Reorganized the code by functional modules

I have reorganized the code into modules, hopefully improving cohesion:

```yaml
Application\
    Cli\ # cli commands
    # container stuff
Model\ # Repository, File, …
Module\
    Markdown\
        Step\  # LoadMarkdownFiles, RenderMarkdown, …
        Model\ # MarkdownFile
    Bower\
    Template\
    Config\
    …
Deployer.php
Generator.php
```

Hopefully the organization in modules is much clearer. Want to add support for RestructuredText? Just add a module…

I wish also to work on installing modules on demand. For example the Bower module requires a PHP lib with *a lot* of dependencies. If this module could be installed on demand (per the configuration in Couscous.yml) that would be awesome. I'd love to be able to offer optional modules (RST, Textile, Bower, Less, whatever, …)