Come on... Just convert them to something the reader is comfortable with and be done with it. Probably PDF or HTML. You can use Calibre.
This whole thing of "hundreds and hundreds of thousands of documents" thing doesn't work for me. You should focus on quality instead of quantity. Think of it this way, out of those hundreds of documents, which ones are more important and you plan on using at the moment ? Convert those first. Then slowly convert more once you're done with them.
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