General developer forum

You didn't specify which Moodle version you're using so I'll assume it's a 3.X version.

clean.js is the correct file and the functions are _cleanHTML() and _cleanPasteHTML()

In order for any changes to take hold, you'll need to compile the file using shifter and then purge cache.

However, this isn't the recommended choice, because this is a core change, meaning that in the next version update your changes will be overridden.

I had the same issue and found the solution in overriding the original code through an added script.

Here's an example of what I did for one of the functions.

function EditorAddon() {}
EditorAddon.prototype = {
    _cleanHTML: function(content) {
        var rules = [
            // Put here all the rules from the original function.
            // Add here all your new rules.
        ];
        return this._filterContentWithRules(content, rules);
    }
};
// This line will replace the original function with the new one.
Y.Base.mix(Y.M.editor_atto.Editor, [EditorAddon], true, 1);

I don't know if this is the best solution but it worked well for me so far.