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There is the Cluny museumhttps://www.musee-moyenage.fr/en/home.html
There is also the Armee museum (Invalides) which covers 1000+ years of history. I guess they do have a book shop.
Three very good bookshops just near musee de Cluny, Gilbert Joseph, Boulinier, Anne Lamort and Bonnefoi. CheersMatt