I was recently faced with the task of scanning a lot of documents and wanted to preserve them as multi-page pdfs. Converting the raw jpegs to pdfs proved to be quite easy using ImageMagick's convert that I got from http://stackoverflow.com/questions/8955425/how-can-i-convert-a-series-of-images-to-a-pdf-from-the-command-line-on-linux. But, the file sizes of the pdfs was really large when using convert to create multi-page documents. A little bit of googling and I found pdfunite which was perfect and I was able to create reasonably sized multi-page pdfs from a set of single page pdfs :)
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