Clean up the root directory a bit

Remove dead things, move specific things, rename things.

- Drop the unmaintained Vagrantfile
- Drop the SSL cert
- Drop MANIFEST.in for setuptools_git (Close #1329)
- Move install docs into docs
- Move config files into config

karma.config.js → h/static/scripts/karma.config.js

 // Karma configuration
-// Generated on Mon Jul 14 2014 14:06:50 GMT+0200 (CEST)
 var path = require('path');
 
 module.exports = function(config) {
   config.set({
 
     // base path that will be used to resolve all patterns (eg. files, exclude)
-    basePath: 'h/static/scripts',
+    basePath: './',
 
 
     // frameworks to use