Most UNIX commands take arguments which are specified after the command -- often with a "-".
Paths that start with "~" or "/" are absolute pathnames because they refer to a specific starting point. Other paths are relative, and constructed starting from the directory you're in. The example above was absolute and will work no matter where I am. In contrast, "../foo" will go back one level from the current directory and look for foo.
pwd prints the working directory you're in.
cd name changes you into the the named directory.
ls lists the files in the current directory. Subdirectories are marked with a "/".
ls -l gives you the long version of the above. You get the dates the files were created, their sizes, and plenty of other stuff that won't be important.
ls -a lists all the files in a directory. Filenames which start with ".", so-called dot files, are not printed otherwise. Dot files usually contain configuration information for various programs.
ls name lists the contents of the named directory.
cp name new-name copies a file to a new name or location.
mv name new-name moves a file. If new-name is a directory, the file will be moved to that location. If it is a filename, it will be renamed to that name.
rm name removes a file (No warning!).
mkdir name makes a new directory.
rmdir name removes a directory.
cat name prints the contents of name. You can give cat multiple files, and their contents will be concatenated together and output. This is the mnemonic for this command (concatenate).
head name prints out just the first 10 lines of name. This is handy if want to remind yourself of what a file contains. head has many other options; see the man page (see below).
You can also re-edit previous commands by using the arrow keys to scroll through them. The MSCC machines seem to be set up in such a way that this isn't completely straightforward. Type bind emacs to make it work intuitively. Put this line in your .cshrc to have it be run automatically for you at every login (.cshrc contains commands that will be run whenever a new shell is started).