I'm curious how software can be created and evolve over time. I'm afraid that at some point, we'll realize there are issues with the software we're using that can only be remedied by massive changes or a complete rewrite.
Are there any instances of this happening? Where something is designed with a flaw that doesn't get realized until much later, necessitating scrapping the whole thing and starting from scratch?
Indeed. Assembly is(can be) used to implement them.
As in who (user foo) tried to do what (open/read/write/delete/...) to which object (e.g. which socket, which file, which Linux namespace, which memory mapping,...).
Kernel implements it in software(except memory mappings, it is implemented in MMU). There are no sockets, files and namespaces in ISA.