I'd recommend Unix Power Tools - it's a collection of like 10 O'reilly books + Usenet articles etc. in one 1000+ page book
. It'll cover heaps of commands, shell scripting, text editors, directory structures, inodes and more. It's really worth a read and it might be available online from O'reilly's website (It's probably 10-15 years of republishing now and I have no idea what edition it is up to now) I know that the second edition doesn't go into X but the latest one might. If you want to lean about X I'd suggest "The Joy of X".