Not a lot. They both have directory structures derived from UNIX.
Linux is just a kernel. Period. In order to run the kernel you need the GCC Libraries which come with the GNU Tools -- this is deliberate. The Gnu Tools got their start as attempt to write a free alternative to UNIX ten years before the Linux kernel, and when they didn't have a kernel of their own, Mr. Torvalds just sat down and wrote his own in consultation with some Minix hackers. The GUI, X-Windows, got its start in the mid-eighties as an OS-Independent GUI. While most commonly used on Linux and UNIX systems (including FreeBSD and Solaris) there are actually users of the Amiga and BeOS operating systems still out there, who also use it (as both OSes were released into Open Source after having X-Windows ported to them).
That's really the thing to remember: Windows and Linux are profoundly different because Windows is entirely written within one company whose individual teams don't always have access to each others code, while Linux is written by many independent vendors, each of whom delivers only a small part of the system but all of whom have FULL access to each others code because of the GPL.
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