That article is about not throwing away your whole codebase; in fact, he even talks about doing exactly what Jeff Atwood mentions: These problems can be solved

That article is about not throwing away your whole codebase; in fact, he even talks about doing exactly what Jeff Atwood mentions: These problems can be solved, one at a time, by carefully moving code, refactoring, changing interfaces. They can be done by one programmer working carefully and checking in his changes all at once, so that nobody else is disrupted. Even fairly major architectural changes can be done without throwing away the code. Joel, I'm sure, is not advocating never re-writing anything at all, and if you think that, sheesh, I'd hate to see the code you work on...