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don't you work a lot in the command prompt with Linux?
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If you want to fully experience linux, you'll need to become familier with the command line. A lot of software is not pre-configured for each distro, and sooner or later you'll need to learn how to compile and install from the console. It's not hard. The hardest part is probably learning that mounted drives show up in the /mnt/directory and you need to learn how to use the chown, chgrp, and chmod commands to set directory permissions.
When people say they run linux, generally they are saying that they run programs using the linux kernal.. Linux itself is only the part that handles the input and output commands of the computer.. Every-thing else, such as your GUI "Gnome, Blackbox, WM, KDE.." is added onto the linux kernal. You can make your own linux by starting with a minimallistic distro, then adding on the programs that you want..
If you do this, you need to keep in mind that some (actually most) programs built for linux require other programs to work.. The programs needed to make others work are called dependencies. Newer distros, such as red-hat, debian, etc, include tools that will resolve and correct the dependencies in the background, so you don't have to worry about them as much. But it's still a good idea, when you go to install something new, to check if anything else is needed and install it first.