I did some work today to get Nikola properly packaged. This involves some minor changes on the workflow for site authors. I am not 100% sure I have it right yet, so here is a short video showing how it works right now in the packaging branch I am doing.
The new thing is the nikola init foldername command, the rest is all old stuff. Basically, you stop having a full copy of Nikola for each site and everything is in a centralized location.
You can still do your own themes by putting them in themes/themename and add new tasks, files, etc. The configuration dodo.py is unchanged except for the "magic bit" which is slightly different.
So, not really invasive, easy to migrate to, and enables much easier updates in the future, as long as we don't break any important stuff in a non-compatible way.
Here is the video: