When you type ls, files beginning with a dot are not listed.
Traditionally, files which contain configuration information, user preferences,
and so on begin with a dot; these are hidden and out of your way while you do
you day-to-day work. Sample dotfiles are ~/.emacs,
~/.newsrc, ~/.bashrc, ~/.xsession,
~/.fvwmrc, etc... These are used by Emacs, newsreaders, the Bash
shell, the X Window System, and the fvwm window manager,
respectively. It is conventional to end the dotfile name 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 dotfile automatically; for example, Netscape allows you to edit your preferences with a graphical dialog 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 dotfiles, 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 includes all dotfiles except . and .. --- remember that . is the current directory, and .. is the parent of the current directory; since these are guaranteed to be in every directory, there is no real reason to list them with ls. You already know they are there.
It's important to remember that there are two different kinds of configuration on a Debian system. System-wide configuration affects all users. System-wide settings are made in the /etc directory. You might configure the way the system connects to the internet, for example; or have web browsers on the system always start on the company home page. Since you want these settings to apply to all users, you make the changes in /etc. Sample configuration files in /etc include /etc/X11/XF86Config, /etc/lynx.cfg, and /etc/ppp/options. In fact nearly all the files in /etc are configuration files.
Normally you must be root to change system-wide settings.
User configuration affects only a single user. Dotfiles are used for user configuration. For example, the file ~/.newsrc stores a list of which Usenet (discussion group) articles you have read, and which groups you are subscribed to. This allows newsreaders such as trn or Netscape to display unread articles in the groups you're interested in. This information will be different for every user on the system, so each user has their own .newsrc file in their home directory.
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