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Very impressive!
This kind of design style is just what I dreamed: I press one button and you do all the work!!!!!
From algorithm's point of view, I think the most interesting part is the algorithm that detects blocks of contents from the pdf layout. If the program can incorporate the algorithm that breaks lines, it will be able to break 1-page wide blocks to 1/2-page wide block. The program will be a star to handle academic papers then (what a desperate target?). There may be many small things need to be tweaked, but the major function (handle sing-column and double-column) is there.
And, please, please, please keep the current operation style. I understand that you experts like commend line a lot. But this types of clean and intuitive UI is very important to the newbies (Do I need some HCI refences to support this argument?).
At last, a small thing I think may make the output looks better: when segmenting the small block to fit into the 6'' pages, you may want to detect whether a cut may cross some content or not. If it does, we may need to move the cut a little bit higher. This is only a small problem. The current tool is fantastic at this stage.
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