The commands are be scattered around the hd. A command is any file with the execution bit set on.😉
The best way to go is to go to your local library and find any book on unix or bash. There will be some difference between what you read and what is available in X. the man command should key you in on the differences.
A book on Bash would be helpful.
Here is the book that I use:
Mac OS X Tiger in a Nutshell: A Desktop Quick Reference (In a Nutshell (O'Reilly))
This is also good & was in my local library.
Practical Guide to Linux Commands, Editors, and Shell Programming, A (2nd Edition) [Paperback] the book Don't be fooled by the name, the second addition includes Mac OS X.
Advanced Bash Script. premise: Examples for everything. I have revision 6.2.
tldp.org/LDP/abs/abs-guide.pdf
BASH Programming - Introduction HOW-TO
http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO.html#toc14
Apple administrative commands
http://manuals.info.apple.com/en_US/IntroCommandLine_v10.6.pdf
Apple Shell Scripting Primer
https://developer.apple.com/library/mac/documentation/OpenSource/Conceptual/Shel lScripting/ShellScripting.pdf
Check you local library. Any book on Bash syntax will do. There will be minor differences but they will not be great.
Sometimes you can get a good deal on used books in Amazon.
Bash Cookbook, Carol Albing, JP Vossen & Cameron Newham (O'Reilly)