<p>If the battery died, how (and why??) did you re-install Linux?</p>
<p>Did you reformat the computer to re-install Linux? If so, data is probably gone unless /home was on another drive which was not reformatted. /home (which is where each user's home directory is stored at) contains many hidden files and folders, including settings. ( /opt is another place you want to backup as well. )</p>
<p>Realize that most "applications" are really just a GUI front-end for what can be done via the command line. For example, you can use Brasero to record a CD, but you can also use the command line as well. Brasero acts as the front-end for that. Now some things are best done via command line vs a GUI front-end. For example, you can use fwbuilder to configure iptables (which itself is used to configure netfilters), but you'd have a lot more options (and control) configuring iptables from the command line vs from fwbuilder (the GUI front-end for it). point being..... this is where using the command line is really a must. You should learn it if you want to do any advanced work with Linux.</p>