<base href="[[++site_url]]"> <!--20150826: Not sure what this calls or does?-->
This is primarily for FURLs. It provides the base url for the site which is commonly what would be written out in any link on a non-MODX or static site such as
http://domain.com/
If you'll notice, all the links shown in the example code in this thread don't show the
http://domain.com portion of the link. The <base href="[[++site_url]]"> does this for us throughout the site for any link to files or images in the filesystem. It's quite handy.
As Bruno showed above (see, no
http://domain.com/):
<link rel="stylesheet" href="assets/bootstrap/css/bootstrap.min.css">
<script src="assets/bootstrap/js/bootstrap.min.js"></script>
Read this:
https://rtfm.modx.com/revolution/2.x/administering-your-site/using-friendly-urls
It is better to use the CDN version of Bootstrap than the files you've downloaded from Bootstrap. Including them is no different than including files uploaded to whatever path in the filesystem, except for the fact that you'll need to use the full url from the CDN rather than the shortened path that you can with site files as Bruno showed above (with the base url).
Additionally, when debugging CSS not applying to your elements... you are using your browser's inspect tool, right?
Can you see that the CSS file (either in the resource or in a file) is even loading? Chrome's inspector is better at showing all the http requests and their status than Firefox. And if the file is readable, when you inspect the element that needs to be affected by your styles, which CSS selectors are applying? Just because your CSS doesn't apply visually, doesn't mean the file is not being read. It could be that the CSS selector is incorrect, or your trying to apply a value to the wrong selector, or the value is invalid for that particular property or element, etc. Inspecting is your friend, use it whenever you want to see what's actually applying to your elements.
FWIW, all the packages that you downloaded and installed from Package Management aren't going to mess with your site, but if you're learning Bootstrap and MODX at the same time there will be some chunks and perhaps TVs, snippet calls, etc. in there that you can use as examples. I'd keep them around for a bit to reference if you're struggling much with MODX and Bootstrap. For the menus alone, what is coded up and working from those packages can come in quite handy.