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With poppler-utils tools you could first extract single pages with pdfseparate: pdfseparate infile.pdf piece-%d.pdf into pieces like piece-1.pdf, piece-2.pdf ... piece-n.pdf where n is the total number of pages in your original pdf. You could then join them with pdfunite: pdfunite piece-{1..n..2}.pdf odd.pdf pdfunite piece-{2..n..2}.pdf even.pdf ...

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