How do you upgrade applications installed from source?
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If you have the source still, you can go to it and run "make uninstall" to remove the program and then compile the new version. If you don't have the source, you need to manually remove the files.
If your in luck, there's a patch file so you only need to patch your source code and then recompile and install it.
"make uninstall" is not offered by all Makefiles. If you install from source you can most often use checkinstall. It uses installwatch to monitor the install changes and is able to build a package (tgz, deb, rpm ...?) that you can install and uninstall using your distro's package management system. Using this you can do a clean uninstall in most cases.
You can use tools such as stow or encap to install source tarballs. Each will create a subdirectory under /usr/local (/usr/local/stow or /usr/local/encap). Tarballs are installed in subdirectories and symlinked to the locations called for in the tarball. When an updated version of a package comes along, install with stow/encap. They each can detect a pre-existing installation, and upgrade it to the new version.