Add skeleton migration

Resolves https://github.com/cakephp/upgrade/issues/33 and https://github.com/cakephp/upgrade/issues/32

It uses the root composer.json to determine the base path of the application.
Should not be used for plugins.

Also
- added plugin dirs to exclude (logically, those can be run individually if desired)
- some gitignore additions
- fixed some minor issues
That is the one file that will be in the root directory. A little trick to find it. Other than that its not possible to make the current way of running files work with the root directory it seems.