You seem to have two copies of most of the runtime scripts inside scripts.js. Something has gone wrong on your server!
The Numbas compiler collects together all the .js files it can find inside the `runtime` directory and the theme directory, which is `themes/default` if you use the default theme. If you're using a different theme, check that you don't have another copy of the Numbas compiler files inside it.
Can you run `git status` inside your Numbas compiler directory
(should be /srv/numbas/compiler if you followed the installation
instructions exactly), and tell me what it produces?