I've written a mod for your software that implements column auto-detection (for two-column documents) and large block splitting with automatic rotation. Also a way to set resulting PDF's title. The changes currently work as command line parameters and so in batch mode only.
Argument "-t title" sets the resulting PDF's title property.
Argument "-2" enables automatic two-column detection and splitup.
Argument "-r" enables automatic wide block rotation.
Argument "-b ratio" enables the splitting of too large blocks.
So one would use this as:
java -jar briss-0.9.jar -2 -r -b 1.333 -s dogeatdog.pdf -d dogcrop.pdf
The modified briss can be accessed from:
The source code diff is within the archive. Hadn't written any Java in 10 years, so is a bit choppy.