Update scripts.

java-restructuring

models/common-functions.rc

models/dotPic-single-fileConverter.sh

models/logback.xml

models/make-tables-and-images.sh

models/mitgcm/combine-models.sh

models/mitgcm/compare-models.sh

models/mitgcm/compute-statistics.sh

models/mitgcm/console-logger.xml

models/mitgcm/prepare-models-for-inspection.sh

models/mitgcm/run-all.sh

models/mitgcm/run-architecture-analysis.sh

models/mitgcm/run-dynamic-analysis.sh

models/mitgcm/run-dynamic-observation.sh

models/mitgcm/run-static-analysis.sh

models/mitgcm/run-static-code-processing.sh

models/uvic/combine-models.sh

models/uvic/compare-models.sh

models/uvic/compute-statistics.sh

models/uvic/linux_amd64_gfortran_kieker