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It's going to be quite a bit of work.
A few questions,
What text editor do you use? Can it search in selection only?
How many individual short stories are there?
Does it have to be in markdown?
Does any of your text have any other markup apart from headers (###), i.e. bold/italics?
The reason I ask is if we convert it to Textile, it will be easier to do the footnotes.
Do the footnotes need to be able to link back to the place they linked from?
Some readers don't have a backup button, and need to have a link back.
I can see how I'd do it in Textile (my preference txt format), using two different search and replaces, doing each stories text, then its footnotes,
then the next stories text, and then its footnotes.
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