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Navigation links break easily. This is probably harder than it seems, but perhaps abstracting away the headers and links would do the trick:
A global navigation.py:
NAV = {
'some_link': 'http://google.com',
'some_header': 'My Heading Text'
}
Then, a pandoc filter goes through the markdown pages, looking for patterns like '# <symbol>' and '[footext](<symbol>)' and replaces <symbol> with what it finds in NAV.
markdown-page-1.md:
# some_header
Some words about what is supposed to be in this section.
markdown-page-2.md:
...
Some text about something and a [link](some_header) to the thing. Oh, and here's another [link](some_link).
...
Probably this is an oversimplification, but something more like this might work.
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