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Thanks for your request. This requires a lot of work. At the moment we are using Apache Tika as our backend solution. Tika exports XML output (Extractous will support this very soon), which has some structure and can be post processed and converted to Mardown. If you really need Mardown, unfortunately at this moment in time we do not have enough resources to implement such feature.
Hope this answers your question ...
Can you preserve the document structure and output it as a markdown file?
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