Almost all programs that people write are written so that they provably halt (or provably don't halt - as continuing forever is sometimes the desired behavior).
How do we do that? By using known-halting parts, and composing them in known-halting ways. How did we find those parts in the first place, well computer science.. But boiling that down to a codified process, that's where it gets murkier. I think we don't really know exactly how human ingenuity discovers new useful halting parts in the face of the halting problem.
