docrev 0.9.5 → 0.9.7

package/dist/lib/commands/utilities.js

@@ -1,29 +1,9 @@
 /**
- * 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
+ * Utility commands: help, completions, open, upgrade, install-cli-skill, uninstall-cli-skill
  *
- * Miscellaneous utility commands for project management.
+ * Core utility commands that don't fit into a specific domain.
  */
-import { chalk, fs, path, fmt, findFiles, loadBuildConfig, getComments, setCommentStatus, countAnnotations, stripAnnotations, parseAnnotations, getUserName, countWords, } from './context.js';
-/**
- * Recursively add directory contents to a zip archive, filtering by predicate
- */
-function addDirToZip(zip, dir, shouldInclude, 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()) {
-            addDirToZip(zip, fullPath, shouldInclude, entryZipPath);
-        }
-        else {
-            zip.addLocalFile(fullPath, zipPath || undefined);
-        }
-    }
-}
+import { chalk, fs, path, fmt, } from './context.js';
 /**
  * Register utility commands with the program
  */
@@ -99,1210 +79,6 @@ export function register(program, pkg) {
         }
     });
     // ==========================================================================
-    // 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);
-        }
-        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 (_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));
-        }
-        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;
-        };
-        addDirToZip(zip, '.', shouldInclude);
-        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 || 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: ${excluded.join(', ')}`));
-                console.log();
-            }
-        }
-        if (docxFiles.length === 0) {
-            console.log(fmt.status('info', 'No .docx files to archive.'));
-            return;
-        }
-        const projectTitle = projectSlug;
-        // Create archive folder
-        const archiveDir = path.resolve(options.dir || 'archive');
-        if (!options.dryRun && !fs.existsSync(archiveDir)) {
-            fs.mkdirSync(archiveDir, { recursive: true });
-        }
-        console.log(fmt.header('Archive'));
-        console.log();
-        const moved = [];
-        for (const file of docxFiles) {
-            const stat = fs.statSync(file);
-            const mtime = stat.mtime;
-            const timestamp = mtime.toISOString().slice(0, 19).replace(/[-:]/g, '').replace('T', '_');
-            // Determine reviewer name
-            let reviewer = options.by || null;
-            if (!reviewer && options.rename !== false) {
-                try {
-                    const comments = await extractWordComments(file);
-                    const authors = [...new Set(comments.map(c => c.author).filter(a => a && a !== 'Unknown'))];
-                    if (authors.length === 1) {
-                        reviewer = authors[0].replace(/[^a-zA-Z0-9]/g, '-').replace(/^-|-$/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)} → ${chalk.cyan(path.join(options.dir || 'archive', newName))}`);
-            }
-            else {
-                // Handle name collision
-                let finalPath = destPath;
-                let counter = 1;
-                while (fs.existsSync(finalPath)) {
-                    const ext = path.extname(newName);
-                    const base = path.basename(newName, ext);
-                    finalPath = path.join(archiveDir, `${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 ${options.dir || 'archive'}/`));
-        }
-    });
-    // ==========================================================================
-    // EXPORT command - Export project as distributable zip
-    // ==========================================================================
-    program
-        .command('export')
-        .description('Export project as distributable zip')
-        .option('-o, --output <file>', 'Output filename')
-        .option('--include-output', 'Include built PDF/DOCX files')
-        .action(async (options) => {
-        const { default: AdmZip } = await import('adm-zip');
-        const { build } = await import('../build.js');
-        let config = {};
-        try {
-            config = loadBuildConfig('.') || {};
-        }
-        catch {
-            // Not in a rev project, that's ok
-        }
-        // Build first if including output
-        if (options.includeOutput) {
-            console.log(chalk.dim('Building documents...'));
-            await build('.', ['pdf', 'docx']);
-        }
-        const zip = new AdmZip();
-        const projectName = config.title?.replace(/[^a-zA-Z0-9]/g, '-').toLowerCase() || 'project';
-        const outputPath = options.output || `${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;
-        };
-        addDirToZip(zip, '.', shouldInclude);
-        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, _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);
-        }
-        console.log(chalk.dim(`Building ${format}...`));
-        const result = await build('.', [format]);
-        const buildResult = result.results.find(r => r.format === format);
-        if (!buildResult?.success) {
-            const errorMsg = buildResult?.error || 'Unknown error';
-            console.error(chalk.red(`Build failed: ${errorMsg}`));
-            process.exit(1);
-        }
-        const outputFile = buildResult.outputPath;
-        if (!outputFile || !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 result = await build('.', formats);
-                for (const r of result.results) {
-                    if (r.success) {
-                        console.log(chalk.green(`  ✓ ${r.format}: ${r.outputPath}`));
-                    }
-                    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 || 'info'] || 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 readline = await import('readline');
-        const rl = 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 || 'warning'] || 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 existingSections = sections.filter(f => fs.existsSync(f));
-            const result = validateCitations(existingSections, bibFile);
-            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(`   ${totalIssues} warning(s). Review before submission.`));
-        }
-        else {
-            console.log(chalk.green('   ✓ All checks passed! Ready for submission.'));
-        }
-    });
-    // ==========================================================================
     // OPEN command - Open project folder or file
     // ==========================================================================
     program
@@ -1389,200 +165,6 @@ export function register(program, pkg) {
         }
     });
     // ==========================================================================
-    // SPELLING command - Spellcheck with global dictionary
-    // ==========================================================================
-    program
-        .command('spelling')
-        .description('Check spelling in markdown files')
-        .argument('[files...]', 'Files to check (default: section files)')
-        .option('--learn <word>', 'Add word to global dictionary')
-        .option('--learn-project <word>', 'Add word to project dictionary')
-        .option('--forget <word>', 'Remove word from global dictionary')
-        .option('--forget-project <word>', 'Remove word from project dictionary')
-        .option('--list', 'List global dictionary words')
-        .option('--list-project', 'List project dictionary words')
-        .option('--list-all', 'List all custom words (global + project)')
-        .option('--british', 'Use British English dictionary')
-        .option('--add-names', 'Add detected names to global dictionary')
-        .action(async (files, options) => {
-        const spelling = await import('../spelling.js');
-        // Handle dictionary management
-        if (options.learn) {
-            const added = spelling.addWord(options.learn, true);
-            if (added) {
-                console.log(fmt.status('success', `Added "${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: ${globalWords.length + projectWords.length} word(s)`));
-            return;
-        }
-        // Check spelling in files
-        let filesToCheck = files || [];
-        if (filesToCheck.length === 0) {
-            if (fs.existsSync('rev.yaml')) {
-                try {
-                    const config = loadBuildConfig('.');
-                    filesToCheck = config?.sections || [];
-                }
-                catch {
-                    // Ignore errors
-                }
-                if (filesToCheck.length === 0) {
-                    filesToCheck = fs.readdirSync('.')
-                        .filter(f => f.endsWith('.md') && !f.startsWith('.'));
-                }
-            }
-            else {
-                filesToCheck = fs.readdirSync('.')
-                    .filter(f => f.endsWith('.md') && !f.startsWith('.'));
-            }
-        }
-        if (filesToCheck.length === 0) {
-            console.log(chalk.yellow('No markdown files found'));
-            return;
-        }
-        const lang = options.british ? 'en-gb' : 'en';
-        console.log(fmt.header(`Spelling Check (${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
@@ -1644,157 +226,6 @@ export function register(program, pkg) {
             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, ${r.pending || 0} pending`);
-                    break;
-                case 'resolve':
-                    details = r.resolved && r.resolved > 0
-                        ? chalk.green(`${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) {