Fix & enable "JS Chrome app (using Polymer)" + fix other templates

@devoncarew: just a nominal review, there is not much actual app code that's changed.

I'll submit a follow-up PR, which will add a warning to run the CSP Fixer after creating a "JS Chrome app (using Polymer)" and finally move it from under a flag.
To be honest, I wasn't sure myself, switched back and forth 5 times. I just wanted to settle on a unified naming. I've just talked to @sowbug, and the consensus is that historically index.html is ok, although it's a misnomer. And main.js for the main script. I'll rename.