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Clean Pagination uses the same format as Drupal, that is it counts the first page as 0 (or nothing), the second as 1, and so on. I modified Pagination.inc to follow this pattern. Nothing major, a very quick fix. I changed only 3 lines (if I recall correctly!) tagged with comments: "//drupal pattern" . Anyway, it works with Clean Pagination, which would otherwise cause pagers 1 and 2 to link to page 1, pager 3 link to page 2 and so on. The table of contents is also fixed, but the urls generated are not affected by Clean Pagination and thus they are returned as ?page=. Just replace Pagination.inc in pagination/includes with this file (after you rename it to Pagination.inc)