Made changes to module.txt & theme.txt files of all my stuff...

...so the modules don't light up red on dashboard & also to make modules actually work.
The boostrap framework is properly separated now, needs only linking to cdn & versioning in the resource manifest file.
New theme is fully working... theme created by documentation... inherited from bootstrap theme, picked up fluid responsive layout instead default.
The theme properly links to jQuery & Bootstrap modules now.

Lesson learned: take module.txt & theme.txt very seriously...
added modified user.csthml to theme - added register button next to sign up at the top nav bar