Is it possible to track the whole wiki (e.g. ./static; ./templates; ./wikidata) under git?

I'd like to be able to track the whole wiki under git, not just the 'wikidata'. Is there a way to accomplish this? My naive attempt was to:

1) remove the wikidata/.git directory
2) init the repo from the 'parent' of wikidata
3) commit, push, etc.

When I attempt to use the wiki as configured it is unable to find any pages.

Is there a way to work around this?