The popular development methodologies in use are based on some iterative cycle between specification and coding. They largely vary based on the specification artefacts and duration of the cycle time.

Extreme programming is the most artistic process and is great for small teams dealing with many unknowns and learning on-the-fly. The code is the main artefact. Model-based methods (RUP et al) scale better and try to keep the design separate from the implementation. However, these projects are often highly challenged to keep the model and implementation synchronised and the model often gets abandoned. With a lot of skill and discipline, these model-based methods can work but I have not been witness to it. Most enterprises bumble along with something in-between these extremes. The process is often loosely based on a traditional waterfall method but with more iterations.

But at the end of the day, you still wind up with a massive code base of entangled logic that gradually entropies. Current methodologies won’t solve this problem; they just help you get there in a more consistent fashion.