I think you're on the right track with there being a conflict.
Here's a plunk that demonstrates the issue: http://plnkr.co/edit/2sR7F2W0QGJAcXxgez14
In the plunk, if JQuery is still reference by $ and you add the reference to Prototype, you see that Footable stops working. If you use the JQuery NoConflict and then use that instead of $, Footable starts work as expected again.
Here's where I define the scripts:
<head>
<link data-require="bootstrap-css@3.0.2" data-semver="3.0.2" rel="stylesheet" href="//netdna.bootstrapcdn.com/bootstrap/3.0.2/css/bootstrap.min.css" />
<link data-require="jqueryui@*" data-semver="1.10.0" rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/jqueryui/1.10.0/css/smoothness/jquery-ui-1.10.0.custom.min.css" />
<link rel="stylesheet" href="footable.core.css" />
<script data-require="jquery@*" data-semver="2.0.3" src="http://code.jquery.com/jquery-2.0.3.min.js"></script>
<script data-require="jqueryui@*" data-semver="1.10.0" src="//cdnjs.cloudflare.com/ajax/libs/jqueryui/1.10.0/jquery-ui.js"></script>
<script data-require="bootstrap@*" data-semver="3.0.2" src="//netdna.bootstrapcdn.com/bootstrap/3.0.2/js/bootstrap.min.js"></script>
<script>var $j = jQuery.noConflict();</script>
<script src="footable.js"></script>
<script src="footable.filter.js"></script>
<script data-require="prototype@*" data-semver="1.7.1+0" src="//cdnjs.cloudflare.com/ajax/libs/prototype/1.7.1.0/prototype.js"></script>
</head>
Then when I use JQuery and Call footable():
$j(function() {
window.footable.options.filter.filterFunction = function(index) {
var $t = $j(this),
$table = $t.parents('table:first'),
filter = $table.data('current-filter').toUpperCase(),
columns = $t.find('td');
var regEx = new RegExp("\\b" + filter + "\\b");
var result = false;
for (i = 0; i < columns.length; i++) {
var text = $j(columns[i]).text();
result = regEx.test(text.toUpperCase());
if (result === true)
break;
if (!$table.data('filter-text-only')) {
text = $j(columns[i]).data("value");
if (text)
result = regEx.test(text.toString().toUpperCase());
}
if (result === true)
break;
}
return result;
};
$j('table').footable().bind('footable_filtering', function(e) {
var selected = $j('.filter-status').find(':selected').text();
if (selected && selected.length > 0) {
e.filter += (e.filter && e.filter.length > 0) ? ' ' + selected : selected;
e.clear = !e.filter;
}
});
}
If you want to continue to use $ jquery you could do something like: (jQuery and prototype.js conflict, how to keep jQuery as $?)
(function($) {
$('table').footable();
})(jQuery);