[eluser]Phil Sturgeon[/eluser]
Epic post! I started reading this on my iPhone, that was a mistake. :-)
Thanks for your feedback. I recently created the core_modules folder to store modules that should always be there, and clearly overlooked quite a few things.
Tonight I am off on a 9 mile hike which will take up my entire 17:00-sleep but I will definitely get on these soon.
It would be great if you could create issues for these - and any other bugs you might spot - on the GitHub page (link in my signature) or better yet join the team!
You clearly have an eye for bugs and have no problem getting around a completely undocumented system. It would be great to have you aboard.