In a medium saucepan, cover the clementines with water. Bring to a simmer and cook over moderately high heat until the skin softens, about 8 minutes. Drain and let stand until cool enough to handle. Coarsely chop the whole clementines and discard any seeds. Wipe out the saucepan.
In the same saucepan, combine the chopped clementines with the sugar and water. Bring to a simmer and cook over moderate heat until the clementine peel is sweet, about 30 minutes. Add the cranberries and cook over moderately high heat until they burst, about 6 minutes. Scrape into a bowl and refrigerate until chilled, about 3 hours. Fold in the pumpkin seeds and serve.
The conserve can be refrigerated for up to 2 weeks. Fold in the pumpkin seeds just before serving.
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