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Is there a good program to help simplify all the applications and hardware on my computer.. possible consists of multiple applications?
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You can ignore others, or you may 'uninstall' what you don't need. They don't take up memory, they don't generally load unless launched.
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I've noticed that I have multiple programs doing the same functions and conflicting with each other. The "preferred applications" program only has a list for very basic programs.
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So you need more? I thought you wanted to get rid of many. I suppose you wanted a 'launcher' for applications you prefer but not available under "preferred applications" box. This is very easy to do under Ubuntu Gnome. Just read Ubuntu help and how-to.
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I would like some sort of ui were I can see all the hardware on my computer and tell it what programs to use to control specific hardware as well as functions???
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Get familiar with your Menus. They're just there.
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As well as when opening specific files is there a program I can tell to universally open extension "x" with application "y" automatically?
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I'm sorry I don't understand what you exactly mean by 'extension x' and 'application y' and much 'automatically'. One thing important to know: in Linux we "don't respect" dignities of file.extensions; there are no ".exe"s no ".com's. In linux a file's dignity to run is in its contents, regardless of extensions: and everything is but a "FILE" and I mean this 'literally'.
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Really not sure exactly what I'm asking, I just feel my computer is very unorganized and I find myself searching for applications to complete a task that isn't currently available and in doing so I create conflicts system wide and I am not sure how to fix this problem...
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"Everybody falls the first time (of jump)." We went the same road you are now. Don't worry, you'll get by soon, now that you come to this place.
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I am using the Gnome desktop but open to suggestions if there is a better desktop to use..
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There are many windowing managers available; other popular are KDE and XFCE. But for me (only a matter of TASTE not a criticism) Gnome is still the best: though I only use "Fluxbox" and "Xfce" as my mainstay. Your Ubuntu that runs Gnome is the distro that opened many eyes to the world of linux. Manipulation of files are just as easy as "clicking" the way we did in M$oft. Only, you read a little about it.
KDE is more 'Windows'-like appearance and menu-ing system. You can try
download it here. If you install Kubuntu it is most advantageous for you to become a member into Kubuntu community where you can interact with fellow-users for faster answers.
Regardless of distro at hand you will always need a handy tutorial in order to understand Linux and how to control it.
Download this tutorial and make it your reference.
Good luck.