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JARFILE is the name of the hps-java jarfile you used/will be using to reconstruct your data files with the aligned (new) geometry.
The flag -t is needed as some of the parameters in the compact.xml file are already been modified by some expressions introducing physical constraints.
ATTENTION: all rotation offsets have to be summed, which means their sign doesn't have to be flipped when building the new compact.xml file. In some cases two "-" signs appear the the xml file, you need to replace the "- -" string with a "+" (not sure of the overall effect if the correction is not applied - this must be fixed).
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