Putting in new-line characters in the empty lines has fixed copy+paste and made the min-height css unnecessary.

static/index.html

@@ -8,6 +8,6 @@
     <h2>Input org-mode source:</h2>
     <textarea id="org-input" rows="24" cols="80"></textarea>
     <hr/>
-    <div id="parse-output" class="code_block" style="padding-left: calc(2ch + 10px); counter-set: code_line_number 0;"><code>This is line 1</code><code class="highlighted">This is line 2</code><code>This is line 3</code></div>
+    <div id="parse-output" class="code_block" style="counter-set: code_line_number 0;"></div>
   </body>
 </html>