New layers:
company-mode layer has been replaced by the new layer auto-completion.
Org packages have been moved to the new layer org.
Flycheck has been moved to the new layer syntax-checking.
Be sure to update your dotfile to add these layers.

Init functions:
The init function <layer>/init-<package> is now mandatory. Any package
without an explicit init function will be ignored and uninstalled by
Spacemacs.