From MSDN .Net Architecture Center...
The file has been the central container of work in software development for over thirty years. All of a project's structure and logic is ultimately reduced down to files and directories. The tools that surround software development are built around this concept, too. This article explores the concept of file structure, and contrasts it with an emerging view of Model Driven Architecture...Maybe some tools. Not all tools.
It seems clear that the file is a relic that has outlived its usefulness for software development...
The modern development environment has not yet fully caught up to the object-oriented shift. All of the tools still rely on a file to be the container of source code. While some contain modeling capabilities as well, the models exist as different entities than the file and its code.
The article seems to conflate two issues that could benefit from being addressed independently: