There is perhaps no clearer indication that Apple was keen to make a break from its roots than when it removed the giant, blown-up versions of some of the early icons, Clarus included, from what was called the Icon Garden at its campus in Cupertino. You can't argue with the results: since then, Apple's sales figures have rocketed and its appeal has become truly global. And sure, I'm not saying that killing Clarus led directly to this success, but it's likely that it was this unsentimental mindset that helped propel the company to its current position as the world's richest technology company.
Mind you, Apple may never rid itself of a grass-roots proto-anarchy. Despite expunging Clarus, in its documentation for its brand-new programming language, Swift, one of the examples given for naming constants and variables uses the emoji for a dog and a cow (which it says could equal "dogcow"), as lovely a little nod to Clarus's role as a mascot for Apple developers as you could hope to find.
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