A Gold Star ? Ok
I had a similar problem. Your problem is not jQuery.noConflict(); neither is it prototype js but rather that you did not add everything there is to to the noconflict
1 - Fist of all align every other librairie that does not use jquery ex:
<script src="js/scriptaculous/lib/prototype.js" type="text/javascript"></script>
<script src="js/scriptaculous/src/scriptaculous.js" type="text/javascript"></script>
<script language="javascript" src="js/protoplasm/protoplasm.js"></script>
<script>
Protoplasm.use('rte').transform('textarea.richeditor');
</script>
2 - After that insert your jquery file and directly followed up with noconflict before any other library or code that uses jquery
<script type="text/javascript" src="js/jquery/jquery-2.1.1.min.js"></script>
<script type="text/javascript">
$.noConflict();
</script>
3 - And MOST IMPORTANTLY and this is where you are missing the point
Open each and every other javascript code you have as js that uses jquery like Bootstrap.min.js or app.js and if you find jquery inside, then put on top of the code, at the very begin of the file (ex at the begining of bootstrap.min.js) the following code
jQuery( document ).ready(function( $ ) {
// Code that uses jQuery's $ can follow here.
///////////////////////////////////////////////////////////////////////////////
4- At the very end of the code (ex at the end of bootstrap.min.js) put the following code
///////////////////////////////////////////////////////////////////////////////
});
5 - Put also every other code using jquery in your page between another
jQuery( document ).ready(function( $ ) {
// Code that uses jQuery's $ can follow here.
///////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////
});
As you can see jquery noconflict alone is not enough. You really have to add those codes everywhere jquery is being used even in external file if you do not want any interference
You may face some few error in controls.js with firebug but all your codes will work. Even when you remove control.js, as long as scriptaculous.js is on your page, Firebug will always give you and error like TypeError: this.element is null controls.js but all your code will be working perfectly.
Please, do not forget the Gold star. Thanks