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Normally, flight crew members will enter the Schengen area on the basis of a pilot's license or crew certificate (see Annex VII, item 2 of the Schengen Borders Code), which is not to be stamped (see Article 11(2)).
The code does not contain an explicit exemption from the 90/180 rule in such cases, but the explicit exemption of these documents from being stamped is an implicit exemption from the 90/180 rule because the stamps are the record by which presence in the Schengen area is calculated.