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Paco was written to solve this problem in a quite simple fashion.
When installing a package from sources, paco wraps the "make install" command (or whatever command or group of commands are needed to install the files into the system), and saves installation information into a text database.
Paco has many usage options for removing packages, looking at package files, file counts, sorting, missing files, etc. Run "paco -h" on the command line, or "man paco" for more information.