Update file references.

The VERSION file has moved in preparation for the repo split. Update the
build scripts accordingly.
Fix paths to autoload.php file.
Fix cakephp composer.json

The file path prefix is not needed as the core classes all start with
Cake\ which is the same as the directory name. With the prefix composer
cannot locate classes correctly.
Remove Cake autoloader.

We should be relying on composer now.
Move application code down a level.

This is required so that composer's psr-0 autoloader can find code in
the App\ namespace. I decided to not move tmp, webroot and vendor as
they never contain application PHP code.
Add some useful defaults to the gitignore.

Ignore files that generally don't belong in VCS.
Add an install script.

This install script takes care of copying the default config file into
its proper place, and changing permissions on the tmp dir if required.
This will help ease use of the app skeleton. It also gives a place for
application developers to provide their own install script if they want.