[WorldMaker]

It depends on how deep you plan to extend Bootstrap, obviously. I had one project I worked on that did a lot surgery to the Bootstrap files in a branch of fork of the main Bootstrap repository. I don't recommend that if you can avoid, and it was late in that project that I got better at being able to do overrides of the LESS files (as this was Bootstrap 2/3) in other LESS files without needing to edit the Bootstrap sources. There ends up being more duplication by doing it in separate files you control, but it makes it easier to deal with "merge conflicts" from upstream.

From that approach, one useful example I have seen is the infrastructure of the Bootswatch project. [1] Perhaps unsurprisingly for how many themes Bootswatch maintains, their GitHub repository is quite well laid out, easy to learn from, and even easy enough to fork as the basis of your own project.

[1] http://bootswatch.com/