Minor gitignore cleanup and .dist config files

This PR addresses a few git issues which should improve further development.

* Added gitignore for all app/var/data/packages/*.json files except for these which comes with the cms
Currently every installed package creates it's own json file and git isn't sure what to do about them.

* Moved default config files to .dist and added a condition to Engine/Config::_getConfiguration() which creates the (gitignored) php files on the fly.
Currently the php config files are modifiable and git isn't sure what to do about them too.