docrev 0.8.1 → 0.8.5

package/lib/commands/{comments.js → comments.ts}

@@ -4,6 +4,7 @@
  * Commands for viewing, navigating, and managing reviewer comments and track changes.
  */
 
+import { Command } from 'commander';
 import {
   chalk,
   fs,
@@ -16,23 +17,25 @@ import {
   setCommentStatus,
   getTrackChanges,
   applyDecision,
+  cleanupOrphanedMarkers,
   interactiveCommentReview,
-  tuiCommentReview,
+  // tuiCommentReview, // TUI module not yet migrated
   getUserName,
   exitWithError,
   getAnnotationSuggestions,
   requireFile,
 } from './context.js';
+import type { Comment, Annotation } from '../types.js';
 
 /**
  * Add a reply after a comment
- * @param {string} text - Full document text
- * @param {object} comment - Comment object with position and match
- * @param {string} author - Reply author name
- * @param {string} message - Reply message
- * @returns {string} Updated text
+ * @param text - Full document text
+ * @param comment - Comment object with position and match
+ * @param author - Reply author name
+ * @param message - Reply message
+ * @returns Updated text
  */
-function addReply(text, comment, author, message) {
+function addReply(text: string, comment: Comment, author: string, message: string): string {
   const replyAnnotation = `{>>${author}: ${message}<<}`;
   const insertPos = comment.position + comment.match.length;
   return text.slice(0, insertPos) + ' ' + replyAnnotation + text.slice(insertPos);
@@ -41,7 +44,7 @@ function addReply(text, comment, author, message) {
 /**
  * Helper to find section file by name (deterministic priority)
  */
-function findSectionFile(section) {
+function findSectionFile(section: string): string[] {
   const allMd = findFiles('.md');
   const sectionLower = section.toLowerCase();
 
@@ -68,7 +71,9 @@ function findSectionFile(section) {
       if (headerMatch && headerMatch[1].toLowerCase().trim() === sectionLower) {
         return [f];
       }
-    } catch (e) {}
+    } catch {
+      // Skip unreadable files silently - not critical for section matching
+    }
   }
 
   // 4. Header contains (partial match)
@@ -80,7 +85,9 @@ function findSectionFile(section) {
       if (headerMatch && headerMatch[1].toLowerCase().includes(sectionLower)) {
         headerMatches.push(f);
       }
-    } catch (e) {}
+    } catch {
+      // Skip unreadable files silently - not critical for section matching
+    }
   }
   if (headerMatches.length === 1) return headerMatches;
   if (headerMatches.length > 1) {
@@ -93,11 +100,60 @@ function findSectionFile(section) {
   return [section];
 }
 
+interface CommentsOptions {
+  pending?: boolean;
+  resolved?: boolean;
+  author?: string;
+  export?: string;
+  interactive?: boolean;
+  tui?: boolean;
+}
+
+interface ResolveOptions {
+  number?: number;
+  all?: boolean;
+  unresolve?: boolean;
+  dryRun?: boolean;
+}
+
+interface NextOptions {
+  number?: number;
+}
+
+interface PrevOptions {
+  number?: number;
+}
+
+interface AcceptOptions {
+  number?: number;
+  all?: boolean;
+  dryRun?: boolean;
+}
+
+interface RejectOptions {
+  number?: number;
+  all?: boolean;
+  dryRun?: boolean;
+}
+
+interface ReplyOptions {
+  message?: string;
+  number?: number;
+  author?: string;
+  all?: boolean;
+  dryRun?: boolean;
+}
+
+interface ReplyDocOptions {
+  output?: string;
+  context?: boolean;
+  force?: boolean;
+}
+
 /**
  * Register comment commands with the program
- * @param {import('commander').Command} program
  */
-export function register(program) {
+export function register(program: Command): void {
   // ==========================================================================
   // COMMENTS command - List all comments
   // ==========================================================================
@@ -113,33 +169,38 @@ export function register(program) {
     .option('-e, --export <csvFile>', 'Export comments to CSV file')
     .option('-i, --interactive', 'Interactive review mode (reply, resolve, skip)')
     .option('-t, --tui', 'Visual TUI mode for comment review')
-    .action(async (file, options) => {
+    .action(async (file: string, options: CommentsOptions) => {
       requireFile(file, 'Markdown file');
 
       const text = fs.readFileSync(file, 'utf-8');
 
       // TUI review mode
       if (options.tui) {
-        let author = options.author || getUserName();
-        if (!author) {
-          exitWithError('No user name set for replies', getAnnotationSuggestions('no_author'));
-        }
-
-        const result = await tuiCommentReview(text, {
-          author,
-          addReply: (txt, comment, auth, msg) => {
-            const replyAnnotation = `{>>${auth}: ${msg}<<}`;
-            const insertPos = comment.position + comment.match.length;
-            return txt.slice(0, insertPos) + ' ' + replyAnnotation + txt.slice(insertPos);
-          },
-          setStatus: setCommentStatus,
-        });
+        console.error(chalk.yellow('TUI mode is temporarily unavailable (module migration in progress)'));
+        console.error(chalk.dim('Use --interactive mode instead: rev comments --interactive ' + file));
+        process.exit(1);
 
-        if (result.resolved > 0 || result.replied > 0) {
-          fs.writeFileSync(file, result.text, 'utf-8');
-          console.log(fmt.status('success', `Changes saved to ${file}`));
-        }
-        return;
+        // TODO: Re-enable when tui.ts is migrated
+        // let author = options.author || getUserName();
+        // if (!author) {
+        //   exitWithError('No user name set for replies', getAnnotationSuggestions('no_author'));
+        // }
+        //
+        // const result = await tuiCommentReview(text, {
+        //   author,
+        //   addReply: (txt: string, comment: Comment, auth: string, msg: string) => {
+        //     const replyAnnotation = `{>>${auth}: ${msg}<<}`;
+        //     const insertPos = comment.position + comment.match.length;
+        //     return txt.slice(0, insertPos) + ' ' + replyAnnotation + txt.slice(insertPos);
+        //   },
+        //   setStatus: setCommentStatus,
+        // });
+        //
+        // if (result.resolved > 0 || result.replied > 0) {
+        //   fs.writeFileSync(file, result.text, 'utf-8');
+        //   console.log(fmt.status('success', `Changes saved to ${file}`));
+        // }
+        // return;
       }
 
       // Interactive review mode
@@ -151,7 +212,7 @@ export function register(program) {
 
         const result = await interactiveCommentReview(text, {
           author,
-          addReply: (txt, comment, auth, msg) => {
+          addReply: (txt: string, comment: Comment, auth: string, msg: string) => {
             const replyAnnotation = `{>>${auth}: ${msg}<<}`;
             const insertPos = comment.position + comment.match.length;
             return txt.slice(0, insertPos) + ' ' + replyAnnotation + txt.slice(insertPos);
@@ -181,7 +242,7 @@ export function register(program) {
 
       // CSV export mode
       if (options.export) {
-        const csvEscape = (str) => {
+        const csvEscape = (str?: string | number | null): string => {
           if (!str) return '';
           str = String(str);
           if (str.includes(',') || str.includes('"') || str.includes('\n')) {
@@ -257,7 +318,7 @@ export function register(program) {
     .option('-a, --all', 'Mark all comments as resolved')
     .option('-u, --unresolve', 'Mark as pending (unresolve)')
     .option('--dry-run', 'Preview without saving')
-    .action((file, options) => {
+    .action((file: string, options: ResolveOptions) => {
       requireFile(file, 'Markdown file');
 
       let text = fs.readFileSync(file, 'utf-8');
@@ -339,7 +400,7 @@ export function register(program) {
     .description('Show next pending comment')
     .argument('[file]', 'Specific file (default: all markdown files)')
     .option('-n, --number <n>', 'Skip to nth pending comment', parseInt)
-    .action((file, options) => {
+    .action((file: string | undefined, options: NextOptions) => {
       const files = file ? [file] : findFiles('.md');
 
       if (files.length === 0) {
@@ -348,7 +409,7 @@ export function register(program) {
       }
 
       // Collect all pending comments across files
-      const allPending = [];
+      const allPending: Array<Annotation & { file: string; number: number }> = [];
       for (const f of files) {
         if (!fs.existsSync(f)) continue;
         const text = fs.readFileSync(f, 'utf-8');
@@ -404,7 +465,7 @@ export function register(program) {
     .description('Show previous pending comment')
     .argument('[file]', 'Specific file (default: all markdown files)')
     .option('-n, --number <n>', 'Skip to nth pending comment from end', parseInt)
-    .action((file, options) => {
+    .action((file: string | undefined, options: PrevOptions) => {
       const files = file ? [file] : findFiles('.md');
 
       if (files.length === 0) {
@@ -413,7 +474,7 @@ export function register(program) {
       }
 
       // Collect all pending comments across files
-      const allPending = [];
+      const allPending: Array<Annotation & { file: string; number: number }> = [];
       for (const f of files) {
         if (!fs.existsSync(f)) continue;
         const text = fs.readFileSync(f, 'utf-8');
@@ -471,7 +532,7 @@ export function register(program) {
     .command('first')
     .description('Show first comment')
     .argument('[section]', 'Specific file or section name (default: all markdown files)')
-    .action((section) => {
+    .action((section: string | undefined) => {
       const files = section ? findSectionFile(section) : findFiles('.md');
 
       if (files.length === 0) {
@@ -517,7 +578,7 @@ export function register(program) {
     .command('last')
     .description('Show last comment')
     .argument('[section]', 'Specific file or section name (default: all markdown files)')
-    .action((section) => {
+    .action((section: string | undefined) => {
       const files = section ? findSectionFile(section) : findFiles('.md').reverse();
 
       if (files.length === 0) {
@@ -566,7 +627,7 @@ export function register(program) {
     .description('List all pending comments as a checklist')
     .argument('[file]', 'Specific file (default: all markdown files)')
     .option('--by-author', 'Group by author')
-    .action((file, options) => {
+    .action((file: string | undefined, options: { byAuthor?: boolean }) => {
       const files = file ? [file] : findFiles('.md');
 
       if (files.length === 0) {
@@ -575,7 +636,13 @@ export function register(program) {
       }
 
       // Collect all pending comments
-      const todos = [];
+      const todos: Array<{
+        file: string;
+        number: number;
+        line: number;
+        author: string;
+        content: string;
+      }> = [];
       for (const f of files) {
         if (!fs.existsSync(f)) continue;
         const text = fs.readFileSync(f, 'utf-8');
@@ -604,7 +671,7 @@ export function register(program) {
 
       if (options.byAuthor) {
         // Group by author
-        const byAuthor = {};
+        const byAuthor: Record<string, typeof todos> = {};
         for (const t of todos) {
           if (!byAuthor[t.author]) byAuthor[t.author] = [];
           byAuthor[t.author].push(t);
@@ -620,7 +687,7 @@ export function register(program) {
         }
       } else {
         // List by file
-        let currentFile = null;
+        let currentFile: string | null = null;
         for (const t of todos) {
           if (t.file !== currentFile) {
             if (currentFile) console.log();
@@ -648,7 +715,7 @@ export function register(program) {
     .option('-n, --number <n>', 'Accept specific change by number', parseInt)
     .option('-a, --all', 'Accept all changes')
     .option('--dry-run', 'Preview without saving')
-    .action((file, options) => {
+    .action((file: string, options: AcceptOptions) => {
       if (!fs.existsSync(file)) {
         console.error(chalk.red(`Error: File not found: ${file}`));
         process.exit(1);
@@ -668,6 +735,8 @@ export function register(program) {
         for (const change of sorted) {
           text = applyDecision(text, change, true);
         }
+        // Clean up any orphaned CriticMarkup markers that result from interleaved track changes
+        text = cleanupOrphanedMarkers(text);
         if (!options.dryRun) {
           fs.writeFileSync(file, text, 'utf-8');
           console.log(fmt.status('success', `Accepted ${changes.length} change(s)`));
@@ -700,13 +769,15 @@ export function register(program) {
 
       for (let i = 0; i < changes.length; i++) {
         const c = changes[i];
-        let desc;
+        let desc: string;
         if (c.type === 'insert') {
           desc = chalk.green(`+++ "${c.content.slice(0, 40)}${c.content.length > 40 ? '...' : ''}"`);
         } else if (c.type === 'delete') {
           desc = chalk.red(`--- "${c.content.slice(0, 40)}${c.content.length > 40 ? '...' : ''}"`);
         } else if (c.type === 'substitute') {
           desc = chalk.yellow(`~~~ "${c.content.slice(0, 20)}" → "${(c.replacement || '').slice(0, 20)}"`);
+        } else {
+          desc = chalk.dim('???');
         }
         console.log(`  #${i + 1} ${chalk.dim(`L${c.line}`)} ${desc}`);
       }
@@ -728,7 +799,7 @@ export function register(program) {
     .option('-n, --number <n>', 'Reject specific change by number', parseInt)
     .option('-a, --all', 'Reject all changes')
     .option('--dry-run', 'Preview without saving')
-    .action((file, options) => {
+    .action((file: string, options: RejectOptions) => {
       if (!fs.existsSync(file)) {
         console.error(chalk.red(`Error: File not found: ${file}`));
         process.exit(1);
@@ -780,13 +851,15 @@ export function register(program) {
 
       for (let i = 0; i < changes.length; i++) {
         const c = changes[i];
-        let desc;
+        let desc: string;
         if (c.type === 'insert') {
           desc = chalk.green(`+++ "${c.content.slice(0, 40)}${c.content.length > 40 ? '...' : ''}"`);
         } else if (c.type === 'delete') {
           desc = chalk.red(`--- "${c.content.slice(0, 40)}${c.content.length > 40 ? '...' : ''}"`);
         } else if (c.type === 'substitute') {
           desc = chalk.yellow(`~~~ "${c.content.slice(0, 20)}" → "${(c.replacement || '').slice(0, 20)}"`);
+        } else {
+          desc = chalk.dim('???');
         }
         console.log(`  #${i + 1} ${chalk.dim(`L${c.line}`)} ${desc}`);
       }
@@ -809,7 +882,7 @@ export function register(program) {
     .option('-a, --author <name>', 'Override author name')
     .option('--all', 'Reply to all pending comments with the same message (requires -m)')
     .option('--dry-run', 'Preview without saving')
-    .action(async (file, options) => {
+    .action(async (file: string, options: ReplyOptions) => {
       if (!fs.existsSync(file)) {
         console.error(chalk.red(`File not found: ${file}`));
         process.exit(1);
@@ -844,7 +917,7 @@ export function register(program) {
         // Process in reverse order to maintain positions
         const sortedComments = [...comments].sort((a, b) => b.position - a.position);
         for (const comment of sortedComments) {
-          result = addReply(result, comment, author, options.message);
+          result = addReply(result, comment as Comment, author, options.message);
           count++;
         }
         if (options.dryRun) {
@@ -864,7 +937,7 @@ export function register(program) {
           console.error(chalk.red(`Invalid comment number. File has ${allComments.length} comments.`));
           process.exit(1);
         }
-        const result = addReply(text, allComments[idx], author, options.message);
+        const result = addReply(text, allComments[idx] as Comment, author, options.message);
         if (options.dryRun) {
           console.log(fmt.status('info', `Would add reply to comment #${options.number}`));
         } else {
@@ -882,7 +955,7 @@ export function register(program) {
         output: process.stdout,
       });
 
-      const askQuestion = (prompt) =>
+      const askQuestion = (prompt: string): Promise<string> =>
         new Promise((resolve) => rl.question(prompt, resolve));
 
       let result = text;
@@ -904,7 +977,7 @@ export function register(program) {
         }
 
         if (answer.trim()) {
-          result = addReply(result, c, author, answer.trim());
+          result = addReply(result, c as Comment, author, answer.trim());
           repliesAdded++;
           console.log(chalk.green('  ✓ Reply added'));
         }
@@ -919,4 +992,64 @@ export function register(program) {
         console.log(chalk.dim('\nNo replies added.'));
       }
     });
+
+  // ==========================================================================
+  // REPLY-DOC command - Generate reply template document from comments
+  // ==========================================================================
+
+  program
+    .command('reply-doc')
+    .alias('rd')
+    .description('Generate a reply template document from comments')
+    .argument('<file>', 'Markdown file with comments')
+    .option('-o, --output <file>', 'Output file (default: <input>_reply.md)')
+    .option('--no-context', 'Exclude commented text context')
+    .option('--force', 'Overwrite existing output file')
+    .action(async (file: string, options: ReplyDocOptions) => {
+      requireFile(file, 'Markdown file');
+
+      const text = fs.readFileSync(file, 'utf-8');
+      const comments = getComments(text);
+
+      if (comments.length === 0) {
+        console.log(fmt.status('info', 'No comments found in file.'));
+        return;
+      }
+
+      // Determine output filename
+      const baseName = path.basename(file, '.md');
+      const dirName = path.dirname(file);
+      const outputFile = options.output || path.join(dirName, `${baseName}_reply.md`);
+
+      // Check if output exists
+      if (fs.existsSync(outputFile) && !options.force) {
+        console.log(fmt.status('error', `Output file already exists: ${outputFile}`));
+        console.log(chalk.dim('  Use --force to overwrite'));
+        process.exit(1);
+      }
+
+      // Generate reply template
+      const sectionName = baseName.charAt(0).toUpperCase() + baseName.slice(1);
+      let output = `# ${sectionName} - Response to Reviewer Comments\n\n`;
+
+      comments.forEach((c, i) => {
+        const authorName = c.author || 'Anonymous';
+
+        output += `## Comment ${i + 1} (${authorName})\n`;
+        output += `> "${c.content}"\n\n`;
+
+        if (options.context !== false && c.before) {
+          const context = c.before.trim().slice(-80);
+          if (context) {
+            output += `*Context: "...${context}"*\n\n`;
+          }
+        }
+
+        output += `**Response:** \n\n`;
+      });
+
+      fs.writeFileSync(outputFile, output, 'utf-8');
+      console.log(fmt.status('success', `Generated reply template: ${outputFile}`));
+      console.log(chalk.dim(`  ${comments.length} comment(s) extracted`));
+    });
 }

package/lib/commands/{context.js → context.ts}

@@ -13,11 +13,11 @@ import * as fmt from '../format.js';
 export let quietMode = false;
 export let jsonMode = false;
 
-export function setQuietMode(value) {
+export function setQuietMode(value: boolean): void {
   quietMode = value;
 }
 
-export function setJsonMode(value) {
+export function setJsonMode(value: boolean): void {
   jsonMode = value;
   if (value) {
     chalk.level = 0;
@@ -25,12 +25,12 @@ export function setJsonMode(value) {
 }
 
 // JSON output helper
-export function jsonOutput(data) {
+export function jsonOutput(data: unknown): void {
   console.log(JSON.stringify(data, null, 2));
 }
 
 // Find files by extension
-export function findFiles(ext, cwd = process.cwd()) {
+export function findFiles(ext: string, cwd: string = process.cwd()): string[] {
   try {
     return fs.readdirSync(cwd)
       .filter(f => f.endsWith(ext) && !f.startsWith('.'));
@@ -52,6 +52,7 @@ export {
   hasAnnotations,
   getTrackChanges,
   applyDecision,
+  cleanupOrphanedMarkers,
 } from '../annotations.js';
 
 export {
@@ -81,13 +82,16 @@ export {
 export {
   build,
   loadConfig as loadBuildConfig,
+  formatBuildResults,
+} from '../build.js';
+
+export {
   hasPandoc,
   hasPandocCrossref,
-  formatBuildResults,
   hasLatex,
   checkDependencies,
   getInstallInstructions,
-} from '../build.js';
+} from '../dependencies.js';
 
 export {
   getTemplate,
@@ -107,6 +111,8 @@ export {
 
 export { inlineDiffPreview } from '../format.js';
 
+export { countWords } from '../utils.js';
+
 export {
   parseCommentsWithReplies,
   collectComments,
@@ -135,9 +141,12 @@ export {
   isValidDoiFormat,
   lookupDoi,
   lookupMissingDois,
+} from '../doi.js';
+
+export {
   clearDoiCache,
   getDoiCacheStats,
-} from '../doi.js';
+} from '../doi-cache.js';
 
 export {
   formatError,
@@ -162,4 +171,5 @@ export {
   getPluginDirs,
 } from '../plugins.js';
 
-export { tuiCommentReview } from '../tui.js';
+// TUI module not yet migrated to TypeScript
+// export { tuiCommentReview } from '../tui.js';