Nano-machines-Equestria was swarming with nano-machines in one form or another, and acted as the point of interface between magic and ponies. When this was discovered, soon after the Great Shift, there were a lot of questions asked, and very few of them were answered. Eventually, everybody was able to create nano-machines of their own…but was never quite as good as the swarming hordes of invisible nano-machines around them. Only unicorns and alicorns were able to consciously access and control these nano-machines, while the other races used them instinctively. Even this level of control is highly restricted, with very few ponies being able to go beyond a few simple “tricks”. Trying to hack the nano-machines is very difficult to impossible, and Very Bad Things happen to ponies that try.
To this day, the nano-machine technology that makes magic possible seems to follow ponies (and everybody else) everywhere, or is there already. It is definitely a Precursor technology (the very existence of the nano-machines violates several laws of thermodynamics and at least one law of causality), and it is one of the biggest question marks about the existence of the Precursors. Research on them is very tricky-they have very effective self destruct mechanisms and are almost impossible to contain.
(And, this is even cannon!)