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There is a package called "recoll" in the Fedora repository. It keeps an index of all documents in selected directories including words within documents. It handles pdf by default and can index MSWord documents once the necessary helper packages are installed. It has a lot of configuration options, but the vanilla installation is still very useful. Guidance for installing index generation as a cron job is given. Indexing is done incrementally; you don't have to scan the whole directory tree for each iteration.

The project homepage is at http://www.lesbonscomptes.com/recoll/ .