Most software development projects I see are quite good at using version control systems to manage their code. What they don't do as well is tracking their changes. If you make a code change that involves code in multiple classes across multiple packages, you should be able to group those together so you know which versions of the packages go together. If you load just one of the packages, the system doesn't work. In Store, some people do this by always publishing a bundle that contains all the packages. Others explicitly record their changes in a wiki or other mechanisms outside the version control system. Most projects don't track changes at all. When you don't track changes, it becomes much harder to tell what code was submitted and what code needs to be loaded together.
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