Looking at the browsers javascript object graph it seems to me that mootools is not used anywhere (anymore). I also tried some search terms on the codebase and could not find any uses of the mootools library.
I removed mootools from common.inc.php and did some basic UI tests, where everything worked fine. I come to the conclusion that mootools is not used anymore and suggests its removal and the continued use of jQuery, which pretty much does the same things.
Mootools is still used:
- /setup
- js/functions.js (look for "BLOB repository")
- maybe import progress bar
but we are converting to jQuery.