Fix heading detection in fenced code blocks

.vscode/settings.json

@@ -32,5 +32,6 @@
   "[markdown]": {
     "editor.defaultFormatter": "esbenp.prettier-vscode",
     "files.trimTrailingWhitespace": false
-  }
+  },
+  "biome.enabled": false
 }

bin/md-tree.js

@@ -6,10 +6,10 @@
  * A powerful CLI tool for parsing and manipulating markdown files as tree structures.
  */
 
-import { MarkdownTreeParser } from '../lib/markdown-parser.js';
 import fs from 'node:fs/promises';
 import path from 'node:path';
 import { fileURLToPath } from 'node:url';
+import { MarkdownTreeParser } from '../lib/markdown-parser.js';
 
 const __dirname = path.dirname(fileURLToPath(import.meta.url));
 const packagePath = path.join(__dirname, '..', 'package.json');
@@ -352,7 +352,7 @@ For more information, visit: https://github.com/ksylvan/markdown-tree-parser
     if (Object.keys(stats.headings.byLevel).length > 0) {
       console.log('   By level:');
       for (const [level, count] of Object.entries(stats.headings.byLevel).sort(
-        ([a], [b]) => Number.parseInt(a) - Number.parseInt(b)
+        ([a], [b]) => Number.parseInt(a, 10) - Number.parseInt(b, 10)
       )) {
         console.log(`     Level ${level}: ${count}`);
       }
@@ -468,13 +468,13 @@ For more information, visit: https://github.com/ksylvan/markdown-tree-parser
         options.output = args[i + 1];
         i++; // skip next arg
       } else if (arg === '--level' || arg === '-l') {
-        options.level = Number.parseInt(args[i + 1]) || 2;
+        options.level = Number.parseInt(args[i + 1], 10) || 2;
         i++; // skip next arg
       } else if (arg === '--format' || arg === '-f') {
         options.format = args[i + 1] || 'text';
         i++; // skip next arg
       } else if (arg === '--max-level') {
-        options.maxLevel = Number.parseInt(args[i + 1]) || 3;
+        options.maxLevel = Number.parseInt(args[i + 1], 10) || 3;
         i++; // skip next arg
       } else if (arg === '--recursive' || arg === '-r') {
         options.recursive = true;
@@ -517,7 +517,7 @@ For more information, visit: https://github.com/ksylvan/markdown-tree-parser
       console.error(MESSAGES.USAGE_EXTRACT_ALL);
       process.exit(1);
     }
-    const level = args[2] ? Number.parseInt(args[2]) : options.level;
+    const level = args[2] ? Number.parseInt(args[2], 10) : options.level;
     await this.extractAllSections(args[1], level, options.output);
   }
 
@@ -645,9 +645,27 @@ For more information, visit: https://github.com/ksylvan/markdown-tree-parser
     // Find all level 2 headings and their positions
     const sections = [];
     let currentSection = null;
+    let inCodeBlock = false;
 
     for (let i = 0; i < lines.length; i++) {
       const line = lines[i];
+      const trimmed = line.trim();
+
+      // Track fenced code blocks and ignore headings within them
+      if (trimmed.startsWith('```') || trimmed.startsWith('~~~')) {
+        if (currentSection) {
+          currentSection.lines.push(line);
+        }
+        inCodeBlock = !inCodeBlock;
+        continue;
+      }
+
+      if (inCodeBlock) {
+        if (currentSection) {
+          currentSection.lines.push(line);
+        }
+        continue;
+      }
 
       // Check for main title (level 1)
       if (line.match(/^# /)) {
@@ -819,8 +837,20 @@ For more information, visit: https://github.com/ksylvan/markdown-tree-parser
    */
   adjustHeadingLevels(content, adjustment) {
     const lines = content.split('\n');
+    let inCodeBlock = false;
 
     const adjustedLines = lines.map((line) => {
+      // Check for code block boundaries (``` or ~~~)
+      if (line.trim().startsWith('```') || line.trim().startsWith('~~~')) {
+        inCodeBlock = !inCodeBlock;
+        return line;
+      }
+
+      // Skip heading adjustment if we're inside a code block
+      if (inCodeBlock) {
+        return line;
+      }
+
       const headingMatch = line.match(PATTERNS.HEADING_LEVEL_1_5);
       if (headingMatch) {
         const [, hashes, rest] = headingMatch;

index.js

@@ -19,9 +19,9 @@ export default MarkdownTreeParser;
 
 // Export additional utilities that might be useful
 export { unified } from 'unified';
-export { visit } from 'unist-util-visit';
-export { selectAll, select } from 'unist-util-select';
 export { find } from 'unist-util-find';
+export { select, selectAll } from 'unist-util-select';
+export { visit } from 'unist-util-visit';
 
 /**
  * Convenience function to create a new parser instance

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@kayvan/markdown-tree-parser",
-  "version": "1.6.0",
+  "version": "1.6.1",
   "description": "A powerful JavaScript library and CLI tool for parsing and manipulating markdown files as tree structures using the remark/unified ecosystem",
   "type": "module",
   "main": "index.js",
@@ -34,10 +34,10 @@
     "unist-util-visit": "^5.0.0"
   },
   "devDependencies": {
-    "@eslint/js": "^9.29.0",
-    "@types/node": "^24.0.3",
-    "eslint": "^9.29.0",
-    "prettier": "^3.5.3"
+    "@eslint/js": "^9.34.0",
+    "@types/node": "^24.3.0",
+    "eslint": "^9.34.0",
+    "prettier": "^3.6.2"
   },
   "engines": {
     "node": ">=16.0.0"