How do I get full CKEditor working?
There's more interaction and integration between core and CKEditor's plugins than we see in D7. In fact, in researching your question, I've learned that Drupal and the CKEditor team are actively collaborating, which is cool to know. But let's first note that the ckeditor js libraries and plugins (version 4.5.5 as of Drupal 8.0.1) live at core/assets/vendor/ckeditor, not core/modules/ckeditor. Also note that enabling ckeditor plugins requires explicit supporting code, such as noted here and here. 

So, rather than "the kitchen sink" approach — it might be better to identify which CKEditor plugins you need enabled, that are not in core, and use the code examples in the URLS above to implement them. FWIW, it's much easier to manage such projects after delivery anyhow, even with D7.

Finally, as a nag, I presume kittens still get it bad when you overwrite drupal-managed code with your own code. In other words, I'd figure how to extend Drupal without changing code in core/ so that when I perform a later core update, I won't loose those changes.