configure allowed content in Drupal 7

Hi! I'm using Drupal 7 with CKEditor 4.2 and want to allow certain custom content. So I added the following config to sites/all/modules/ckeditor/ckeditor/config.js:

CKEDITOR.editorConfig = function( config ) {
  ...
  config.extraAllowedContent = 'pre (!command-line); span (!command, comment, output); em';
};

Still, content such as the following which I enter through CKEditor in plain-text mode is cleaned/removed:

<pre class="command-line">
    <span class="command"> ... <em>...</em></span>
    <span class="comment">...</span>
    <span class="output">...</span>
</pre>

Since I don't really understand the difference, I also tried using allowedContent instead of extraAllowedContent without any effect. In either case the format is cleaned. Maybe my configuration is being ignored by CKEditor or it's wrong in itself? Any advice would be appreciated.