Earlier, I wrote:
But how to deal with templates we want to include? Is there a programmatic way to mirror all the templates we need once a day automatically and to semi-protect our copies of those templates?
Even though nobody has responded to the above question, I have another question :-)
When bringing stuff over from Wikipedia, how could we prevent most links from showing up as red links like they do in many annex.wikia.com articles[1]?
We could mirror some or all of Wikipedia (and possibly images); but I bet it'd be better to somehow programmatically make red links repoint to enwiki if an article of that name on enwiki exists. And I bet it'd be preferable to do this at render time instead of modifying the stored wikitext, so that it'd be easier to move the stuff back to Wikipedia if necessary.
Cheers, -j
^ [1]. e.g. http://annex.wikia.com/wiki/Aarakocra