Good questions.
Calypso isn’t an update to WordPress proper, it’s a new dashboard for logged-in users on WordPress.com, a free blogging service provided by Automattic. Calypso is designed to provide a new interface for creating and editing your own posts and pages, reading other blogs you are subscribed to, and managing all the blogs for which you are an admin. It is also, through the magic of JavaScript, what powers the WP desktop and mobile apps. And it can be used to manage both WordPress.com blogs and self-hosted .org installs connected via the JetPack plugin.
That’s a lot, and it’s a big update for WordPress.com/JetPack users, but it’s not replacing the standard PHP WordPress application. Calypso does all that it does by communicating with a WordPress installation over a new REST API, which allows external apps to communicate with WordPress. To work, it still depends on WordPress the PHP app to be installed and running as usual.
Which is all to say: developing plugins/themes in PHP for WordPress is not likely to go away anytime soon. And WordPress proper will still need to use a MySQL database as it does now. What is new is that now external apps, such as calypso, can be connected to WordPress and provide new kinds of functionality via the API. Those apps could be written in JavaScript (or really any language that can interface with the API), but they will all still need to have a good old fashioned PHP WordPress installation with MySQL running behind the scenes.
Hope that makes sense and helps clarify things. Welcome to the WordPress community.
