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I've downloaded IntelliJ idea IDE from their website. I've putted it inside /usr/local/bin and then configured my PATH var and the program work correctly. the program folder has these two folders inside it, bin and lib. I know that if I moved their content to my /usr/local/bin and /usr/local/lib/ the program will work. However, it will be a problem to remove it later because I won't be able to distinguish its files from what was already there inside /usr/local/bin and /usr/local/lib/. I know that software centre doesn’t keep them in folders but it sprat them to /usr/bin, /usr/lib and other folders.

So my question is in what way should I organize these type of programs ?

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Don't fix what ain't broken. There's no real need to move those files anywhere. (Or is there?) So, leave as it is.

If you want to do something fancy, create a deb package from it so you can easily install and uninstall.

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