The shell takes commands in the following format:
program [argument1 ...]
When you see notation like this, it is not meant to be copy and pasted directly. Underlined words are placeholders for something, otherwise the word should be typed as written. [words in brackets] are optional arguments which should either be present or absent. A ... means that additional arguments can optionally follow.
All file or directory arguments are paths. For a refresher on how to write paths, see Unix Filesystem section on the ECE 120 wiki.
man 1 program 
 Get detailed help on usage of program. On most systems, you can scroll with the arrow keys and hit "q" to quit.
man 3 function 
 [C Programming] Get detailed help on usage of library function function.
pwd 
 Print the absolute path for the current working directory
ls [directory] 
 List contents of directory, or current working directory if directory is absent.
cd directory 
 Change current working directory to directory.
mkdir directory 
 Create a new directory directory
touch file 
 Create a new empty file file
mv source destination 
 Move a file or directory source to file or directory destination. If destination is an existing directory, move source into it. Otherwise move and rename (if names are different) source to destination.
cp [-r] source destination 
 Copy a file or directory source to file or directory destination. Behaves like mv, but copies instead of moving. If a directory is being copied, all of its contents will be copied and the -r flag must be present.
rm [-r] path 
 Delete a file or directory path. This cannot be undone. If a directory is being deleted, all of its contents will be deleted and the -r flag must be present.
gedit file [&] 
 Edit file using gedit (GUI text editor). If file doesn't exist, create it when you click on "save". Appending the & will tell the shell to launch a separate process for gedit.
nano file 
 Edit file using nano (command line text editor). Useful if you don't have access to the GUI. Nano "commands" will appear at the bottom of the screen, which are control key sequences. For example, ^X: Exit means hit Control-x to exit back to the shell.
exit 
 Terminate the shell (which will also close your terminal emulator window on most systems)