How to truely install a tar.gz file on Linux, and register it to the sytem (eg: what to do after I compile something?)

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http://unix.stackexchange.com – I see all these links explaining packages and .debs... I know that... and there are many kludges to get tar.gz files working (eg: update-alternatives for Java or manually dropping the file in /usr/local/bin (or somewhere else, which I had deduced from hours of searching)). If packages are so smart, how are so few Linux applications available in packages or .debs/rpms? I'm speaking as a new user; I know experts probably know it better (I think I can download a compilable version of Eclipse?). Like netbeans and chrome are .sh, eclipse is a plain, launchable directory, java requires this update-a (HowTos)