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There are pdf2txt utitilities on linux that extract the text from a pdf, so this shouldn't be the problem when scripting. You only get in trouble when the text in the pdf is in fact no text but a bitmap. The even the acrobat reader will fail searching for text.
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Like what LiquidAcid said, there's no certain way to search for words if the words are actually image files. But if they ARE text, there's an option to search within pdf files in an entire directory in Adobe Acrobat Reader itself. The function's the Full Reader Search I believe.
Jam it back in, in the dark.