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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/bun /usr/lib and other folders.

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

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up vote 1 down vote accepted

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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