It will definitely take in the order of millions of years to recover from what humans have done to destroy the habitat. The species will destroy will likely never return, the planet in a million years time will bear the scars of the Holocene extinction.
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Pretty certain cd and pwd have changed over the years. The kernel hasn't remained the same so the commands that use it wont and now we have faster methods to do various things like getting file data the commands that depend on it will change. Less quickly than something that is still gaining features but bit rot is a very real effect since every single part of software is in constant flux.