I did quite a lot. Too much to describe here, actually :)

modified:   ../../../skeleton/modules/myJuliaModule.jl
modified:   ../../../skeleton/modules/myMatlabModule.m
modified:   ../../../skeleton/modules/myPythonModule.py
modified:   ../../../skeleton/modules/myRModule.R
modified:   ../../../skeleton/myPipeline.pipe

modified:   ../../../src/julia/jterator/api/mscript.jl
modified:   ../../../src/python/jterator/checker.py
modified:   ../../../src/python/jterator/module.py
modified:   ../../../src/python/jterator/runner.py

new file:   handles/IdentifyNuclei.handles
deleted:    handles/IdentifyPrimary.handles
modified:   handles/IllumCorr.handles
renamed:    handles/MeasurePrimary.handles -> handles/MeasureObjects.handles
renamed:    handles/Plot.handles -> handles/PlotMeasurements.handles
modified:   handles/PrimeRawData.handles

new file:   modules/IdentifyNuclei.m
deleted:    modules/IdentifyPrimary.jt
renamed:    modules/IllumCorr.jt -> modules/IllumCorr.m
renamed:    modules/MeasurePrimary.jt -> modules/MeasureObjects.py
renamed:    modules/Plot.jt -> modules/PlotMeasurements.R
deleted:    modules/PrimeRawData.jt
new file:   modules/PrimeRawData.py
renamed:    modules/Whatever.jt -> modules/Whatever.jl

renamed:    subfunctions/JTthreshold.m -> subfunctions/+subfunctions/ImageThreshold.m
new file:   subfunctions/+subfunctions/PerimeterAnalysis.m
new file:   subfunctions/+subfunctions/PerimeterWatershedSegmentation.m
new file:   subfunctions/+subfunctions/SelectObjects.m