How can I output custom html inlcuding js files I'm trying to output a JS based frontend app through one controller action.

To achieve this I need this action to output a very specific html layout, inlcuding some js files.

As far as i know I can return a symfony response object to bypass drupals render stack, inlcuding themeing mechanism. 
But how to deal with the js files that should be included? Right now they are located inside my module folder, and I definitly don't want to link to this location inside my custom html output.
If i understand u want to output custom HTML for module, for smoething like this best practice is to preprocess output with twig template, in twig u can generate custom HTML for your needs and of course attach js and css with libraries.
See: Theme system overview.