There's also some notes on how to make a portable install
in the Calibre user manual.
As for batch converting: Use
ebook-convert, as noted before, and use the scripting tools your OS offers for running conversions on folder contents. For example, on Windows, I've had good results using the "for" command.
The trivial way, I think, would of course be just stuffing all of the files in the GUI, converting and exporting them
