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Is there a way to index file shares on a windows file server so that they can be quickly searched by end users, that isn't part of sharepoint?

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you can use Windows Search (or the built in Vista/Win7 search to index shares. The downside is that each client maintains their own index. This seem like a less than optimum solution. Alternative might be to use a web-based indexer like SharePoint, Google, etc. to do it. Microsoft has a high-end indexing solution too. There are open source indexers as well like Apache's lucene

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Use the Search Service, built in to windows server. (Formerly called: Index Server)

Details to set up:

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