diff --git a/.vscode/settings.json b/.vscode/settings.json
index 7714619..970b181 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -32,5 +32,6 @@
   "[markdown]": {
     "editor.defaultFormatter": "esbenp.prettier-vscode",
     "files.trimTrailingWhitespace": false
-  }
+  },
+  "biome.enabled": false
 }
diff --git a/bin/md-tree.js b/bin/md-tree.js
index d7de8f9..d8825f6 100755
--- a/bin/md-tree.js
+++ b/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;
diff --git a/index.js b/index.js
index 6707204..ac6cd9e 100644
--- a/index.js
+++ b/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
diff --git a/package-lock.json b/package-lock.json
index 674385e..ba56b0d 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "@kayvan/markdown-tree-parser",
-  "version": "1.5.0",
+  "version": "1.6.1",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "@kayvan/markdown-tree-parser",
-      "version": "1.5.0",
+      "version": "1.6.1",
       "license": "MIT",
       "dependencies": {
         "remark-parse": "^11.0.0",
@@ -20,10 +20,10 @@
         "md-tree": "bin/md-tree.js"
       },
       "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"
@@ -76,9 +76,9 @@
       }
     },
     "node_modules/@eslint/config-array": {
-      "version": "0.20.1",
-      "resolved": "https://registry.npmjs.org/@eslint/config-array/-/config-array-0.20.1.tgz",
-      "integrity": "sha512-OL0RJzC/CBzli0DrrR31qzj6d6i6Mm3HByuhflhl4LOBiWxN+3i6/t/ZQQNii4tjksXi8r2CRW1wMpWA2ULUEw==",
+      "version": "0.21.0",
+      "resolved": "https://registry.npmjs.org/@eslint/config-array/-/config-array-0.21.0.tgz",
+      "integrity": "sha512-ENIdc4iLu0d93HeYirvKmrzshzofPw6VkZRKQGe9Nv46ZnWUzcF1xV01dcvEg/1wXUR61OmmlSfyeyO7EvjLxQ==",
       "dev": true,
       "license": "Apache-2.0",
       "dependencies": {
@@ -91,9 +91,9 @@
       }
     },
     "node_modules/@eslint/config-helpers": {
-      "version": "0.2.3",
-      "resolved": "https://registry.npmjs.org/@eslint/config-helpers/-/config-helpers-0.2.3.tgz",
-      "integrity": "sha512-u180qk2Um1le4yf0ruXH3PYFeEZeYC3p/4wCTKrr2U1CmGdzGi3KtY0nuPDH48UJxlKCC5RDzbcbh4X0XlqgHg==",
+      "version": "0.3.1",
+      "resolved": "https://registry.npmjs.org/@eslint/config-helpers/-/config-helpers-0.3.1.tgz",
+      "integrity": "sha512-xR93k9WhrDYpXHORXpxVL5oHj3Era7wo6k/Wd8/IsQNnZUTzkGS29lyn3nAT05v6ltUuTFVCCYDEGfy2Or/sPA==",
       "dev": true,
       "license": "Apache-2.0",
       "engines": {
@@ -101,9 +101,9 @@
       }
     },
     "node_modules/@eslint/core": {
-      "version": "0.14.0",
-      "resolved": "https://registry.npmjs.org/@eslint/core/-/core-0.14.0.tgz",
-      "integrity": "sha512-qIbV0/JZr7iSDjqAc60IqbLdsj9GDt16xQtWD+B78d/HAlvysGdZZ6rpJHGAc2T0FQx1X6thsSPdnoiGKdNtdg==",
+      "version": "0.15.2",
+      "resolved": "https://registry.npmjs.org/@eslint/core/-/core-0.15.2.tgz",
+      "integrity": "sha512-78Md3/Rrxh83gCxoUc0EiciuOHsIITzLy53m3d9UyiW8y9Dj2D29FeETqyKA+BRK76tnTp6RXWb3pCay8Oyomg==",
       "dev": true,
       "license": "Apache-2.0",
       "dependencies": {
@@ -138,9 +138,9 @@
       }
     },
     "node_modules/@eslint/js": {
-      "version": "9.29.0",
-      "resolved": "https://registry.npmjs.org/@eslint/js/-/js-9.29.0.tgz",
-      "integrity": "sha512-3PIF4cBw/y+1u2EazflInpV+lYsSG0aByVIQzAgb1m1MhHFSbqTyNqtBKHgWf/9Ykud+DhILS9EGkmekVhbKoQ==",
+      "version": "9.34.0",
+      "resolved": "https://registry.npmjs.org/@eslint/js/-/js-9.34.0.tgz",
+      "integrity": "sha512-EoyvqQnBNsV1CWaEJ559rxXL4c8V92gxirbawSmVUOWXlsRxxQXl6LmCpdUblgxgSkDIqKnhzba2SjRTI/A5Rw==",
       "dev": true,
       "license": "MIT",
       "engines": {
@@ -161,32 +161,19 @@
       }
     },
     "node_modules/@eslint/plugin-kit": {
-      "version": "0.3.2",
-      "resolved": "https://registry.npmjs.org/@eslint/plugin-kit/-/plugin-kit-0.3.2.tgz",
-      "integrity": "sha512-4SaFZCNfJqvk/kenHpI8xvN42DMaoycy4PzKc5otHxRswww1kAt82OlBuwRVLofCACCTZEcla2Ydxv8scMXaTg==",
+      "version": "0.3.5",
+      "resolved": "https://registry.npmjs.org/@eslint/plugin-kit/-/plugin-kit-0.3.5.tgz",
+      "integrity": "sha512-Z5kJ+wU3oA7MMIqVR9tyZRtjYPr4OC004Q4Rw7pgOKUOKkJfZ3O24nz3WYfGRpMDNmcOi3TwQOmgm7B7Tpii0w==",
       "dev": true,
       "license": "Apache-2.0",
       "dependencies": {
-        "@eslint/core": "^0.15.0",
+        "@eslint/core": "^0.15.2",
         "levn": "^0.4.1"
       },
       "engines": {
         "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
       }
     },
-    "node_modules/@eslint/plugin-kit/node_modules/@eslint/core": {
-      "version": "0.15.0",
-      "resolved": "https://registry.npmjs.org/@eslint/core/-/core-0.15.0.tgz",
-      "integrity": "sha512-b7ePw78tEWWkpgZCDYkbqDOP8dmM6qe+AOC6iuJqlq1R/0ahMAeH3qynpnqKFGkMltrp44ohV4ubGyvLX28tzw==",
-      "dev": true,
-      "license": "Apache-2.0",
-      "dependencies": {
-        "@types/json-schema": "^7.0.15"
-      },
-      "engines": {
-        "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
-      }
-    },
     "node_modules/@humanfs/core": {
       "version": "0.19.1",
       "resolved": "https://registry.npmjs.org/@humanfs/core/-/core-0.19.1.tgz",
@@ -292,13 +279,13 @@
       "license": "MIT"
     },
     "node_modules/@types/node": {
-      "version": "24.0.3",
-      "resolved": "https://registry.npmjs.org/@types/node/-/node-24.0.3.tgz",
-      "integrity": "sha512-R4I/kzCYAdRLzfiCabn9hxWfbuHS573x+r0dJMkkzThEa7pbrcDWK+9zu3e7aBOouf+rQAciqPFMnxwr0aWgKg==",
+      "version": "24.3.0",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-24.3.0.tgz",
+      "integrity": "sha512-aPTXCrfwnDLj4VvXrm+UUCQjNEvJgNA8s5F1cvwQU+3KNltTOkBm1j30uNLyqqPNe7gE3KFzImYoZEfLhp4Yow==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
-        "undici-types": "~7.8.0"
+        "undici-types": "~7.10.0"
       }
     },
     "node_modules/@types/unist": {
@@ -484,9 +471,9 @@
       }
     },
     "node_modules/css-selector-parser": {
-      "version": "3.1.2",
-      "resolved": "https://registry.npmjs.org/css-selector-parser/-/css-selector-parser-3.1.2.tgz",
-      "integrity": "sha512-WfUcL99xWDs7b3eZPoRszWVfbNo8ErCF15PTvVROjkShGlAfjIkG6hlfj/sl6/rfo5Q9x9ryJ3VqVnAZDA+gcw==",
+      "version": "3.1.3",
+      "resolved": "https://registry.npmjs.org/css-selector-parser/-/css-selector-parser-3.1.3.tgz",
+      "integrity": "sha512-gJMigczVZqYAk0hPVzx/M4Hm1D9QOtqkdQk9005TNzDIUGzo5cnHEDiKUT7jGPximL/oYb+LIitcHFQ4aKupxg==",
       "funding": [
         {
           "type": "github",
@@ -517,9 +504,9 @@
       }
     },
     "node_modules/decode-named-character-reference": {
-      "version": "1.1.0",
-      "resolved": "https://registry.npmjs.org/decode-named-character-reference/-/decode-named-character-reference-1.1.0.tgz",
-      "integrity": "sha512-Wy+JTSbFThEOXQIR2L6mxJvEs+veIzpmqD7ynWxMXGpnk3smkHQOp6forLdHsKpAMW9iJpaBBIxz285t1n1C3w==",
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/decode-named-character-reference/-/decode-named-character-reference-1.2.0.tgz",
+      "integrity": "sha512-c6fcElNV6ShtZXmsgNgFFV5tVX2PaV4g+MOAkb8eXHvn6sryJBrZa9r0zV6+dtTyoCKxtDy5tyQ5ZwQuidtd+Q==",
       "license": "MIT",
       "dependencies": {
         "character-entities": "^2.0.0"
@@ -572,20 +559,20 @@
       }
     },
     "node_modules/eslint": {
-      "version": "9.29.0",
-      "resolved": "https://registry.npmjs.org/eslint/-/eslint-9.29.0.tgz",
-      "integrity": "sha512-GsGizj2Y1rCWDu6XoEekL3RLilp0voSePurjZIkxL3wlm5o5EC9VpgaP7lrCvjnkuLvzFBQWB3vWB3K5KQTveQ==",
+      "version": "9.34.0",
+      "resolved": "https://registry.npmjs.org/eslint/-/eslint-9.34.0.tgz",
+      "integrity": "sha512-RNCHRX5EwdrESy3Jc9o8ie8Bog+PeYvvSR8sDGoZxNFTvZ4dlxUB3WzQ3bQMztFrSRODGrLLj8g6OFuGY/aiQg==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
         "@eslint-community/eslint-utils": "^4.2.0",
         "@eslint-community/regexpp": "^4.12.1",
-        "@eslint/config-array": "^0.20.1",
-        "@eslint/config-helpers": "^0.2.1",
-        "@eslint/core": "^0.14.0",
+        "@eslint/config-array": "^0.21.0",
+        "@eslint/config-helpers": "^0.3.1",
+        "@eslint/core": "^0.15.2",
         "@eslint/eslintrc": "^3.3.1",
-        "@eslint/js": "9.29.0",
-        "@eslint/plugin-kit": "^0.3.1",
+        "@eslint/js": "9.34.0",
+        "@eslint/plugin-kit": "^0.3.5",
         "@humanfs/node": "^0.16.6",
         "@humanwhocodes/module-importer": "^1.0.1",
         "@humanwhocodes/retry": "^0.4.2",
@@ -1662,9 +1649,9 @@
       }
     },
     "node_modules/prettier": {
-      "version": "3.5.3",
-      "resolved": "https://registry.npmjs.org/prettier/-/prettier-3.5.3.tgz",
-      "integrity": "sha512-QQtaxnoDJeAkDvDKWCLiwIXkTgRhwYDEQCghU9Z6q03iyek/rxRh/2lC3HB7P8sWT2xC/y5JDctPLBIGzHKbhw==",
+      "version": "3.6.2",
+      "resolved": "https://registry.npmjs.org/prettier/-/prettier-3.6.2.tgz",
+      "integrity": "sha512-I7AIg5boAr5R0FFtJ6rCfD+LFsWHp81dolrFD8S79U9tb8Az2nGrJncnMSnys+bpQJfRUzqs9hnA81OAA3hCuQ==",
       "dev": true,
       "license": "MIT",
       "bin": {
@@ -1801,9 +1788,9 @@
       }
     },
     "node_modules/undici-types": {
-      "version": "7.8.0",
-      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.8.0.tgz",
-      "integrity": "sha512-9UJ2xGDvQ43tYyVMpuHlsgApydB8ZKfVYTsLDhXkFL/6gfkp+U8xTGdh8pMJv1SpZna0zxG1DwsKZsreLbXBxw==",
+      "version": "7.10.0",
+      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.10.0.tgz",
+      "integrity": "sha512-t5Fy/nfn+14LuOc2KNYg75vZqClpAiqscVvMygNnlsHBFpSXdJaYtXMcdNLpl/Qvc3P2cB3s6lOV51nqsFq4ag==",
       "dev": true,
       "license": "MIT"
     },
@@ -1938,9 +1925,9 @@
       }
     },
     "node_modules/vfile-message": {
-      "version": "4.0.2",
-      "resolved": "https://registry.npmjs.org/vfile-message/-/vfile-message-4.0.2.tgz",
-      "integrity": "sha512-jRDZ1IMLttGj41KcZvlrYAaI3CfqpLpfpf+Mfig13viT6NKvRzWZ+lXz0Y5D60w6uJIBAOGq9mSHf0gktF0duw==",
+      "version": "4.0.3",
+      "resolved": "https://registry.npmjs.org/vfile-message/-/vfile-message-4.0.3.tgz",
+      "integrity": "sha512-QTHzsGd1EhbZs4AsQ20JX1rC3cOlt/IWJruk893DfLRr57lcnOeMaWG4K0JrRta4mIJZKth2Au3mM3u03/JWKw==",
       "license": "MIT",
       "dependencies": {
         "@types/unist": "^3.0.0",
diff --git a/package.json b/package.json
index 76ce735..697c197 100644
--- a/package.json
+++ b/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"
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 4a87277..01620e5 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -28,17 +28,17 @@ importers:
         version: 5.0.0
     devDependencies:
       '@eslint/js':
-        specifier: ^9.29.0
-        version: 9.29.0
+        specifier: ^9.34.0
+        version: 9.34.0
       '@types/node':
-        specifier: ^24.0.3
-        version: 24.0.3
+        specifier: ^24.3.0
+        version: 24.3.0
       eslint:
-        specifier: ^9.29.0
-        version: 9.29.0
+        specifier: ^9.34.0
+        version: 9.34.0
       prettier:
-        specifier: ^3.5.3
-        version: 3.5.3
+        specifier: ^3.6.2
+        version: 3.6.2
 
 packages:
 
@@ -52,36 +52,32 @@ packages:
     resolution: {integrity: sha512-CCZCDJuduB9OUkFkY2IgppNZMi2lBQgD2qzwXkEia16cge2pijY/aXi96CJMquDMn3nJdlPV1A5KrJEXwfLNzQ==}
     engines: {node: ^12.0.0 || ^14.0.0 || >=16.0.0}
 
-  '@eslint/config-array@0.20.1':
-    resolution: {integrity: sha512-OL0RJzC/CBzli0DrrR31qzj6d6i6Mm3HByuhflhl4LOBiWxN+3i6/t/ZQQNii4tjksXi8r2CRW1wMpWA2ULUEw==}
+  '@eslint/config-array@0.21.0':
+    resolution: {integrity: sha512-ENIdc4iLu0d93HeYirvKmrzshzofPw6VkZRKQGe9Nv46ZnWUzcF1xV01dcvEg/1wXUR61OmmlSfyeyO7EvjLxQ==}
     engines: {node: ^18.18.0 || ^20.9.0 || >=21.1.0}
 
-  '@eslint/config-helpers@0.2.3':
-    resolution: {integrity: sha512-u180qk2Um1le4yf0ruXH3PYFeEZeYC3p/4wCTKrr2U1CmGdzGi3KtY0nuPDH48UJxlKCC5RDzbcbh4X0XlqgHg==}
+  '@eslint/config-helpers@0.3.1':
+    resolution: {integrity: sha512-xR93k9WhrDYpXHORXpxVL5oHj3Era7wo6k/Wd8/IsQNnZUTzkGS29lyn3nAT05v6ltUuTFVCCYDEGfy2Or/sPA==}
     engines: {node: ^18.18.0 || ^20.9.0 || >=21.1.0}
 
-  '@eslint/core@0.14.0':
-    resolution: {integrity: sha512-qIbV0/JZr7iSDjqAc60IqbLdsj9GDt16xQtWD+B78d/HAlvysGdZZ6rpJHGAc2T0FQx1X6thsSPdnoiGKdNtdg==}
-    engines: {node: ^18.18.0 || ^20.9.0 || >=21.1.0}
-
-  '@eslint/core@0.15.0':
-    resolution: {integrity: sha512-b7ePw78tEWWkpgZCDYkbqDOP8dmM6qe+AOC6iuJqlq1R/0ahMAeH3qynpnqKFGkMltrp44ohV4ubGyvLX28tzw==}
+  '@eslint/core@0.15.2':
+    resolution: {integrity: sha512-78Md3/Rrxh83gCxoUc0EiciuOHsIITzLy53m3d9UyiW8y9Dj2D29FeETqyKA+BRK76tnTp6RXWb3pCay8Oyomg==}
     engines: {node: ^18.18.0 || ^20.9.0 || >=21.1.0}
 
   '@eslint/eslintrc@3.3.1':
     resolution: {integrity: sha512-gtF186CXhIl1p4pJNGZw8Yc6RlshoePRvE0X91oPGb3vZ8pM3qOS9W9NGPat9LziaBV7XrJWGylNQXkGcnM3IQ==}
     engines: {node: ^18.18.0 || ^20.9.0 || >=21.1.0}
 
-  '@eslint/js@9.29.0':
-    resolution: {integrity: sha512-3PIF4cBw/y+1u2EazflInpV+lYsSG0aByVIQzAgb1m1MhHFSbqTyNqtBKHgWf/9Ykud+DhILS9EGkmekVhbKoQ==}
+  '@eslint/js@9.34.0':
+    resolution: {integrity: sha512-EoyvqQnBNsV1CWaEJ559rxXL4c8V92gxirbawSmVUOWXlsRxxQXl6LmCpdUblgxgSkDIqKnhzba2SjRTI/A5Rw==}
     engines: {node: ^18.18.0 || ^20.9.0 || >=21.1.0}
 
   '@eslint/object-schema@2.1.6':
     resolution: {integrity: sha512-RBMg5FRL0I0gs51M/guSAj5/e14VQ4tpZnQNWwuDT66P14I43ItmPfIZRhO9fUVIPOAQXU47atlywZ/czoqFPA==}
     engines: {node: ^18.18.0 || ^20.9.0 || >=21.1.0}
 
-  '@eslint/plugin-kit@0.3.2':
-    resolution: {integrity: sha512-4SaFZCNfJqvk/kenHpI8xvN42DMaoycy4PzKc5otHxRswww1kAt82OlBuwRVLofCACCTZEcla2Ydxv8scMXaTg==}
+  '@eslint/plugin-kit@0.3.5':
+    resolution: {integrity: sha512-Z5kJ+wU3oA7MMIqVR9tyZRtjYPr4OC004Q4Rw7pgOKUOKkJfZ3O24nz3WYfGRpMDNmcOi3TwQOmgm7B7Tpii0w==}
     engines: {node: ^18.18.0 || ^20.9.0 || >=21.1.0}
 
   '@humanfs/core@0.19.1':
@@ -119,8 +115,8 @@ packages:
   '@types/ms@2.1.0':
     resolution: {integrity: sha512-GsCCIZDE/p3i96vtEqx+7dBUGXrc7zeSK3wwPHIaRThS+9OhWIXRqzs4d6k1SVU8g91DrNRWxWUGhp5KXQb2VA==}
 
-  '@types/node@24.0.3':
-    resolution: {integrity: sha512-R4I/kzCYAdRLzfiCabn9hxWfbuHS573x+r0dJMkkzThEa7pbrcDWK+9zu3e7aBOouf+rQAciqPFMnxwr0aWgKg==}
+  '@types/node@24.3.0':
+    resolution: {integrity: sha512-aPTXCrfwnDLj4VvXrm+UUCQjNEvJgNA8s5F1cvwQU+3KNltTOkBm1j30uNLyqqPNe7gE3KFzImYoZEfLhp4Yow==}
 
   '@types/unist@3.0.3':
     resolution: {integrity: sha512-ko/gIFJRv177XgZsZcBwnqJN5x/Gien8qNOn0D5bQU/zAzVf9Zt3BlcUiLqhV9y4ARk0GbT3tnUiPNgnTXzc/Q==}
@@ -182,8 +178,8 @@ packages:
     resolution: {integrity: sha512-uV2QOWP2nWzsy2aMp8aRibhi9dlzF5Hgh5SHaB9OiTGEyDTiJJyx0uy51QXdyWbtAHNua4XJzUKca3OzKUd3vA==}
     engines: {node: '>= 8'}
 
-  css-selector-parser@3.1.2:
-    resolution: {integrity: sha512-WfUcL99xWDs7b3eZPoRszWVfbNo8ErCF15PTvVROjkShGlAfjIkG6hlfj/sl6/rfo5Q9x9ryJ3VqVnAZDA+gcw==}
+  css-selector-parser@3.1.3:
+    resolution: {integrity: sha512-gJMigczVZqYAk0hPVzx/M4Hm1D9QOtqkdQk9005TNzDIUGzo5cnHEDiKUT7jGPximL/oYb+LIitcHFQ4aKupxg==}
 
   debug@4.4.1:
     resolution: {integrity: sha512-KcKCqiftBJcZr++7ykoDIEwSa3XWowTfNPo92BYxjXiyYEVrUQh2aLyhxBCwww+heortUFxEJYcRzosstTEBYQ==}
@@ -194,8 +190,8 @@ packages:
       supports-color:
         optional: true
 
-  decode-named-character-reference@1.1.0:
-    resolution: {integrity: sha512-Wy+JTSbFThEOXQIR2L6mxJvEs+veIzpmqD7ynWxMXGpnk3smkHQOp6forLdHsKpAMW9iJpaBBIxz285t1n1C3w==}
+  decode-named-character-reference@1.2.0:
+    resolution: {integrity: sha512-c6fcElNV6ShtZXmsgNgFFV5tVX2PaV4g+MOAkb8eXHvn6sryJBrZa9r0zV6+dtTyoCKxtDy5tyQ5ZwQuidtd+Q==}
 
   deep-is@0.1.4:
     resolution: {integrity: sha512-oIPzksmTg4/MriiaYGO+okXDT7ztn/w3Eptv/+gSIdMdKsJo0u4CfYNFJPy+4SKMuCqGw2wxnA+URMg3t8a/bQ==}
@@ -223,8 +219,8 @@ packages:
     resolution: {integrity: sha512-Uhdk5sfqcee/9H/rCOJikYz67o0a2Tw2hGRPOG2Y1R2dg7brRe1uG0yaNQDHu+TO/uQPF/5eCapvYSmHUjt7JQ==}
     engines: {node: ^18.18.0 || ^20.9.0 || >=21.1.0}
 
-  eslint@9.29.0:
-    resolution: {integrity: sha512-GsGizj2Y1rCWDu6XoEekL3RLilp0voSePurjZIkxL3wlm5o5EC9VpgaP7lrCvjnkuLvzFBQWB3vWB3K5KQTveQ==}
+  eslint@9.34.0:
+    resolution: {integrity: sha512-RNCHRX5EwdrESy3Jc9o8ie8Bog+PeYvvSR8sDGoZxNFTvZ4dlxUB3WzQ3bQMztFrSRODGrLLj8g6OFuGY/aiQg==}
     engines: {node: ^18.18.0 || ^20.9.0 || >=21.1.0}
     hasBin: true
     peerDependencies:
@@ -467,8 +463,8 @@ packages:
     resolution: {integrity: sha512-vkcDPrRZo1QZLbn5RLGPpg/WmIQ65qoWWhcGKf/b5eplkkarX0m9z8ppCat4mlOqUsWpyNuYgO3VRyrYHSzX5g==}
     engines: {node: '>= 0.8.0'}
 
-  prettier@3.5.3:
-    resolution: {integrity: sha512-QQtaxnoDJeAkDvDKWCLiwIXkTgRhwYDEQCghU9Z6q03iyek/rxRh/2lC3HB7P8sWT2xC/y5JDctPLBIGzHKbhw==}
+  prettier@3.6.2:
+    resolution: {integrity: sha512-I7AIg5boAr5R0FFtJ6rCfD+LFsWHp81dolrFD8S79U9tb8Az2nGrJncnMSnys+bpQJfRUzqs9hnA81OAA3hCuQ==}
     engines: {node: '>=14'}
     hasBin: true
 
@@ -509,8 +505,8 @@ packages:
     resolution: {integrity: sha512-XleUoc9uwGXqjWwXaUTZAmzMcFZ5858QA2vvx1Ur5xIcixXIP+8LnFDgRplU30us6teqdlskFfu+ae4K79Ooew==}
     engines: {node: '>= 0.8.0'}
 
-  undici-types@7.8.0:
-    resolution: {integrity: sha512-9UJ2xGDvQ43tYyVMpuHlsgApydB8ZKfVYTsLDhXkFL/6gfkp+U8xTGdh8pMJv1SpZna0zxG1DwsKZsreLbXBxw==}
+  undici-types@7.10.0:
+    resolution: {integrity: sha512-t5Fy/nfn+14LuOc2KNYg75vZqClpAiqscVvMygNnlsHBFpSXdJaYtXMcdNLpl/Qvc3P2cB3s6lOV51nqsFq4ag==}
 
   unified@11.0.5:
     resolution: {integrity: sha512-xKvGhPWw3k84Qjh8bI3ZeJjqnyadK+GEFtazSfZv/rKeTkTjOJho6mFqh2SM96iIcZokxiOpg78GazTSg8+KHA==}
@@ -536,8 +532,8 @@ packages:
   uri-js@4.4.1:
     resolution: {integrity: sha512-7rKUyy33Q1yc98pQ1DAmLtwX109F7TIfWlW1Ydo8Wl1ii1SeHieeh0HHfPeL2fMXK6z0s8ecKs9frCuLJvndBg==}
 
-  vfile-message@4.0.2:
-    resolution: {integrity: sha512-jRDZ1IMLttGj41KcZvlrYAaI3CfqpLpfpf+Mfig13viT6NKvRzWZ+lXz0Y5D60w6uJIBAOGq9mSHf0gktF0duw==}
+  vfile-message@4.0.3:
+    resolution: {integrity: sha512-QTHzsGd1EhbZs4AsQ20JX1rC3cOlt/IWJruk893DfLRr57lcnOeMaWG4K0JrRta4mIJZKth2Au3mM3u03/JWKw==}
 
   vfile@6.0.3:
     resolution: {integrity: sha512-KzIbH/9tXat2u30jf+smMwFCsno4wHVdNmzFyL+T/L3UGqqk6JKfVqOFOZEpZSHADH1k40ab6NUIXZq422ov3Q==}
@@ -560,14 +556,14 @@ packages:
 
 snapshots:
 
-  '@eslint-community/eslint-utils@4.7.0(eslint@9.29.0)':
+  '@eslint-community/eslint-utils@4.7.0(eslint@9.34.0)':
     dependencies:
-      eslint: 9.29.0
+      eslint: 9.34.0
       eslint-visitor-keys: 3.4.3
 
   '@eslint-community/regexpp@4.12.1': {}
 
-  '@eslint/config-array@0.20.1':
+  '@eslint/config-array@0.21.0':
     dependencies:
       '@eslint/object-schema': 2.1.6
       debug: 4.4.1
@@ -575,13 +571,9 @@ snapshots:
     transitivePeerDependencies:
       - supports-color
 
-  '@eslint/config-helpers@0.2.3': {}
-
-  '@eslint/core@0.14.0':
-    dependencies:
-      '@types/json-schema': 7.0.15
+  '@eslint/config-helpers@0.3.1': {}
 
-  '@eslint/core@0.15.0':
+  '@eslint/core@0.15.2':
     dependencies:
       '@types/json-schema': 7.0.15
 
@@ -599,13 +591,13 @@ snapshots:
     transitivePeerDependencies:
       - supports-color
 
-  '@eslint/js@9.29.0': {}
+  '@eslint/js@9.34.0': {}
 
   '@eslint/object-schema@2.1.6': {}
 
-  '@eslint/plugin-kit@0.3.2':
+  '@eslint/plugin-kit@0.3.5':
     dependencies:
-      '@eslint/core': 0.15.0
+      '@eslint/core': 0.15.2
       levn: 0.4.1
 
   '@humanfs/core@0.19.1': {}
@@ -635,9 +627,9 @@ snapshots:
 
   '@types/ms@2.1.0': {}
 
-  '@types/node@24.0.3':
+  '@types/node@24.3.0':
     dependencies:
-      undici-types: 7.8.0
+      undici-types: 7.10.0
 
   '@types/unist@3.0.3': {}
 
@@ -694,13 +686,13 @@ snapshots:
       shebang-command: 2.0.0
       which: 2.0.2
 
-  css-selector-parser@3.1.2: {}
+  css-selector-parser@3.1.3: {}
 
   debug@4.4.1:
     dependencies:
       ms: 2.1.3
 
-  decode-named-character-reference@1.1.0:
+  decode-named-character-reference@1.2.0:
     dependencies:
       character-entities: 2.0.2
 
@@ -723,16 +715,16 @@ snapshots:
 
   eslint-visitor-keys@4.2.1: {}
 
-  eslint@9.29.0:
+  eslint@9.34.0:
     dependencies:
-      '@eslint-community/eslint-utils': 4.7.0(eslint@9.29.0)
+      '@eslint-community/eslint-utils': 4.7.0(eslint@9.34.0)
       '@eslint-community/regexpp': 4.12.1
-      '@eslint/config-array': 0.20.1
-      '@eslint/config-helpers': 0.2.3
-      '@eslint/core': 0.14.0
+      '@eslint/config-array': 0.21.0
+      '@eslint/config-helpers': 0.3.1
+      '@eslint/core': 0.15.2
       '@eslint/eslintrc': 3.3.1
-      '@eslint/js': 9.29.0
-      '@eslint/plugin-kit': 0.3.2
+      '@eslint/js': 9.34.0
+      '@eslint/plugin-kit': 0.3.5
       '@humanfs/node': 0.16.6
       '@humanwhocodes/module-importer': 1.0.1
       '@humanwhocodes/retry': 0.4.3
@@ -865,7 +857,7 @@ snapshots:
     dependencies:
       '@types/mdast': 4.0.4
       '@types/unist': 3.0.3
-      decode-named-character-reference: 1.1.0
+      decode-named-character-reference: 1.2.0
       devlop: 1.1.0
       mdast-util-to-string: 4.0.0
       micromark: 4.0.2
@@ -901,7 +893,7 @@ snapshots:
 
   micromark-core-commonmark@2.0.3:
     dependencies:
-      decode-named-character-reference: 1.1.0
+      decode-named-character-reference: 1.2.0
       devlop: 1.1.0
       micromark-factory-destination: 2.0.1
       micromark-factory-label: 2.0.1
@@ -976,7 +968,7 @@ snapshots:
 
   micromark-util-decode-string@2.0.1:
     dependencies:
-      decode-named-character-reference: 1.1.0
+      decode-named-character-reference: 1.2.0
       micromark-util-character: 2.1.1
       micromark-util-decode-numeric-character-reference: 2.0.2
       micromark-util-symbol: 2.0.1
@@ -1014,7 +1006,7 @@ snapshots:
     dependencies:
       '@types/debug': 4.1.12
       debug: 4.4.1
-      decode-named-character-reference: 1.1.0
+      decode-named-character-reference: 1.2.0
       devlop: 1.1.0
       micromark-core-commonmark: 2.0.3
       micromark-factory-space: 2.0.1
@@ -1071,7 +1063,7 @@ snapshots:
 
   prelude-ls@1.2.1: {}
 
-  prettier@3.5.3: {}
+  prettier@3.6.2: {}
 
   punycode@2.3.1: {}
 
@@ -1110,7 +1102,7 @@ snapshots:
     dependencies:
       prelude-ls: 1.2.1
 
-  undici-types@7.8.0: {}
+  undici-types@7.10.0: {}
 
   unified@11.0.5:
     dependencies:
@@ -1135,7 +1127,7 @@ snapshots:
   unist-util-select@5.1.0:
     dependencies:
       '@types/unist': 3.0.3
-      css-selector-parser: 3.1.2
+      css-selector-parser: 3.1.3
       devlop: 1.1.0
       nth-check: 2.1.1
       zwitch: 2.0.4
@@ -1159,7 +1151,7 @@ snapshots:
     dependencies:
       punycode: 2.3.1
 
-  vfile-message@4.0.2:
+  vfile-message@4.0.3:
     dependencies:
       '@types/unist': 3.0.3
       unist-util-stringify-position: 4.0.0
@@ -1167,7 +1159,7 @@ snapshots:
   vfile@6.0.3:
     dependencies:
       '@types/unist': 3.0.3
-      vfile-message: 4.0.2
+      vfile-message: 4.0.3
 
   which@2.0.2:
     dependencies:
diff --git a/test/test-cli.js b/test/test-cli.js
index be59fd5..d29501c 100644
--- a/test/test-cli.js
+++ b/test/test-cli.js
@@ -275,6 +275,27 @@ async function runTests() {
     );
   });
 
+  await test('CLI explode handles # inside code blocks', async () => {
+    const bugFile = path.join(testDir, 'truncation.md');
+    const bugContent = `# Bug Doc\n\n## Section\n\nBefore code block.\n\n\`\`\`bash\n# inside code block\necho done\n\`\`\`\n\nAfter code block.\n`;
+    await fs.writeFile(bugFile, bugContent, 'utf-8');
+
+    const outputDir = path.join(testDir, 'truncation-exploded');
+    const result = await runCLI(['explode', bugFile, outputDir]);
+
+    assert(result.code === 0, 'Explode should succeed');
+    const sectionPath = path.join(outputDir, 'section.md');
+    const sectionContent = await fs.readFile(sectionPath, 'utf-8');
+    assert(
+      sectionContent.includes('# inside code block'),
+      'Should keep code block comment'
+    );
+    assert(
+      sectionContent.includes('After code block.'),
+      'Should include text after code block'
+    );
+  });
+
   await test('CLI explode error handling', async () => {
     // Test with non-existent file
     const result = await runCLI(['explode', 'non-existent.md', testDir]);
diff --git a/test/test.js b/test/test.js
index d9415ae..8b3e40e 100644
--- a/test/test.js
+++ b/test/test.js
@@ -4,11 +4,11 @@
  * Basic tests for markdown-tree-parser
  */
 
-import { MarkdownTreeParser, createParser, extractSection } from '../index.js';
-import { MarkdownCLI } from '../bin/md-tree.js'; // Added for checkLinks test
 import fs from 'node:fs/promises';
 import path from 'node:path';
 import { fileURLToPath } from 'node:url';
+import { MarkdownTreeParser, createParser, extractSection } from '../index.js';
+import { MarkdownCLI } from '../bin/md-tree.js'; // Added for checkLinks test
 
 const __dirname = path.dirname(fileURLToPath(import.meta.url));