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There were buffer overflows in the Linux kernel in 2012 ( http://www.securityfocus.com/bid/53401 ). Should we not have filesystems in the kernel either?

Certainly the string library, of all places, should be using secure code.

I'm sure there are sooo many people running Linux on pre-OSX Mac harddrives formatted with HFS that could be hacked with a buffer overflow.

Are you seriously arguing that buffer overflows in the kernel are not a big deal?

Well... No, if you're a proponent of the micro-kernel design.