Move config directory and core directory to be nested under new system directory
Remove lib submodule and change directories of config and core back to before in preparation for new submodule structure
Added submodule, but incorrectly
Add config and core files back to system directory and provide files to ready for submodule creation
Move correct core directory to system folder and incorrect directory out
Remove lib submodule from system directory
Remove submodule again, trying to get this right
Add submodule back on its own
Move application-specific directories under one main application directory, and update .gitignore and paths.php to match