How to integrate Bootstrap template with typo3, since bootstrap depends on JQuery and JQuery is in conflict with scriptaculous? I'm not quite sure if typo3 is the one using scriptaculous or is someone of the extensions i'm using.
If you stumbled upon this question: Current versions (7.6.x, 8.x) don't use scriptaculous and jQuery is only loaded in backend by default. If using jQuery or JS in backend, please use requireJS. Take a look at https://scripting-base.de/blog/requirejs-backend-1.html
For the frontend, use whatever you like as there is all done by you.