Isolate the visible part of an application inside a public folder.

`index.php` and `install.php` are specialized for bootstrapping the
application.

This is essential when you have to hide files like `composer.json` or
`phinx.yml` containing sensitive information.

Although this will wipe Minion call from `index.php`. At this point, we should have a dedicated script for it anyway in the project root.
My mistake, I took the comments from `3.3/master` as at first I thought it wouldn't make sense to load minion from there. But if it has to be done, it would be in another commit.

I just rebased this commit.