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I use Linux for 2 years at my work and I still confused where should my installed programs remain. Now I use /opt/<program> e.g. I've installed vim73 from sources there (reason not to use package manager is there is no 7.3 version of VIM in my sources e.g. /etc/apt/sources.list on my Ubuntu).

But all my programs I installed from sources previously are scattered among FS everywhere like PHP 5.3.6 remains in /opt/local/php53, apache in /etc/, vlc in /etc/mutimedia etc.

Is there some convention I can follow?

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Absolutely. It's called the Filesystem Hierarchy Standard.

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    So to answer the question, according to the FHS linked above you should install programs in /opt.
    – Air
    Commented Feb 23, 2014 at 15:20

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