Comment by Bender

Adding to this they also provided programming feedback loops to the Federation that would lead to improvements in existing star-ships and substantial improvements in newer models. This was absolutely required to fight the Borg. Shields and phasers had to be reprogrammed to make continuous and random changes in modulation. This evolution of hardware and software evident in each generation of Star Trek.

There were also incidents that lead to a greater understanding of technology that could also be considered programming such as Reginald Barclay reprogramming via the holodeck the existing tech on the Enterprise to fold space and travel to the center of the galaxy. There were many other similar incidents.