Many plugins fail to generate slicer XML files due to a bug in JIST CLI:

java edu.jhu.ece.iacl.jist.cli.run edu.jhu.cs.cisst.plugins.segmentation.PlugInGACWithoutEdges3DConstant -xml
cli Usage: edu.jhu.ece.iacl.jist.cli.run [classname] -help
cli Usage: edu.jhu.ece.iacl.jist.cli.run [classname] [run options]
cli PARSE Error: Index: 1, Size: 1
java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
at java.util.LinkedList.checkElementIndex(LinkedList.java:553)
at java.util.LinkedList.get(LinkedList.java:474)
at edu.jhu.ece.iacl.jist.cli.JistCLI.getSlicerXML(JistCLI.java:260)
at edu.jhu.ece.iacl.jist.cli.run.main(run.java:68)

Here is a *somewhat* comprehensive list:
edu.jhu.cs.cisst.plugins.segmentation.PlugInGACWithoutEdges3DConstant
edu.jhu.cs.cisst.plugins.segmentation.PlugInGeodesicActiveContour3D
edu.jhu.cs.cisst.plugins.segmentation.PlugInGACWithoutEdges2DMumfordShah
edu.jhu.cs.cisst.plugins.segmentation.PlugInGeodesicActiveContour2D
edu.jhu.cs.cisst.plugins.segmentation.PlugInGACWithoutEdges3DChanEsedogluNikolova
edu.jhu.cs.cisst.plugins.segmentation.PlugInGACWithoutEdges2DChanEsedogluNikolova
edu.jhu.cs.cisst.plugins.segmentation.PlugInGACWithoutEdges3DRudinOsherFatemi
edu.jhu.cs.cisst.plugins.segmentation.PlugInGACWithoutEdges2DRudinOsherFatemi
edu.jhu.cs.cisst.plugins.segmentation.PlugInGACWithoutEdges3DMumfordShah
edu.jhu.cs.cisst.plugins.segmentation.PlugInGACWithoutEdges2DConstant
edu.jhu.ece.iacl.jist.applicationplugins.JISTApplicationPluginInterface
edu.jhu.ece.iacl.jist.applicationplugins.JISTPluginContext
edu.jhu.ece.iacl.jist.plugins.AbstractProcessingAlgorithmInterface
edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmSurfaceLabelStatistics
edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmLabelCombine
edu.jhu.ece.iacl.plugins.mapping.MedicAlgorithmSurface2Sphere2009
edu.jhu.ece.iacl.plugins.utilities.roi.AlgorithmROIRangeStats
edu.jhu.ece.iacl.plugins.utilities.roi.AlgorithmROIStats
edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter2
edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmArithmetic
edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmDeserializeVolumes
edu.jhu.ece.iacl.plugins.comp_geom.MedicAlgorithmMultiResolutionDecomposition
edu.jhu.ece.iacl.plugins.comp_geom.MedicAlgorithmSmoothSurface
edu.jhu.ece.iacl.plugins.comp_geom.MedicAlgorithmMultiResolutionSmoothing
edu.jhu.ece.iacl.plugins.measure.statistics.MedicAlgorithmVolumeStatistic
edu.jhu.ece.iacl.plugins.measure.statistics.MedicAlgorithmSurfaceStatistics
edu.jhu.ece.iacl.plugins.measure.statistics.MedicAlgorithmIsoLevelSurfaceLandmarks
edu.jhu.ece.iacl.plugins.measure.thickness.MedicAlgorithmThickness
edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCaminoFileCollection
edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCaminoFileCollection
edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCamino
edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoFileCollection
edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoRESTOREVariableNoiseField
edu.jhu.ece.iacl.plugins.dti.MetaImageData4D
edu.jhu.ece.iacl.plugins.dti.spine.MedicAlgorithmSpineGeoCorrection
edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmWildBootTrac
edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmApplyFiberDOTS
edu.jhu.ece.iacl.plugins.dti.DWITensorEstCamino
edu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE
edu.jhu.ece.iacl.plugins.dti.AlgorithmDWIMotionCorrection
edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiGradientTableCreator
edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCamino
edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSmoothBrainMask
edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2009
edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmRemoveDura09
edu.jhu.ece.iacl.plugins.segmentation.cruise.MedicAlgorithmCRUISEplus
edu.jhu.ece.iacl.plugins.JistPluginUtil
edu.vanderbilt.VUIIS.plugins.JistMSWASSRMasked
edu.vanderbilt.masi.plugins.classification.LearnerPlugin
edu.vanderbilt.masi.plugins.labelfusion.AbstractVotingFusionPlugin
edu.vanderbilt.masi.plugins.labelfusion.AbstractStatisticalFusionPlugin
edu.umcu.plugins.utilities.roi.AlgorithmROIRangeStats


The problem results from trying to index citations while looping over authors. Should be an easy fix.

Fixed. Update will be reflected in the nightly build. More updates for specific modules in the works.