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"From scratch" is relative but I guess you mean just without a CMS.

My favorite stack for the last year or two has been CoffeeScript (and now ToffeeScript which is even better) and Node.js with good old ExpressJS.

I also think AngularJS is probably the best starting point for many web applications these days. So actually most of your efforts would be with AngularJS since the front end is often going to be much more complex than the back end.

The most convenient way to store data I think is in JSON files or with MongoDB or RethinkDB. Or maybe better take a look at a CRUD framework like https://npmjs.org/package/auto-crud . Again, 'from scratch' is a relative term and actually the farther you stay away from that the better probably. But of course no one, including me, can learn everything, so you have to pick a set of tools and become comfortable with them and that is subjective.

Node has the most advantageous module/package system out there (npm) with the support for semantic versioning and the sheer number of packages available in the registry (more than 41,000 at the moment).

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