Reorganize App to make it easier to limit IO in main loop.

Previously we used liftIO fairly liberally.  The code has
been restructured to avoid this.

A small behavior change is that pandoc will now fall back
to latin1 encoding for inputs that can't be read as UTF-8.
This is what it did previously for content fetched from
the web and not marked as to content type. It makes sense
to do the same for local files.

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