When you type ls, files beginning with a dot are not listed. Traditionally, files that contain configuration information, user preferences, and so on begin with a dot; these are hidden and out of your way while you do your day-to-day work. Sample dot files are ~/.emacs, ~/.newsrc, ~/.bashrc, ~/.xsession, and ~/.fvwmrc. These are used by Emacs, news readers, the Bash shell, the X Window system, and the fvwm window manager, respectively. It is conventional to end the dot filename with rc, but some programs don’t. There are also directories beginning with a dot, such as ~/.gimp and ~/.netscape, which store preferences for the Gimp and Netscape.
Sometimes a program will create a dot file automatically; for example, Netscape allows you to edit your preferences with a graphical dialog box and then it saves your choices. Other times you will create them yourself using a text editor; this is the traditional way to do it, but you have to learn the peculiar format of each file – inconvenient at first, but it can give you a lot of power.
To see dot files, you must use the -a option to ls. The long form of -a is --all, if you find that easier to remember. You can also use -A or --almost-all, which displays all dot files except . and ... Remember that . is the current directory, and .. is the parent of the current directory; because these are guaranteed to be in every directory, there is no real reason to list them with ls. You already know they are there.