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From InDesign CS2 it has been possible to insert linked footnotes into your content (Type > Insert Footnote). InDesign’s method of insertion offers several advantages over adding footnote text by hand, not least being automatic renumbering, and the reflow of footnotes with the text.
The system works by adding a reference number at the insertion point in your text, and a footnote at the foot of the column.
For information on using footnotes in InDesign, see the InDesign documentation.
Atomik Xport SE supports the extraction of InDesign footnotes by adding tagged footnote text at the insertion point.