Fix column layouts to be correct
Ensure all base Hybrid Core features are correctly configured
Move header tweak into correct file. Removing unwanted extra include file.

@neilberry001 not sure why we had this modify-wp-header.php file. Let's
try and keep the includes as clean as possible.
Add rule to remove WP generator from WP head
Removed unwanted register nav menus file. All menu registration now handeled by Hybrid Core. Was previously duplicated in both files!
Remove reference to deleted file