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the model of shells

Starting from the hardware, every layer of programs can be seen as shells which cover the underlying structures.

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The kernel is wrapped around the hardware. All Application Programs (shells are applications, too) use system calls to the kernel that in turn changes states in the hardware.
Shells remove the need of dealing with system calls; e.g. the program rm uses the system call unlink(2) to delete a reference to a file. If this reference is the last one (no further links), the file is deleted.

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