
+        ['Tables', Math.round(totalTables)],
+        ['Citations', citations.size],
+        ['Comments', `${totalComments} (${pendingComments} pending)`],
+      ];
+
+      for (const [label, value] of stats) {
+        console.log(`  ${chalk.dim(label.padEnd(12))} ${chalk.bold(value)}`);
+      }
+
+      // Bibliography stats
+      const bibPath = config.bibliography || 'references.bib';
+      if (fs.existsSync(bibPath)) {
+        const bibContent = fs.readFileSync(bibPath, 'utf-8');
+        const bibEntries = (bibContent.match(/@\w+\s*\{/g) || []).length;
+        console.log(`  ${chalk.dim('Bib entries'.padEnd(12))} ${chalk.bold(bibEntries)}`);
+      }
+
+      console.log();
+    });
+
+  // ==========================================================================
+  // SEARCH command - Search across section files
+  // ==========================================================================
+
+  program
+    .command('search')
+    .description('Search across all section files')
+    .argument('<query>', 'Search query (supports regex)')
+    .option('-i, --ignore-case', 'Case-insensitive search')
+    .option('-c, --context <lines>', 'Show context lines', parseInt, 1)
+    .action((query, options) => {
+      let config = {};
+      try {
+        config = loadBuildConfig() || {};
+      } catch {
+        // Not in a rev project, that's ok
+      }
+      let sections = config.sections || [];
+
+      if (sections.length === 0) {
+        sections = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') && !['README.md', 'CLAUDE.md'].includes(f)
+        );
+      }
+
+      const flags = options.ignoreCase ? 'gi' : 'g';
+      let pattern;
+      try {
+        pattern = new RegExp(query, flags);
+      } catch {
+        pattern = new RegExp(query.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'), flags);
+      }
+
+      let totalMatches = 0;
+
+      for (const section of sections) {
+        if (!fs.existsSync(section)) continue;
+        const text = fs.readFileSync(section, 'utf-8');
+        const lines = text.split('\n');
+
+        const matches = [];
+        for (let i = 0; i < lines.length; i++) {
+          if (pattern.test(lines[i])) {
+            matches.push({ line: i + 1, text: lines[i] });
+            pattern.lastIndex = 0;
+          }
+        }
+
+        if (matches.length > 0) {
+          console.log(chalk.cyan.bold(`\n${section}`));
+          for (const match of matches) {
+            const highlighted = match.text.replace(pattern, (m) => chalk.yellow.bold(m));
+            console.log(`  ${chalk.dim(match.line + ':')} ${highlighted}`);
+          }
+          totalMatches += matches.length;
+        }
+      }
+
+      if (totalMatches === 0) {
+        console.log(chalk.yellow(`No matches found for "${query}"`));
+      } else {
+        console.log(chalk.dim(`\n${totalMatches} match${totalMatches === 1 ? '' : 'es'} found`));
+      }
+    });
+
+  // ==========================================================================
+  // BACKUP command - Timestamped project backup
+  // ==========================================================================
+
+  program
+    .command('backup')
+    .description('Create timestamped project backup')
+    .option('-n, --name <name>', 'Custom backup name')
+    .option('-o, --output <dir>', 'Output directory', '.')
+    .action(async (options) => {
+      const { default: AdmZip } = await import('adm-zip');
+      const zip = new AdmZip();
+
+      const date = new Date().toISOString().slice(0, 10);
+      const name = options.name || `backup-${date}`;
+      const outputPath = path.join(options.output, `${name}.zip`);
+
+      // Files to exclude
+      const excludePatterns = [
+        'node_modules', '.git', '.DS_Store', '*.zip',
+        'paper.md' // Generated file
+      ];
+
+      const shouldInclude = (file) => {
+        for (const pattern of excludePatterns) {
+          if (file.includes(pattern.replace('*', ''))) return false;
+        }
+        return true;
+      };
+
+      const addDir = (dir, zipPath = '') => {
+        const entries = fs.readdirSync(dir, { withFileTypes: true });
+        for (const entry of entries) {
+          const fullPath = path.join(dir, entry.name);
+          const entryZipPath = path.join(zipPath, entry.name);
+
+          if (!shouldInclude(entry.name)) continue;
+
+          if (entry.isDirectory()) {
+            addDir(fullPath, entryZipPath);
+          } else {
+            zip.addLocalFile(fullPath, zipPath || undefined);
+          }
+        }
+      };
+
+      // Add current directory
+      const entries = fs.readdirSync('.', { withFileTypes: true });
+      for (const entry of entries) {
+        if (!shouldInclude(entry.name)) continue;
+
+        if (entry.isDirectory()) {
+          addDir(entry.name, entry.name);
+        } else if (entry.isFile()) {
+          zip.addLocalFile(entry.name);
+        }
+      }
+
+      zip.writeZip(outputPath);
+      console.log(fmt.status('success', `Backup created: ${outputPath}`));
+    });
+
+  // ==========================================================================
+  // ARCHIVE command - Archive reviewer docx files
+  // ==========================================================================
+
+  program
+    .command('archive')
+    .description('Move reviewer .docx files to archive folder')
+    .argument('[files...]', 'Specific files to archive (default: all .docx)')
+    .option('-d, --dir <folder>', 'Archive folder name', 'archive')
+    .option('--by <name>', 'Reviewer name (auto-detected if single commenter)')
+    .option('--no-rename', 'Keep original filenames')
+    .option('--dry-run', 'Preview without moving files')
+    .action(async (files, options) => {
+      const { extractWordComments } = await import('../import.js');
+      const { default: YAML } = await import('yaml');
+
+      // Find docx files to archive
+      let docxFiles = files && files.length > 0
+        ? files.filter(f => f.endsWith('.docx') && fs.existsSync(f))
+        : findFiles('.docx');
+
+      // Exclude our own build outputs
+      let projectSlug = null;
+      const configPath = path.join(process.cwd(), 'rev.yaml');
+      if (fs.existsSync(configPath)) {
+        try {
+          const config = YAML.parse(fs.readFileSync(configPath, 'utf-8'));
+          if (config.title) {
+            projectSlug = config.title
+              .toLowerCase()
+              .replace(/[^a-z0-9]+/g, '-')
+              .replace(/^-|-$/g, '')
+              .slice(0, 50);
+          }
+        } catch (e) {
+          // Ignore config errors
+        }
+      }
+
+      // Filter out build outputs
+      if (projectSlug && files.length === 0) {
+        const buildPatterns = [
+          `${projectSlug}.docx`,
+          `${projectSlug}_comments.docx`,
+          `${projectSlug}-changes.docx`,
+          'paper.docx',
+          'paper_comments.docx',
+          'paper-changes.docx',
+        ];
+        const excluded = [];
+        docxFiles = docxFiles.filter(f => {
+          const base = path.basename(f).toLowerCase();
+          const isBuilt = buildPatterns.includes(base);
+          if (isBuilt) excluded.push(f);
+          return !isBuilt;
+        });
+        if (excluded.length > 0) {
+          console.log(chalk.dim(`  Skipping build outputs: ${excluded.join(', ')}`));
+          console.log();
+        }
+      }
+
+      if (docxFiles.length === 0) {
+        console.log(fmt.status('info', 'No .docx files to archive.'));
+        return;
+      }
+
+      const projectTitle = projectSlug;
+
+      // Create archive folder
+      const archiveDir = path.resolve(options.dir);
+      if (!options.dryRun && !fs.existsSync(archiveDir)) {
+        fs.mkdirSync(archiveDir, { recursive: true });
+      }
+
+      console.log(fmt.header('Archive'));
+      console.log();
+
+      const moved = [];
+      for (const file of docxFiles) {
+        const stat = fs.statSync(file);
+        const mtime = stat.mtime;
+        const timestamp = mtime.toISOString().slice(0, 19).replace(/[-:]/g, '').replace('T', '_');
+
+        // Determine reviewer name
+        let reviewer = options.by || null;
+        if (!reviewer && options.rename !== false) {
+          try {
+            const comments = await extractWordComments(file);
+            const authors = [...new Set(comments.map(c => c.author).filter(a => a && a !== 'Unknown'))];
+            if (authors.length === 1) {
+              reviewer = authors[0].replace(/[^a-zA-Z0-9]/g, '-').replace(/^-|-$/g, '');
+            }
+          } catch (e) {
+            // Ignore extraction errors
+          }
+        }
+
+        // Generate new name
+        let newName;
+        if (options.rename === false) {
+          newName = path.basename(file);
+        } else {
+          const base = path.basename(file, '.docx');
+          if (/^\d{8}_\d{6}_/.test(base)) {
+            newName = path.basename(file);
+          } else {
+            const namePart = projectTitle || base;
+            if (reviewer) {
+              newName = `${timestamp}_${reviewer}_${namePart}.docx`;
+            } else {
+              newName = `${timestamp}_${namePart}.docx`;
+            }
+          }
+        }
+
+        const destPath = path.join(archiveDir, newName);
+
+        if (options.dryRun) {
+          console.log(`  ${chalk.dim(file)} → ${chalk.cyan(path.join(options.dir, newName))}`);
+        } else {
+          // Handle name collision
+          let finalPath = destPath;
+          let counter = 1;
+          while (fs.existsSync(finalPath)) {
+            const ext = path.extname(newName);
+            const base = path.basename(newName, ext);
+            finalPath = path.join(archiveDir, `${base}_${counter}${ext}`);
+            counter++;
+          }
+          fs.renameSync(file, finalPath);
+          console.log(`  ${chalk.dim(file)} → ${chalk.green(path.relative(process.cwd(), finalPath))}`);
+        }
+        moved.push(file);
+      }
+
+      console.log();
+      if (options.dryRun) {
+        console.log(fmt.status('info', `Would archive ${moved.length} file(s). Run without --dry-run to proceed.`));
+      } else {
+        console.log(fmt.status('success', `Archived ${moved.length} file(s) to ${options.dir}/`));
+      }
+    });
+
+  // ==========================================================================
+  // EXPORT command - Export project as distributable zip
+  // ==========================================================================
+
+  program
+    .command('export')
+    .description('Export project as distributable zip')
+    .option('-o, --output <file>', 'Output filename')
+    .option('--include-output', 'Include built PDF/DOCX files')
+    .action(async (options) => {
+      const { default: AdmZip } = await import('adm-zip');
+      const { build } = await import('../build.js');
+
+      let config = {};
+      try {
+        config = loadBuildConfig() || {};
+      } catch {
+        // Not in a rev project, that's ok
+      }
+
+      // Build first if including output
+      if (options.includeOutput) {
+        console.log(chalk.dim('Building documents...'));
+        await build(['pdf', 'docx']);
+      }
+
+      const zip = new AdmZip();
+      const projectName = config.title?.replace(/[^a-zA-Z0-9]/g, '-').toLowerCase() || 'project';
+      const outputPath = options.output || `${projectName}-export.zip`;
+
+      const exclude = ['node_modules', '.git', '.DS_Store', '*.zip'];
+
+      const shouldInclude = (name) => {
+        if (!options.includeOutput && (name.endsWith('.pdf') || name.endsWith('.docx'))) {
+          return false;
+        }
+        for (const pattern of exclude) {
+          if (name === pattern || name.includes(pattern.replace('*', ''))) return false;
+        }
+        return true;
+      };
+
+      const addDir = (dir, zipPath = '') => {
+        const entries = fs.readdirSync(dir, { withFileTypes: true });
+        for (const entry of entries) {
+          const fullPath = path.join(dir, entry.name);
+          const entryZipPath = path.join(zipPath, entry.name);
+
+          if (!shouldInclude(entry.name)) continue;
+
+          if (entry.isDirectory()) {
+            addDir(fullPath, entryZipPath);
+          } else {
+            zip.addLocalFile(fullPath, zipPath || undefined);
+          }
+        }
+      };
+
+      const entries = fs.readdirSync('.', { withFileTypes: true });
+      for (const entry of entries) {
+        if (!shouldInclude(entry.name)) continue;
+
+        if (entry.isDirectory()) {
+          addDir(entry.name, entry.name);
+        } else if (entry.isFile()) {
+          zip.addLocalFile(entry.name);
+        }
+      }
+
+      zip.writeZip(outputPath);
+      console.log(fmt.status('success', `Exported: ${outputPath}`));
+    });
+
+  // ==========================================================================
+  // PREVIEW command - Build and open document
+  // ==========================================================================
+
+  program
+    .command('preview')
+    .description('Build and open document in default app')
+    .argument('[format]', 'Format to preview: pdf, docx', 'pdf')
+    .action(async (format) => {
+      const { exec } = await import('child_process');
+      const { build } = await import('../build.js');
+
+      let config = {};
+      try {
+        config = loadBuildConfig() || {};
+      } catch (err) {
+        console.error(chalk.red('Not in a rev project directory (no rev.yaml found)'));
+        process.exit(1);
+      }
+
+      console.log(chalk.dim(`Building ${format}...`));
+      const results = await build([format]);
+
+      const result = results.find(r => r.format === format);
+      if (!result?.success) {
+        console.error(chalk.red(`Build failed: ${result?.error || 'Unknown error'}`));
+        process.exit(1);
+      }
+
+      const outputFile = result.output;
+      if (!fs.existsSync(outputFile)) {
+        console.error(chalk.red(`Output file not found: ${outputFile}`));
+        process.exit(1);
+      }
+
+      // Open with system default
+      const openCmd = process.platform === 'darwin' ? 'open' :
+                      process.platform === 'win32' ? 'start' : 'xdg-open';
+
+      exec(`${openCmd} "${outputFile}"`, (err) => {
+        if (err) {
+          console.error(chalk.red(`Could not open file: ${err.message}`));
+        } else {
+          console.log(fmt.status('success', `Opened ${outputFile}`));
+        }
+      });
+    });
+
+  // ==========================================================================
+  // WATCH command - Auto-rebuild on changes
+  // ==========================================================================
+
+  program
+    .command('watch')
+    .description('Watch files and auto-rebuild on changes')
+    .argument('[format]', 'Format to build: pdf, docx, all', 'pdf')
+    .option('--no-open', 'Do not open after first build')
+    .action(async (format, options) => {
+      const { exec } = await import('child_process');
+      const { build } = await import('../build.js');
+
+      let config = {};
+      try {
+        config = loadBuildConfig() || {};
+      } catch (err) {
+        console.error(chalk.red('Not in a rev project directory (no rev.yaml found)'));
+        process.exit(1);
+      }
+      let sections = config.sections || [];
+
+      if (sections.length === 0) {
+        sections = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f)
+        );
+      }
+
+      const filesToWatch = [
+        ...sections,
+        'rev.yaml',
+        config.bibliography || 'references.bib'
+      ].filter(f => fs.existsSync(f));
+
+      console.log(fmt.header('Watch Mode'));
+      console.log(chalk.dim(`Watching: ${filesToWatch.join(', ')}`));
+      console.log(chalk.dim('Press Ctrl+C to stop\n'));
+
+      let building = false;
+      let pendingBuild = false;
+
+      const doBuild = async () => {
+        if (building) {
+          pendingBuild = true;
+          return;
+        }
+
+        building = true;
+        console.log(chalk.dim(`\n[${new Date().toLocaleTimeString()}] Rebuilding...`));
+
+        try {
+          const formats = format === 'all' ? ['pdf', 'docx'] : [format];
+          const results = await build(formats);
+
+          for (const r of results) {
+            if (r.success) {
+              console.log(chalk.green(`  ✓ ${r.format}: ${r.output}`));
+            } else {
+              console.log(chalk.red(`  ✗ ${r.format}: ${r.error}`));
+            }
+          }
+        } catch (err) {
+          console.error(chalk.red(`  Build error: ${err.message}`));
+        }
+
+        building = false;
+        if (pendingBuild) {
+          pendingBuild = false;
+          doBuild();
+        }
+      };
+
+      // Initial build
+      await doBuild();
+
+      // Open after first build
+      if (options.open) {
+        const outputFile = format === 'docx' ?
+          (config.title?.replace(/[^a-zA-Z0-9]/g, '-').toLowerCase() || 'paper') + '.docx' :
+          (config.title?.replace(/[^a-zA-Z0-9]/g, '-').toLowerCase() || 'paper') + '.pdf';
+
+        if (fs.existsSync(outputFile)) {
+          const openCmd = process.platform === 'darwin' ? 'open' :
+                          process.platform === 'win32' ? 'start' : 'xdg-open';
+          exec(`${openCmd} "${outputFile}"`);
+        }
+      }
+
+      // Watch files
+      for (const file of filesToWatch) {
+        fs.watch(file, { persistent: true }, (eventType) => {
+          if (eventType === 'change') {
+            doBuild();
+          }
+        });
+      }
+    });
+
+  // ==========================================================================
+  // LINT command - Check for common issues
+  // ==========================================================================
+
+  program
+    .command('lint')
+    .description('Check for common issues in the project')
+    .option('--fix', 'Auto-fix issues where possible')
+    .action(async (options) => {
+      let config = {};
+      try {
+        config = loadBuildConfig() || {};
+      } catch {
+        // Not in a rev project, that's ok
+      }
+      let sections = config.sections || [];
+
+      if (sections.length === 0) {
+        sections = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f)
+        );
+      }
+
+      const issues = [];
+      const warnings = [];
+
+      // Collect all content
+      let allText = '';
+      for (const section of sections) {
+        if (fs.existsSync(section)) {
+          allText += fs.readFileSync(section, 'utf-8') + '\n';
+        }
+      }
+
+      // Check 1: Broken cross-references
+      const figAnchors = new Set();
+      const tblAnchors = new Set();
+      const eqAnchors = new Set();
+
+      const anchorPattern = /\{#(fig|tbl|eq):([^}]+)\}/g;
+      let match;
+      while ((match = anchorPattern.exec(allText)) !== null) {
+        if (match[1] === 'fig') figAnchors.add(match[2]);
+        else if (match[1] === 'tbl') tblAnchors.add(match[2]);
+        else if (match[1] === 'eq') eqAnchors.add(match[2]);
+      }
+
+      const refPattern = /@(fig|tbl|eq):([a-zA-Z0-9_-]+)/g;
+      while ((match = refPattern.exec(allText)) !== null) {
+        const type = match[1];
+        const label = match[2];
+        const anchors = type === 'fig' ? figAnchors : type === 'tbl' ? tblAnchors : eqAnchors;
+
+        if (!anchors.has(label)) {
+          issues.push({
+            type: 'error',
+            message: `Broken reference: @${type}:${label}`,
+            fix: null
+          });
+        }
+      }
+
+      // Check 2: Orphaned figures
+      for (const label of figAnchors) {
+        if (!allText.includes(`@fig:${label}`)) {
+          warnings.push({
+            type: 'warning',
+            message: `Unreferenced figure: {#fig:${label}}`,
+          });
+        }
+      }
+
+      // Check 3: Missing citations
+      const bibPath = config.bibliography || 'references.bib';
+      if (fs.existsSync(bibPath)) {
+        const bibContent = fs.readFileSync(bibPath, 'utf-8');
+        const bibKeys = new Set();
+        const bibPattern = /@\w+\s*\{\s*([^,]+)/g;
+        while ((match = bibPattern.exec(bibContent)) !== null) {
+          bibKeys.add(match[1].trim());
+        }
+
+        const citePattern = /@([a-zA-Z][a-zA-Z0-9_-]*)(?![:\w])/g;
+        while ((match = citePattern.exec(allText)) !== null) {
+          const key = match[1];
+          if (!bibKeys.has(key) && !['fig', 'tbl', 'eq'].includes(key)) {
+            issues.push({
+              type: 'error',
+              message: `Missing citation: @${key}`,
+            });
+          }
+        }
+      }
+
+      // Check 4: Unresolved comments
+      const comments = getComments(allText);
+      const pending = comments.filter(c => !c.resolved);
+      if (pending.length > 0) {
+        warnings.push({
+          type: 'warning',
+          message: `${pending.length} unresolved comment${pending.length === 1 ? '' : 's'}`,
+        });
+      }
+
+      // Check 5: Empty sections
+      for (const section of sections) {
+        if (fs.existsSync(section)) {
+          const content = fs.readFileSync(section, 'utf-8').trim();
+          if (content.length < 50) {
+            warnings.push({
+              type: 'warning',
+              message: `Section appears empty: ${section}`,
+            });
+          }
+        }
+      }
+
+      // Output results
+      console.log(fmt.header('Lint Results'));
+      console.log();
+
+      if (issues.length === 0 && warnings.length === 0) {
+        console.log(chalk.green('✓ No issues found'));
+        return;
+      }
+
+      for (const issue of issues) {
+        console.log(chalk.red(`  ✗ ${issue.message}`));
+      }
+
+      for (const warning of warnings) {
+        console.log(chalk.yellow(`  ⚠ ${warning.message}`));
+      }
+
+      console.log();
+      console.log(chalk.dim(`${issues.length} error${issues.length === 1 ? '' : 's'}, ${warnings.length} warning${warnings.length === 1 ? '' : 's'}`));
+
+      if (issues.length > 0) {
+        process.exit(1);
+      }
+    });
+
+  // ==========================================================================
+  // GRAMMAR command - Check grammar and style
+  // ==========================================================================
+
+  program
+    .command('grammar')
+    .description('Check grammar and style issues')
+    .argument('[files...]', 'Markdown files to check')
+    .option('--learn <word>', 'Add word to custom dictionary')
+    .option('--forget <word>', 'Remove word from custom dictionary')
+    .option('--list', 'List custom dictionary words')
+    .option('--rules', 'List available grammar rules')
+    .option('--no-scientific', 'Disable scientific writing rules')
+    .option('-s, --severity <level>', 'Minimum severity: error, warning, info', 'info')
+    .action(async (files, options) => {
+      const {
+        checkGrammar,
+        getGrammarSummary,
+        loadDictionary,
+        addToDictionary,
+        removeFromDictionary,
+        listRules,
+      } = await import('../grammar.js');
+
+      // Handle dictionary management
+      if (options.learn) {
+        const added = addToDictionary(options.learn);
+        if (added) {
+          console.log(fmt.status('success', `Added "${options.learn}" to dictionary`));
+        } else {
+          console.log(chalk.dim(`"${options.learn}" already in dictionary`));
+        }
+        return;
+      }
+
+      if (options.forget) {
+        const removed = removeFromDictionary(options.forget);
+        if (removed) {
+          console.log(fmt.status('success', `Removed "${options.forget}" from dictionary`));
+        } else {
+          console.log(chalk.yellow(`"${options.forget}" not in dictionary`));
+        }
+        return;
+      }
+
+      if (options.list) {
+        const words = loadDictionary();
+        console.log(fmt.header('Custom Dictionary'));
+        console.log();
+        if (words.size === 0) {
+          console.log(chalk.dim('  No custom words defined'));
+          console.log(chalk.dim('  Use --learn <word> to add words'));
+        } else {
+          const sorted = [...words].sort();
+          for (const word of sorted) {
+            console.log(`  ${word}`);
+          }
+          console.log();
+          console.log(chalk.dim(`${words.size} word(s)`));
+        }
+        return;
+      }
+
+      if (options.rules) {
+        const rules = listRules(options.scientific);
+        console.log(fmt.header('Grammar Rules'));
+        console.log();
+        for (const rule of rules) {
+          const icon = rule.severity === 'error' ? chalk.red('●') :
+                       rule.severity === 'warning' ? chalk.yellow('●') :
+                       chalk.blue('●');
+          console.log(`  ${icon} ${chalk.bold(rule.id)}`);
+          console.log(chalk.dim(`     ${rule.message}`));
+        }
+        return;
+      }
+
+      // Get files to check
+      let mdFiles = files;
+      if (!mdFiles || mdFiles.length === 0) {
+        let config = {};
+        try {
+          config = loadBuildConfig() || {};
+        } catch {
+          // Not in a rev project
+        }
+        mdFiles = config.sections || [];
+
+        if (mdFiles.length === 0) {
+          mdFiles = fs.readdirSync('.').filter(f =>
+            f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f)
+          );
+        }
+      }
+
+      if (mdFiles.length === 0) {
+        console.error(chalk.red('No markdown files found'));
+        process.exit(1);
+      }
+
+      console.log(fmt.header('Grammar Check'));
+      console.log();
+
+      const severityLevels = { error: 3, warning: 2, info: 1 };
+      const minSeverity = severityLevels[options.severity] || 1;
+
+      let allIssues = [];
+
+      for (const file of mdFiles) {
+        if (!fs.existsSync(file)) continue;
+
+        const text = fs.readFileSync(file, 'utf-8');
+        const issues = checkGrammar(text, { scientific: options.scientific });
+
+        // Filter by severity
+        const filtered = issues.filter(i => severityLevels[i.severity] >= minSeverity);
+
+        if (filtered.length > 0) {
+          console.log(chalk.cyan.bold(file));
+
+          for (const issue of filtered) {
+            const icon = issue.severity === 'error' ? chalk.red('●') :
+                         issue.severity === 'warning' ? chalk.yellow('●') :
+                         chalk.blue('●');
+
+            console.log(`  ${chalk.dim(`L${issue.line}:`)} ${icon} ${issue.message}`);
+            console.log(chalk.dim(`      "${issue.match}" in: ${issue.context.slice(0, 60)}...`));
+          }
+          console.log();
+          allIssues.push(...filtered.map(i => ({ ...i, file })));
+        }
+      }
+
+      const summary = getGrammarSummary(allIssues);
+
+      if (summary.total === 0) {
+        console.log(chalk.green('✓ No issues found'));
+      } else {
+        console.log(chalk.dim(`Found ${summary.total} issue(s): ${summary.errors} errors, ${summary.warnings} warnings, ${summary.info} info`));
+        console.log();
+        console.log(chalk.dim('Tip: Use --learn <word> to add words to dictionary'));
+      }
+    });
+
+  // ==========================================================================
+  // ANNOTATE command - Add comments to Word document
+  // ==========================================================================
+
+  program
+    .command('annotate')
+    .description('Add comment to Word document')
+    .argument('<docx>', 'Word document')
+    .option('-m, --message <text>', 'Comment text')
+    .option('-s, --search <text>', 'Text to attach comment to')
+    .option('-a, --author <name>', 'Comment author')
+    .action(async (docxPath, options) => {
+      if (!fs.existsSync(docxPath)) {
+        console.error(chalk.red(`File not found: ${docxPath}`));
+        process.exit(1);
+      }
+
+      if (!options.message) {
+        console.error(chalk.red('Comment message required (-m)'));
+        process.exit(1);
+      }
+
+      const { default: AdmZip } = await import('adm-zip');
+      const zip = new AdmZip(docxPath);
+
+      // Read document.xml
+      const docEntry = zip.getEntry('word/document.xml');
+      if (!docEntry) {
+        console.error(chalk.red('Invalid Word document'));
+        process.exit(1);
+      }
+
+      let docXml = zip.readAsText(docEntry);
+
+      // Read or create comments.xml
+      let commentsEntry = zip.getEntry('word/comments.xml');
+      let commentsXml;
+      let nextCommentId = 1;
+
+      if (commentsEntry) {
+        commentsXml = zip.readAsText(commentsEntry);
+        const idMatches = commentsXml.match(/w:id="(\d+)"/g) || [];
+        for (const m of idMatches) {
+          const id = parseInt(m.match(/\d+/)[0]);
+          if (id >= nextCommentId) nextCommentId = id + 1;
+        }
+      } else {
+        commentsXml = `<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<w:comments xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main">
+</w:comments>`;
+      }
+
+      const author = options.author || getUserName() || 'Claude';
+      const date = new Date().toISOString();
+      const commentId = nextCommentId;
+
+      // Add comment to comments.xml
+      const newComment = `<w:comment w:id="${commentId}" w:author="${author}" w:date="${date}">
+  <w:p><w:r><w:t>${options.message}</w:t></w:r></w:p>
+</w:comment>`;
+
+      commentsXml = commentsXml.replace('</w:comments>', `${newComment}\n</w:comments>`);
+
+      // Find text and add comment markers
+      if (options.search) {
+        const searchText = options.search;
+        const textPattern = new RegExp(`(<w:t[^>]*>)([^<]*${searchText.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}[^<]*)(<\/w:t>)`, 'i');
+
+        if (textPattern.test(docXml)) {
+          docXml = docXml.replace(textPattern, (match, start, text, end) => {
+            return `<w:commentRangeStart w:id="${commentId}"/>${start}${text}${end}<w:commentRangeEnd w:id="${commentId}"/><w:r><w:commentReference w:id="${commentId}"/></w:r>`;
+          });
+        } else {
+          console.log(chalk.yellow(`Text "${searchText}" not found in document. Comment added without anchor.`));
+        }
+      }
+
+      // Update zip
+      zip.updateFile('word/document.xml', Buffer.from(docXml));
+
+      if (commentsEntry) {
+        zip.updateFile('word/comments.xml', Buffer.from(commentsXml));
+      } else {
+        zip.addFile('word/comments.xml', Buffer.from(commentsXml));
+
+        // Update [Content_Types].xml
+        const ctEntry = zip.getEntry('[Content_Types].xml');
+        if (ctEntry) {
+          let ctXml = zip.readAsText(ctEntry);
+          if (!ctXml.includes('comments.xml')) {
+            ctXml = ctXml.replace('</Types>',
+              '<Override PartName="/word/comments.xml" ContentType="application/vnd.openxmlformats-officedocument.wordprocessingml.comments+xml"/>\n</Types>');
+            zip.updateFile('[Content_Types].xml', Buffer.from(ctXml));
+          }
+        }
+
+        // Update document.xml.rels
+        const relsEntry = zip.getEntry('word/_rels/document.xml.rels');
+        if (relsEntry) {
+          let relsXml = zip.readAsText(relsEntry);
+          if (!relsXml.includes('comments.xml')) {
+            const newRelId = `rId${Date.now()}`;
+            relsXml = relsXml.replace('</Relationships>',
+              `<Relationship Id="${newRelId}" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/comments" Target="comments.xml"/>\n</Relationships>`);
+            zip.updateFile('word/_rels/document.xml.rels', Buffer.from(relsXml));
+          }
+        }
+      }
+
+      // Write back
+      zip.writeZip(docxPath);
+      console.log(fmt.status('success', `Added comment to ${docxPath}`));
+    });
+
+  // ==========================================================================
+  // APPLY command - Apply MD annotations as Word track changes
+  // ==========================================================================
+
+  program
+    .command('apply')
+    .description('Apply markdown annotations to Word document as track changes')
+    .argument('<md>', 'Markdown file with annotations')
+    .argument('<docx>', 'Output Word document')
+    .option('-a, --author <name>', 'Author name for track changes')
+    .action(async (mdPath, docxPath, options) => {
+      if (!fs.existsSync(mdPath)) {
+        console.error(chalk.red(`File not found: ${mdPath}`));
+        process.exit(1);
+      }
+
+      const mdContent = fs.readFileSync(mdPath, 'utf-8');
+      const annotations = parseAnnotations(mdContent);
+
+      if (annotations.length === 0) {
+        console.log(chalk.yellow('No annotations found in markdown file'));
+      }
+
+      const author = options.author || getUserName() || 'Author';
+
+      // Build document with track changes
+      const { buildWithTrackChanges } = await import('../trackchanges.js');
+
+      try {
+        const result = await buildWithTrackChanges(mdPath, docxPath, { author });
+
+        if (result.success) {
+          console.log(fmt.status('success', result.message));
+          console.log(chalk.dim(`  ${annotations.length} annotations applied as track changes`));
+        } else {
+          console.error(chalk.red(result.message));
+          process.exit(1);
+        }
+      } catch (err) {
+        console.error(chalk.red(`Error: ${err.message}`));
+        process.exit(1);
+      }
+    });
+
+  // ==========================================================================
+  // COMMENT command - Interactive comment addition to DOCX
+  // ==========================================================================
+
+  program
+    .command('comment')
+    .description('Add comments to Word document interactively')
+    .argument('<docx>', 'Word document')
+    .option('-a, --author <name>', 'Comment author')
+    .action(async (docxPath, options) => {
+      if (!fs.existsSync(docxPath)) {
+        console.error(chalk.red(`File not found: ${docxPath}`));
+        process.exit(1);
+      }
+
+      const { default: AdmZip } = await import('adm-zip');
+      const rl = (await import('readline')).createInterface({
+        input: process.stdin,
+        output: process.stdout,
+      });
+
+      const ask = (prompt) => new Promise((resolve) => rl.question(prompt, resolve));
+
+      const author = options.author || getUserName() || 'Reviewer';
+
+      console.log(fmt.header('Interactive Comment Mode'));
+      console.log(chalk.dim(`  Document: ${docxPath}`));
+      console.log(chalk.dim(`  Author: ${author}`));
+      console.log(chalk.dim('  Type your comment, then the text to attach it to.'));
+      console.log(chalk.dim('  Enter empty comment to quit.\n'));
+
+      let commentsAdded = 0;
+
+      while (true) {
+        const message = await ask(chalk.cyan('Comment: '));
+
+        if (!message.trim()) {
+          break;
+        }
+
+        const searchText = await ask(chalk.cyan('Attach to text: '));
+
+        // Load document fresh each time
+        const zip = new AdmZip(docxPath);
+        const docEntry = zip.getEntry('word/document.xml');
+
+        if (!docEntry) {
+          console.error(chalk.red('Invalid Word document'));
+          rl.close();
+          process.exit(1);
+        }
+
+        let docXml = zip.readAsText(docEntry);
+
+        // Read or create comments.xml
+        let commentsEntry = zip.getEntry('word/comments.xml');
+        let commentsXml;
+        let nextCommentId = 1;
+
+        if (commentsEntry) {
+          commentsXml = zip.readAsText(commentsEntry);
+          const idMatches = commentsXml.match(/w:id="(\d+)"/g) || [];
+          for (const m of idMatches) {
+            const id = parseInt(m.match(/\d+/)[0]);
+            if (id >= nextCommentId) nextCommentId = id + 1;
+          }
+        } else {
+          commentsXml = `<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<w:comments xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main">
+</w:comments>`;
+        }
+
+        const date = new Date().toISOString();
+        const commentId = nextCommentId;
+
+        // Add comment to comments.xml
+        const newComment = `<w:comment w:id="${commentId}" w:author="${author}" w:date="${date}">
+  <w:p><w:r><w:t>${message}</w:t></w:r></w:p>
+</w:comment>`;
+
+        commentsXml = commentsXml.replace('</w:comments>', `${newComment}\n</w:comments>`);
+
+        // Find text and add comment markers
+        if (searchText.trim()) {
+          const escapedSearch = searchText.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+          const textPattern = new RegExp(`(<w:t[^>]*>)([^<]*${escapedSearch}[^<]*)(<\/w:t>)`, 'i');
+
+          if (textPattern.test(docXml)) {
+            docXml = docXml.replace(textPattern, (match, start, text, end) => {
+              return `<w:commentRangeStart w:id="${commentId}"/>${start}${text}${end}<w:commentRangeEnd w:id="${commentId}"/><w:r><w:commentReference w:id="${commentId}"/></w:r>`;
+            });
+            console.log(chalk.green(`  ✓ Comment added at "${searchText}"`));
+          } else {
+            console.log(chalk.yellow(`  Text not found. Comment added without anchor.`));
+          }
+        } else {
+          console.log(chalk.dim(`  Comment added without anchor.`));
+        }
+
+        // Update zip
+        zip.updateFile('word/document.xml', Buffer.from(docXml));
+
+        if (commentsEntry) {
+          zip.updateFile('word/comments.xml', Buffer.from(commentsXml));
+        } else {
+          zip.addFile('word/comments.xml', Buffer.from(commentsXml));
+
+          // Update [Content_Types].xml
+          const ctEntry = zip.getEntry('[Content_Types].xml');
+          if (ctEntry) {
+            let ctXml = zip.readAsText(ctEntry);
+            if (!ctXml.includes('comments.xml')) {
+              ctXml = ctXml.replace('</Types>',
+                '<Override PartName="/word/comments.xml" ContentType="application/vnd.openxmlformats-officedocument.wordprocessingml.comments+xml"/>\n</Types>');
+              zip.updateFile('[Content_Types].xml', Buffer.from(ctXml));
+            }
+          }
+
+          // Update document.xml.rels
+          const relsEntry = zip.getEntry('word/_rels/document.xml.rels');
+          if (relsEntry) {
+            let relsXml = zip.readAsText(relsEntry);
+            if (!relsXml.includes('comments.xml')) {
+              const newRelId = `rId${Date.now()}`;
+              relsXml = relsXml.replace('</Relationships>',
+                `<Relationship Id="${newRelId}" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/comments" Target="comments.xml"/>\n</Relationships>`);
+              zip.updateFile('word/_rels/document.xml.rels', Buffer.from(relsXml));
+            }
+          }
+        }
+
+        zip.writeZip(docxPath);
+        commentsAdded++;
+        console.log();
+      }
+
+      rl.close();
+      console.log();
+
+      if (commentsAdded > 0) {
+        console.log(fmt.status('success', `Added ${commentsAdded} comment(s) to ${docxPath}`));
+      } else {
+        console.log(chalk.dim('No comments added.'));
+      }
+    });
+
+  // ==========================================================================
+  // CLEAN command - Remove generated files
+  // ==========================================================================
+
+  program
+    .command('clean')
+    .description('Remove generated files (paper.md, PDFs, DOCXs)')
+    .option('-n, --dry-run', 'Show what would be deleted without deleting')
+    .option('--all', 'Also remove backup and export zips')
+    .action((options) => {
+      let config = {};
+      try {
+        config = loadBuildConfig() || {};
+      } catch {
+        // Not in a rev project, that's ok
+      }
+
+      const projectName = config.title?.toLowerCase().replace(/\s+/g, '-') || 'paper';
+
+      // Files to clean
+      const patterns = [
+        'paper.md',
+        '*.pdf',
+        `${projectName}.docx`,
+        `${projectName}.pdf`,
+        `${projectName}.tex`,
+        '.paper-*.md', // Temp build files
+      ];
+
+      if (options.all) {
+        patterns.push('*.zip', 'backup-*.zip', '*-export.zip');
+      }
+
+      const toDelete = [];
+
+      for (const pattern of patterns) {
+        if (pattern.includes('*')) {
+          const regex = new RegExp('^' + pattern.replace(/\./g, '\\.').replace(/\*/g, '.*') + '$');
+          const files = fs.readdirSync('.').filter(f => regex.test(f));
+          toDelete.push(...files);
+        } else if (fs.existsSync(pattern)) {
+          toDelete.push(pattern);
+        }
+      }
+
+      if (toDelete.length === 0) {
+        console.log(chalk.dim('No generated files to clean.'));
+        return;
+      }
+
+      console.log(fmt.header('Clean'));
+      console.log();
+
+      for (const file of toDelete) {
+        if (options.dryRun) {
+          console.log(chalk.dim(`  Would delete: ${file}`));
+        } else {
+          fs.unlinkSync(file);
+          console.log(chalk.red(`  Deleted: ${file}`));
+        }
+      }
+
+      console.log();
+      if (options.dryRun) {
+        console.log(chalk.dim(`Would delete ${toDelete.length} file(s). Run without --dry-run to delete.`));
+      } else {
+        console.log(fmt.status('success', `Cleaned ${toDelete.length} file(s)`));
+      }
+    });
+
+  // ==========================================================================
+  // CHECK command - Pre-submission check
+  // ==========================================================================
+
+  program
+    .command('check')
+    .description('Run all checks before submission (lint + grammar + citations)')
+    .option('--fix', 'Auto-fix issues where possible')
+    .option('-s, --severity <level>', 'Minimum grammar severity', 'warning')
+    .action(async (options) => {
+      const { validateCitations } = await import('../citations.js');
+      const { checkGrammar, getGrammarSummary } = await import('../grammar.js');
+
+      console.log(fmt.header('Pre-Submission Check'));
+      console.log();
+
+      let hasErrors = false;
+      let totalIssues = 0;
+
+      // 1. Run lint
+      console.log(chalk.cyan.bold('1. Linting...'));
+      let config = {};
+      try {
+        config = loadBuildConfig() || {};
+      } catch {
+        // Not in a rev project
+      }
+
+      let sections = config.sections || [];
+      if (sections.length === 0) {
+        sections = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f)
+        );
+      }
+
+      const lintIssues = [];
+      const lintWarnings = [];
+
+      for (const file of sections) {
+        if (!fs.existsSync(file)) continue;
+        const content = fs.readFileSync(file, 'utf-8');
+
+        // Check for broken cross-references
+        const refs = content.match(/@(fig|tbl|eq|sec):\w+/g) || [];
+        const anchors = content.match(/\{#(fig|tbl|eq|sec):[^}]+\}/g) || [];
+        const anchorLabels = anchors.map(a => a.match(/#([^}]+)/)[1]);
+
+        for (const ref of refs) {
+          const label = ref.slice(1);
+          if (!anchorLabels.includes(label)) {
+            lintIssues.push({ file, message: `Broken reference: ${ref}` });
+          }
+        }
+
+        // Check for unresolved comments
+        const unresolvedComments = (content.match(/\{>>[^<]*<<\}/g) || [])
+          .filter(c => !c.includes('[RESOLVED]'));
+        if (unresolvedComments.length > 0) {
+          lintWarnings.push({ file, message: `${unresolvedComments.length} unresolved comment(s)` });
+        }
+      }
+
+      if (lintIssues.length > 0) {
+        for (const issue of lintIssues) {
+          console.log(chalk.red(`   ✗ ${issue.file}: ${issue.message}`));
+        }
+        hasErrors = true;
+        totalIssues += lintIssues.length;
+      }
+      for (const warning of lintWarnings) {
+        console.log(chalk.yellow(`   ⚠ ${warning.file}: ${warning.message}`));
+        totalIssues++;
+      }
+      if (lintIssues.length === 0 && lintWarnings.length === 0) {
+        console.log(chalk.green('   ✓ No lint issues'));
+      }
+      console.log();
+
+      // 2. Run grammar check
+      console.log(chalk.cyan.bold('2. Grammar check...'));
+
+      const severityLevels = { error: 3, warning: 2, info: 1 };
+      const minSeverity = severityLevels[options.severity] || 2;
+      let grammarIssues = [];
+
+      for (const file of sections) {
+        if (!fs.existsSync(file)) continue;
+        const text = fs.readFileSync(file, 'utf-8');
+        const issues = checkGrammar(text, { scientific: true });
+        const filtered = issues.filter(i => severityLevels[i.severity] >= minSeverity);
+        grammarIssues.push(...filtered.map(i => ({ ...i, file })));
+      }
+
+      const grammarSummary = getGrammarSummary(grammarIssues);
+      if (grammarSummary.errors > 0) {
+        hasErrors = true;
+      }
+      totalIssues += grammarSummary.total;
+
+      if (grammarSummary.total > 0) {
+        console.log(chalk.yellow(`   ⚠ ${grammarSummary.total} grammar issue(s): ${grammarSummary.errors} errors, ${grammarSummary.warnings} warnings`));
+      } else {
+        console.log(chalk.green('   ✓ No grammar issues'));
+      }
+      console.log();
+
+      // 3. Run citation check
+      console.log(chalk.cyan.bold('3. Citation check...'));
+      const bibFile = config.bibliography || 'references.bib';
+      if (fs.existsSync(bibFile)) {
+        const allContent = sections
+          .filter(f => fs.existsSync(f))
+          .map(f => fs.readFileSync(f, 'utf-8'))
+          .join('\n');
+        const bibContent = fs.readFileSync(bibFile, 'utf-8');
+
+        const result = validateCitations(allContent, bibContent);
+
+        if (result.missing.length > 0) {
+          console.log(chalk.red(`   ✗ ${result.missing.length} missing citation(s): ${result.missing.slice(0, 3).join(', ')}${result.missing.length > 3 ? '...' : ''}`));
+          hasErrors = true;
+          totalIssues += result.missing.length;
+        }
+        if (result.unused.length > 0) {
+          console.log(chalk.yellow(`   ⚠ ${result.unused.length} unused citation(s)`));
+          totalIssues += result.unused.length;
+        }
+        if (result.missing.length === 0 && result.unused.length === 0) {
+          console.log(chalk.green('   ✓ All citations valid'));
+        }
+      } else {
+        console.log(chalk.dim('   - No bibliography file found'));
+      }
+      console.log();
+
+      // Summary
+      console.log(chalk.bold('Summary'));
+      if (hasErrors) {
+        console.log(chalk.red(`   ${totalIssues} issue(s) found. Please fix before submission.`));
+        process.exit(1);
+      } else if (totalIssues > 0) {
+        console.log(chalk.yellow(`   ${totalIssues} warning(s). Review before submission.`));
+      } else {
+        console.log(chalk.green('   ✓ All checks passed! Ready for submission.'));
+      }
+    });
+
+  // ==========================================================================
+  // OPEN command - Open project folder or file
+  // ==========================================================================
+
+  program
+    .command('open')
+    .description('Open project folder or file in default app')
+    .argument('[file]', 'File to open (default: project folder)')
+    .action(async (file) => {
+      const { exec } = await import('child_process');
+      const target = file || '.';
+
+      if (!fs.existsSync(target)) {
+        console.error(chalk.red(`File not found: ${target}`));
+        process.exit(1);
+      }
+
+      const platform = process.platform;
+      let command;
+
+      if (platform === 'darwin') {
+        command = `open "${target}"`;
+      } else if (platform === 'win32') {
+        command = `start "" "${target}"`;
+      } else {
+        command = `xdg-open "${target}"`;
+      }
+
+      exec(command, (err) => {
+        if (err) {
+          console.error(chalk.red(`Failed to open: ${err.message}`));
+          process.exit(1);
+        }
+        console.log(fmt.status('success', `Opened ${target}`));
+      });
+    });
+
+  // ==========================================================================
+  // INSTALL-CLI-SKILL command - Install Claude Code skill
+  // ==========================================================================
+
+  program
+    .command('install-cli-skill')
+    .description('Install docrev skill for Claude Code')
+    .action(() => {
+      const homedir = process.env.HOME || process.env.USERPROFILE;
+      const skillDir = path.join(homedir, '.claude', 'skills', 'docrev');
+      const sourceDir = path.join(import.meta.dirname, '..', '..', 'skill');
+
+      // Check if source skill files exist
+      const skillFile = path.join(sourceDir, 'SKILL.md');
+      if (!fs.existsSync(skillFile)) {
+        console.error(chalk.red('Skill files not found in package'));
+        process.exit(1);
+      }
+
+      // Create skill directory
+      fs.mkdirSync(skillDir, { recursive: true });
+
+      // Copy skill files
+      const files = ['SKILL.md', 'REFERENCE.md'];
+      for (const file of files) {
+        const src = path.join(sourceDir, file);
+        const dest = path.join(skillDir, file);
+        if (fs.existsSync(src)) {
+          fs.copyFileSync(src, dest);
+        }
+      }
+
+      console.log(fmt.status('success', 'Installed docrev skill for Claude Code'));
+      console.log(chalk.dim(`  Location: ${skillDir}`));
+      console.log(chalk.dim('  Restart Claude Code to activate'));
+    });
+
+  program
+    .command('uninstall-cli-skill')
+    .description('Remove docrev skill from Claude Code')
+    .action(() => {
+      const homedir = process.env.HOME || process.env.USERPROFILE;
+      const skillDir = path.join(homedir, '.claude', 'skills', 'docrev');
+
+      if (fs.existsSync(skillDir)) {
+        fs.rmSync(skillDir, { recursive: true });
+        console.log(fmt.status('success', 'Removed docrev skill from Claude Code'));
+      } else {
+        console.log(chalk.yellow('Skill not installed'));
+      }
+    });
+
+  // ==========================================================================
+  // SPELLING command - Spellcheck with global dictionary
+  // ==========================================================================
+
+  program
+    .command('spelling')
+    .description('Check spelling in markdown files')
+    .argument('[files...]', 'Files to check (default: section files)')
+    .option('--learn <word>', 'Add word to global dictionary')
+    .option('--learn-project <word>', 'Add word to project dictionary')
+    .option('--forget <word>', 'Remove word from global dictionary')
+    .option('--forget-project <word>', 'Remove word from project dictionary')
+    .option('--list', 'List global dictionary words')
+    .option('--list-project', 'List project dictionary words')
+    .option('--list-all', 'List all custom words (global + project)')
+    .option('--british', 'Use British English dictionary')
+    .option('--add-names', 'Add detected names to global dictionary')
+    .action(async (files, options) => {
+      const spelling = await import('../spelling.js');
+
+      // Handle dictionary management
+      if (options.learn) {
+        const added = spelling.addWord(options.learn, true);
+        if (added) {
+          console.log(fmt.status('success', `Added "${options.learn}" to global dictionary`));
+        } else {
+          console.log(chalk.yellow(`"${options.learn}" already in dictionary`));
+        }
+        return;
+      }
+
+      if (options.learnProject) {
+        const added = spelling.addWord(options.learnProject, false);
+        if (added) {
+          console.log(fmt.status('success', `Added "${options.learnProject}" to project dictionary`));
+        } else {
+          console.log(chalk.yellow(`"${options.learnProject}" already in dictionary`));
+        }
+        return;
+      }
+
+      if (options.forget) {
+        const removed = spelling.removeWord(options.forget, true);
+        if (removed) {
+          console.log(fmt.status('success', `Removed "${options.forget}" from global dictionary`));
+        } else {
+          console.log(chalk.yellow(`"${options.forget}" not in dictionary`));
+        }
+        return;
+      }
+
+      if (options.forgetProject) {
+        const removed = spelling.removeWord(options.forgetProject, false);
+        if (removed) {
+          console.log(fmt.status('success', `Removed "${options.forgetProject}" from project dictionary`));
+        } else {
+          console.log(chalk.yellow(`"${options.forgetProject}" not in dictionary`));
+        }
+        return;
+      }
+
+      if (options.list) {
+        const words = spelling.listWords(true);
+        console.log(fmt.header('Global Dictionary'));
+        if (words.length === 0) {
+          console.log(chalk.dim('  No custom words'));
+          console.log(chalk.dim('  Use --learn <word> to add words'));
+        } else {
+          for (const word of words) {
+            console.log(`  ${word}`);
+          }
+          console.log(chalk.dim(`\n${words.length} word(s)`));
+        }
+        return;
+      }
+
+      if (options.listProject) {
+        const words = spelling.listWords(false);
+        console.log(fmt.header('Project Dictionary'));
+        if (words.length === 0) {
+          console.log(chalk.dim('  No custom words'));
+          console.log(chalk.dim('  Use --learn-project <word> to add words'));
+        } else {
+          for (const word of words) {
+            console.log(`  ${word}`);
+          }
+          console.log(chalk.dim(`\n${words.length} word(s)`));
+        }
+        return;
+      }
+
+      if (options.listAll) {
+        const globalWords = spelling.listWords(true);
+        const projectWords = spelling.listWords(false);
+
+        console.log(fmt.header('Global Dictionary'));
+        if (globalWords.length === 0) {
+          console.log(chalk.dim('  No custom words'));
+        } else {
+          for (const word of globalWords) {
+            console.log(`  ${word}`);
+          }
+        }
+
+        console.log(fmt.header('Project Dictionary'));
+        if (projectWords.length === 0) {
+          console.log(chalk.dim('  No custom words'));
+        } else {
+          for (const word of projectWords) {
+            console.log(`  ${word}`);
+          }
+        }
+
+        console.log(chalk.dim(`\nTotal: ${globalWords.length + projectWords.length} word(s)`));
+        return;
+      }
+
+      // Check spelling in files
+      let filesToCheck = files;
+
+      if (filesToCheck.length === 0) {
+        if (fs.existsSync('rev.yaml')) {
+          const { getSectionFiles } = await import('../sections.js');
+          filesToCheck = getSectionFiles('.');
+        } else {
+          filesToCheck = fs.readdirSync('.')
+            .filter(f => f.endsWith('.md') && !f.startsWith('.'));
+        }
+      }
+
+      if (filesToCheck.length === 0) {
+        console.log(chalk.yellow('No markdown files found'));
+        return;
+      }
+
+      const lang = options.british ? 'en-gb' : 'en';
+      console.log(fmt.header(`Spelling Check (${options.british ? 'British' : 'US'} English)`));
+      let totalMisspelled = 0;
+      const allNames = new Set();
+
+      for (const file of filesToCheck) {
+        if (!fs.existsSync(file)) {
+          console.log(chalk.yellow(`File not found: ${file}`));
+          continue;
+        }
+
+        const result = await spelling.checkFile(file, { projectDir: '.', lang });
+        const { misspelled, possibleNames } = result;
+
+        // Collect names
+        for (const n of possibleNames) {
+          allNames.add(n.word);
+        }
+
+        if (misspelled.length > 0) {
+          console.log(chalk.cyan(`\n${file}:`));
+          for (const issue of misspelled) {
+            const suggestions = issue.suggestions.length > 0
+              ? chalk.dim(` → ${issue.suggestions.join(', ')}`)
+              : '';
+            console.log(`  ${chalk.yellow(issue.word)} ${chalk.dim(`(line ${issue.line})`)}${suggestions}`);
+          }
+          totalMisspelled += misspelled.length;
+        }
+      }
+
+      // Show possible names separately
+      if (allNames.size > 0) {
+        const nameList = [...allNames].sort();
+
+        if (options.addNames) {
+          console.log(fmt.header('Adding Names to Dictionary'));
+          for (const name of nameList) {
+            spelling.addWord(name, true);
+            console.log(chalk.green(`  ✓ ${name}`));
+          }
+          console.log(chalk.dim(`\nAdded ${nameList.length} name(s) to global dictionary`));
+        } else {
+          console.log(fmt.header('Possible Names'));
+          console.log(chalk.dim(`  ${nameList.join(', ')}`));
+          console.log(chalk.dim(`\n  Run with --add-names to add all to dictionary`));
+        }
+      }
+
+      if (totalMisspelled === 0 && allNames.size === 0) {
+        console.log(fmt.status('success', 'No spelling errors found'));
+      } else {
+        if (totalMisspelled > 0) {
+          console.log(chalk.yellow(`\n${totalMisspelled} spelling error(s)`));
+        }
+        if (allNames.size > 0) {
+          console.log(chalk.blue(`${allNames.size} possible name(s)`));
+        }
+        console.log(chalk.dim('Use --learn <word> to add words to dictionary'));
+      }
+    });
+
+  // ==========================================================================
+  // UPGRADE command - Self-update via npm
+  // ==========================================================================
+
+  program
+    .command('upgrade')
+    .description('Check for updates and upgrade docrev')
+    .option('--check', 'Only check for updates, do not install')
+    .action(async (options) => {
+      const { execSync, spawn } = await import('child_process');
+
+      console.log(chalk.cyan('Checking for updates...'));
+
+      try {
+        // Get current version
+        const currentVersion = pkg?.version || 'unknown';
+
+        // Get latest version from npm
+        let latestVersion;
+        try {
+          latestVersion = execSync('npm view docrev version', { encoding: 'utf-8' }).trim();
+        } catch {
+          console.error(chalk.red('Failed to check npm registry'));
+          console.error(chalk.dim('Check your internet connection'));
+          process.exit(1);
+        }
+
+        if (currentVersion === latestVersion) {
+          console.log(fmt.status('success', `Already on latest version (${currentVersion})`));
+          return;
+        }
+
+        console.log(`  Current: ${chalk.yellow(currentVersion)}`);
+        console.log(`  Latest:  ${chalk.green(latestVersion)}`);
+        console.log();
+
+        if (options.check) {
+          console.log(chalk.cyan('Run "rev upgrade" to install the update'));
+          return;
+        }
+
+        console.log(chalk.cyan('Upgrading...'));
+
+        // Run npm update
+        const child = spawn('npm', ['install', '-g', 'docrev@latest'], {
+          stdio: 'inherit',
+          shell: true,
+        });
+
+        child.on('close', (code) => {
+          if (code === 0) {
+            console.log();
+            console.log(fmt.status('success', `Upgraded to ${latestVersion}`));
+          } else {
+            console.error(chalk.red('Upgrade failed'));
+            console.error(chalk.dim('Try running: npm install -g docrev@latest'));
+            process.exit(1);
+          }
+        });
+
+        child.on('error', (err) => {
+          console.error(chalk.red(`Upgrade failed: ${err.message}`));
+          console.error(chalk.dim('Try running: npm install -g docrev@latest'));
+          process.exit(1);
+        });
+      } catch (err) {
+        console.error(chalk.red(`Error: ${err.message}`));
+        process.exit(1);
+      }
+    });
+
+  // ==========================================================================
+  // BATCH command - Run operations on multiple documents
+  // ==========================================================================
+
+  program
+    .command('batch')
+    .description('Run operations on multiple documents')
+    .argument('<command>', 'Command to run (status, strip, resolve)')
+    .argument('[pattern]', 'File pattern (default: *.md)')
+    .option('--parallel', 'Run operations in parallel')
+    .option('--dry-run', 'Preview files without running')
+    .option('-a, --all', 'Include all .md files (not just sections)')
+    .action(async (command, pattern, options) => {
+      const validCommands = ['status', 'strip', 'resolve', 'comments'];
+
+      if (!validCommands.includes(command)) {
+        console.error(fmt.status('error', `Unknown batch command: ${command}`));
+        console.error(chalk.dim(`Available: ${validCommands.join(', ')}`));
+        process.exit(1);
+      }
+
+      // Find files
+      let files = [];
+      if (pattern) {
+        if (pattern.includes('*')) {
+          files = fs.readdirSync('.').filter(f =>
+            f.endsWith('.md') && !['README.md', 'CLAUDE.md', 'paper.md'].includes(f)
+          );
+        } else {
+          files = [pattern];
+        }
+      } else {
+        files = fs.readdirSync('.').filter(f =>
+          f.endsWith('.md') &&
+          (options.all || !['README.md', 'CLAUDE.md', 'paper.md'].includes(f))
+        );
+      }
+
+      if (files.length === 0) {
+        console.error(fmt.status('error', 'No files found'));
+        process.exit(1);
+      }
+
+      console.log(fmt.header(`Batch ${command} on ${files.length} file(s)`));
+      console.log();
+
+      if (options.dryRun) {
+        console.log(chalk.dim('Dry run - files that would be processed:'));
+        for (const file of files) {
+          console.log(chalk.dim(`  ${file}`));
+        }
+        return;
+      }
+
+      // Process files
+      const results = [];
+      const progressBar = fmt.progressBar(files.length, 'Processing');
+      progressBar.update(0);
+
+      for (let i = 0; i < files.length; i++) {
+        const file = files[i];
+        progressBar.update(i + 1);
+
+        if (!fs.existsSync(file)) {
+          results.push({ file, status: 'not found' });
+          continue;
+        }
+
+        try {
+          const text = fs.readFileSync(file, 'utf-8');
+          let result = { file, status: 'ok' };
+
+          switch (command) {
+            case 'status': {
+              const counts = countAnnotations(text);
+              const comments = getComments(text);
+              result.annotations = counts.total;
+              result.comments = comments.length;
+              result.pending = comments.filter(c => !c.resolved).length;
+              break;
+            }
+
+            case 'comments': {
+              const comments = getComments(text);
+              result.total = comments.length;
+              result.pending = comments.filter(c => !c.resolved).length;
+              result.resolved = comments.filter(c => c.resolved).length;
+              break;
+            }
+
+            case 'resolve': {
+              const comments = getComments(text);
+              const pending = comments.filter(c => !c.resolved);
+              if (pending.length > 0) {
+                let newText = text;
+                for (const c of pending) {
+                  newText = setCommentStatus(newText, c, true);
+                }
+                fs.writeFileSync(file, newText, 'utf-8');
+                result.resolved = pending.length;
+              } else {
+                result.resolved = 0;
+              }
+              break;
+            }
+
+            case 'strip': {
+              const clean = stripAnnotations(text, { keepComments: false });
+              const hasChanges = clean !== text;
+              if (hasChanges) {
+                fs.writeFileSync(file, clean, 'utf-8');
+                result.stripped = true;
+              } else {
+                result.stripped = false;
+              }
+              break;
+            }
+          }
+
+          results.push(result);
+        } catch (err) {
+          results.push({ file, status: 'error', error: err.message });
+        }
+      }
+
+      progressBar.done();
+      console.log();
+
+      // Show results
+      console.log(fmt.header('Results'));
+      console.log();
+
+      for (const r of results) {
+        const statusIcon = r.status === 'ok'
+          ? chalk.green('✓')
+          : r.status === 'error'
+            ? chalk.red('✗')
+            : chalk.yellow('?');
+
+        let details = '';
+        switch (command) {
+          case 'status':
+            details = chalk.dim(`${r.annotations || 0} annotations, ${r.pending || 0} pending comments`);
+            break;
+          case 'comments':
+            details = chalk.dim(`${r.total || 0} total, ${r.pending || 0} pending`);
+            break;
+          case 'resolve':
+            details = r.resolved > 0
+              ? chalk.green(`${r.resolved} resolved`)
+              : chalk.dim('no pending');
+            break;
+          case 'strip':
+            details = r.stripped
+              ? chalk.green('cleaned')
+              : chalk.dim('no changes');
+            break;
+        }
+
+        console.log(`  ${statusIcon} ${r.file} ${details}`);
+        if (r.error) {
+          console.log(chalk.red(`    ${r.error}`));
+        }
+      }
+
+      // Summary
+      console.log();
+      const successful = results.filter(r => r.status === 'ok').length;
+      const failed = results.filter(r => r.status === 'error').length;
+      console.log(chalk.dim(`${successful} succeeded, ${failed} failed`));
+    });
+}
+
+// Helper functions for help text
+
+function showFullHelp(pkg) {
+  console.log(`
+${chalk.bold.cyan('rev')} ${chalk.dim(`v${pkg?.version || 'unknown'}`)} - Revision workflow for Word ↔ Markdown round-trips
+
+${chalk.bold('DESCRIPTION')}
+  Handle reviewer feedback when collaborating on academic papers.
+  Import changes from Word, review them interactively, and preserve
+  comments for discussion with Claude.
+
+${chalk.bold('GLOBAL OPTIONS')}
+
+  ${chalk.bold('--no-color')}               Disable colored output
+  ${chalk.bold('-q, --quiet')}              Suppress non-essential output
+  ${chalk.bold('--json')}                   Output in JSON format (for scripting)
+
+${chalk.bold('TYPICAL WORKFLOW')}
+
+  ${chalk.dim('1.')} Build and send: ${chalk.green('rev build docx')} ${chalk.dim('(or rev b docx)')}
+  ${chalk.dim('2.')} Reviewers return ${chalk.yellow('reviewed.docx')} with edits and comments
+  ${chalk.dim('3.')} Sync their feedback: ${chalk.green('rev sync reviewed.docx')}
+  ${chalk.dim('4.')} Work through comments: ${chalk.green('rev next')} ${chalk.dim('(n)')} / ${chalk.green('rev todo')} ${chalk.dim('(t)')}
+  ${chalk.dim('5.')} Accept/reject changes: ${chalk.green('rev accept -a')} ${chalk.dim('(a)')} or ${chalk.green('rev review')}
+  ${chalk.dim('6.')} Rebuild: ${chalk.green('rev build docx')}
+  ${chalk.dim('7.')} Archive old files: ${chalk.green('rev archive')}
+
+${chalk.bold('MORE HELP')}
+
+  rev help workflow    Detailed workflow guide
+  rev help syntax      Annotation syntax reference
+  rev help commands    All commands with options
+`);
+}
+
+function showWorkflowHelp() {
+  console.log(`
+${chalk.bold.cyan('rev')} ${chalk.dim('- Workflow Guide')}
+
+${chalk.bold('OVERVIEW')}
+
+  The rev workflow solves a common problem: you write in Markdown,
+  but collaborators review in Word. When they return edited documents,
+  you need to merge their changes back into your source files.
+
+${chalk.bold('STEP 1: BUILD & SEND')}
+
+  ${chalk.green('rev build docx')}
+  ${chalk.dim('# Send the .docx to reviewers')}
+
+${chalk.bold('STEP 2: RECEIVE FEEDBACK')}
+
+  Reviewers edit the document, adding:
+  ${chalk.dim('•')} Track changes (insertions, deletions)
+  ${chalk.dim('•')} Comments (questions, suggestions)
+
+${chalk.bold('STEP 3: SYNC CHANGES')}
+
+  ${chalk.green('rev sync reviewed.docx')}
+  ${chalk.dim('# Or just: rev sync (auto-detects most recent .docx)')}
+
+  Your markdown files now contain their feedback as annotations.
+
+${chalk.bold('STEP 4: WORK THROUGH COMMENTS')}
+
+  ${chalk.green('rev todo')}              ${chalk.dim('# See all pending comments')}
+  ${chalk.green('rev next')}              ${chalk.dim('# Show next pending comment')}
+  ${chalk.green('rev reply file.md -n 1 -m "Done"')}
+  ${chalk.green('rev resolve file.md -n 1')}
+
+${chalk.bold('STEP 5: ACCEPT/REJECT CHANGES')}
+
+  ${chalk.green('rev accept file.md -a')} ${chalk.dim('# Accept all changes')}
+  ${chalk.green('rev reject file.md -n 2')} ${chalk.dim('# Reject specific change')}
+  ${chalk.dim('# Or use interactive mode:')}
+  ${chalk.green('rev review file.md')}
+
+${chalk.bold('STEP 6: REBUILD')}
+
+  ${chalk.green('rev build docx')}
+  ${chalk.green('rev build docx --dual')} ${chalk.dim('# Clean + comments version')}
+
+${chalk.bold('STEP 7: ARCHIVE & REPEAT')}
+
+  ${chalk.green('rev archive')}           ${chalk.dim('# Move reviewer files to archive/')}
+  ${chalk.dim('# Send new .docx, repeat cycle')}
+`);
+}
+
+function showSyntaxHelp() {
+  console.log(`
+${chalk.bold.cyan('rev')} ${chalk.dim('- Annotation Syntax (CriticMarkup)')}
+
+${chalk.bold('INSERTIONS')}
+
+  Syntax:  ${chalk.green('{++inserted text++}')}
+  Meaning: This text was added by the reviewer
+
+  Example:
+    We ${chalk.green('{++specifically++}')} focused on neophytes.
+    → Reviewer added the word "specifically"
+
+${chalk.bold('DELETIONS')}
+
+  Syntax:  ${chalk.red('{--deleted text--}')}
+  Meaning: This text was removed by the reviewer
+
+  Example:
+    We focused on ${chalk.red('{--recent--}')} neophytes.
+    → Reviewer removed the word "recent"
+
+${chalk.bold('SUBSTITUTIONS')}
+
+  Syntax:  ${chalk.yellow('{~~old text~>new text~~}')}
+  Meaning: Text was changed from old to new
+
+  Example:
+    The effect was ${chalk.yellow('{~~significant~>substantial~~}')}.
+    → Reviewer changed "significant" to "substantial"
+
+${chalk.bold('COMMENTS')}
+
+  Syntax:  ${chalk.blue('{>>Author: comment text<<}')}
+  Meaning: Reviewer left a comment at this location
+
+  Example:
+    The results were significant. ${chalk.blue('{>>Dr. Smith: Add p-value<<}')}
+    → Dr. Smith commented asking for a p-value
+
+  Comments are placed ${chalk.bold('after')} the text they reference.
+`);
+}
+
+function showCommandsHelp() {
+  console.log(`
+${chalk.bold.cyan('rev')} ${chalk.dim('- Command Reference')}
+
+${chalk.bold('rev import')} <docx> <original-md>
+
+  Import changes from a Word document by comparing against your
+  original Markdown source.
+
+  ${chalk.bold('Arguments:')}
+    docx          Word document from reviewer
+    original-md   Your original Markdown file
+
+  ${chalk.bold('Options:')}
+    -o, --output <file>   Write to different file (default: overwrites original)
+    -a, --author <name>   Author name for changes (default: "Reviewer")
+    --dry-run             Preview changes without saving
+
+${chalk.bold('rev review')} <file>
+
+  Interactively review and accept/reject track changes.
+  Comments are preserved; only track changes are processed.
+
+  ${chalk.bold('Keys:')}
+    a   Accept this change
+    r   Reject this change
+    s   Skip (decide later)
+    A   Accept all remaining changes
+    L   Reject all remaining changes
+    q   Quit without saving
+
+${chalk.bold('rev strip')} <file>
+
+  Remove annotations, outputting clean Markdown.
+  Track changes are applied (insertions kept, deletions removed).
+
+  ${chalk.bold('Options:')}
+    -o, --output <file>   Write to file (default: stdout)
+    -c, --keep-comments   Keep comment annotations
+
+${chalk.bold('rev help')} [topic]
+
+  Show help. Optional topics:
+    workflow    Step-by-step workflow guide
+    syntax      Annotation syntax reference
+    commands    This command reference
+`);
+}