Keeping track of installs and where everything goes...
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to get a list of installed packages, i can also use it to install/uninstall and i can check the website for dependencies. Works fine for me. Also has the AUR to create packages from source and install via pacman, to keep track of em.
Every package manager should be able to list contents of a package, in Ubuntu it's very easy trough Synaptic for example. If you know which package you want to query, you can query it to see what files are inside, and if the system is smart enough, it tells where the files were installed. This is true for binary packages, if it was unclear. If you remove a package in Ubuntu, the basic removal doesn't remove config files (usually); that's because if you later install it again, you don't lose your settings. To remove everything the package installs, use the purge option (that's the way to go with other package managers too than apt, I guess).
Source code software is another thing. With binary packages the tracking and removal of installed files is easy, as that all can be done and set in the package information, and since it's a binary package, it stays so. A list can be created during the package creation and that list can be used when the package is removed. If you compile source code, however, the result depends on multiple things like prefix and other configuration options. There's no one single way to remove everything; "make uninstall" works for some, some have an uninstallation script of their own. Then there is software that you use when running the final step, usually "make install", of a source code project: I don't remember it's name (but you'll find it with google or altavista or something) but basically it keeps an eye of what "make install" step does, creates a "log" about it and when you want to remove the installed stuff, you run the program with the created "log" file and it uses that information to remove all stuff no matter where on the system they were copied. Basically a reverse "make install", except that it's "third-party", not something that comes with every source code project. Also I'm not sure where it's limits are, i.e. what kind of compilation+installs it can handle, but last time I read it sound great.
Just a brief note - you're right, removing a package leaves some things behind, like configuration files. If you want to remove everything, drop the the command line and issue an 'apt-get --purge remove <package>'.
And what about make installs? I know how to remove the temp files, but what if I want to remove a compiled application? How can I be sure I'm removing all of it.
Look into the 'checkinstall' package which makes your package manager aware of things you install by compilation, allowing you to easily uninstall it.