As of the latest DIALS/xia2 nightly build (2015-04-24 onwards, available from http://dials.diamond.ac.uk/diamond_builds/), xia2 now supports passing multiple directories or images via the command line, e.g.:
xia2 -dials /path/to/directory1 /path/to/directory2
xia2 -dials image=/path/to/directory1/image_1_0001.cbf image=/path/to/directory2/image_2_0001.cbf
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