astroid: 0.11.1 -> 0.13

Couple of things were updated to make this work.

1. webkitgtk24x-gtk3 that is marked unsafe has been replaced with
   webkitgtk (2.20.*) as astroid has recently indicated that [>= 2.20
   is
   acceptable](https://github.com/astroidmail/astroid/commit/48ce7e3010d2ee99ccba18798b4f5333867bd1a2)
2. protobuf built input was added to satisfy requirements
3. astroid was not functional at all without proper icons so gnome3.defaultIconTheme
   were added to buildInputs
4. By default, astroid will use `gvim` as a setting for the embedded
   editor, however that didn't work well with nixpkgs. vim is now
   bundled with astroid by default. This setting can be overridden
   by the user in astroid's config file.