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If it is not in the man pages or the how-to's this is the place!
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Introduction to Linux - A Hands on Guide
This guide was created as an overview of the Linux Operating System, geared toward new users as an exploration tour and getting started guide, with exercises at the end of each chapter.
For more advanced trainees it can be a desktop reference, and a collection of the base knowledge needed to proceed with system and network administration. This book contains many real life examples derived from the author's experience as a Linux system and network administrator, trainer and consultant. They hope these examples will help you to get a better understanding of the Linux system and that you feel encouraged to try out things on your own.
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There are thousands of documents that might be what you want and
might not be. Can you say more specifically what you're looking for?
Do you just want a list of commands? Do you want a basic syntax guide?
Do you want some type of tutorial or howto guide?
dont forget another built in command is info
I would say look on google for Linux CLI commands. You may also want to search for CLI commands on a particular topic if you want something more specific. If you are looking for new tricks to manage your system look at a few books on hacking Linux.
Suggestions so far just copy what has gone before.
Try reading 'Linux in a NUTshell' as a newbie, it's enough to put anyone off. There is not even a decent index. It is really a reference book for the knowing. Given that, it is authoritative which is a bonus when you are all at sea.
Technical writing is a skill, especially when you are talking to those who are ignorant (positive usage) and few books do that well, even fewer cater for an intermediate level. The confusion may have led from an over simplification earlier?
"Linux Command Line and Shell Scripting Bible" was the only command line "publication" I ever read, and I still use it as reference for somethings, but chrism's list is definitely the best online resources.
If you want a physical book, O'Reilly's "Linux Pocket Guide" is great. It doesn't cover everything, just the commonly used stuff. Makes for a compact (about the size of a Nintendo DS), concise, and cheap book. Includes a primer on bash shell scripting that covers all the basics - variables, ifs, loops, stuff like that.
If I can add to the list and I do not see why a newbie should be put off by the command line unless we want to go back years but it is good to have as a stand by or an alternative, etc but not what a user is looking for at first glance.
Best linux writers include:
Kier Thomas and Christopher Negus.
There are many others but I would recommend the former. 'Beginning SUSE linux' being an example of.
Experts tend to forget their origins!