Just the javascript and everything else not visible
But as I said, and I know not what I say, large sections of the main page could remain as they are with minimal added class=row wrappers and class=table-responsive around any tables to prevent them collapsing. I would imagine that the LHS nav section is governed by a similar set of rules for the whole nav section, and that would take some work to modifiy, but once that pattern was worked out it could be re-applied to most pages. So working on the LHS nav is one job, applying row and table-responsive class divs is another and not much else needs to be changed (says I not having even done a view-source on any page!) Compared to the whmcs structural layout mess, Blesta looks like it could be delightfully consistent to modify once the right approach was worked out.