Install markdown-mode via package.el

* Removed the old lib/markdown-mode.el file
* Updated the requirements.txt file
Re-install nginx-mode via package.el

* Delete lib/nginx-mode.el
* Update config/misc.el
* Update requirements.txt file
Re-install rainbow-delimeters via package.el

* deleted the rainbow-delimeters.el file
* removed the require expression
* update requirements.txt
Removed code for including org mode as it's built-in now
Remove the org-mode submodule
Re-install flymake-cursor.el via package.el

* Removed the file
* Updated the prog.el config
* Updated the requirements.txt file