I have just upgraded from MX 5.00 beta 8 to 5.00 and the bootstrap CSS directories runtime\mxclientsystem\mxui\ui\bootstrap and runtime\mxclientsystem\mxui\ui\bootstrap-rlt seem to be missing. Is this an error or something to do with the new layout templates.
I had the same problem. The bootstrap.min.css is in this directory: deployment\web\lib\bootstrap\css.
Change this in your index.html in your theme package.