Important information is that this site is running on the official e107 2.3.3 pack. I created a repo and uploaded the content of this pack. Then I synced this site directly with this pack. So what you can see is the original e107 2.3.2 GitHub version (developer) was replaced with the official stable pack. 

Then I deleted 2 news folders and synced the site with my version of the news plugin.  The only reason for this is testing - I use it for somebody and I need this to be tested. There is nothing wrong with the core news plugin! For this, my repo for core has two branches, and if you want to use Github Sync plugin too, use only the main repo!

With those steps, I lost all my customization and experimental code, but it is a good thing.  

There is a lot of work here, cleaning up and testing (where my canonical URLs are?), so if something is not working, let me know.