If I am adding oil for flavour, it goes in with the initial batch of water. If I am adding herbs (e.g. olive oil + rosemary...) the rosemary gets similarly crushed small and mixed in with the initial mixing of flour + starter + water.

So far I have been adding nuts + fruit after I've done about half the number of folds I expect to; this means that (1) the gluten gets a chance to develop without being interrupted by Miscellaneous Lumps, but (2) it's possible to mix the additions through relatively easily and relatively gently so they don't end up sort of weirdly swiss-rolled.