I'm well used to e.g. the Rails Asset Pipeline (Sprockets). Does Webstorm offer something similar out of the box?
What do i mean: A 'tool' that collects all .js files in a given order and injects them into my index.html + another configuration for deployment that includes minify etc.
I would consider using Grunt build tool for that, which gets quite popular with time. There's no support for Grunt so far, but you can run it using File Watchers (automatically) or External Tools (manually) features. Please take a look at our blog post regarding file watchers: http://blog.jetbrains.com/webide/2013/03/file-watchers-in-webstormphpstorm-6-a-k-a-background-tasks/