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unset($doc->_scripts[JUri::base(true)'/path/to/file.js'])

is mostly how to do it, some scripts might add the full url and some might not.

So here is a better way to go about it if you want everything removed.

$doc->_scripts = array();
//if you need to re include libraries
JHtml::_('jquery.framework');
JHtml::_('behavior.framework');

//if the array trick does not work you could do
for($i=0;$i<count($doc->_scripts);$i++){
   //in here you could stop it from removing specific files by looking for specific file names
   $get_file = explode('/',$doc->_scripts[$i]);
   $get_file = end($get_file);

   //many more ways to do this, chains of if statements can get messy
   switch($get_file){
      case 'jquery.js':
      case 'boostrap.js';
         break;
      default:
         unset($doc->_scripts[$i]);
         break;
   }
}