Revert "return of the labeled output (should be temporary though)"

This reverts commit 319e479f1e1b1465685b979c227e3a16d6040645.
remove Mesh3D from jar export
Add ROI on duplicated input image (like before) and name them correctly (with digit padding)
fix contour number in overlay to match the final result
Dilate and fill holes in each ROI2DArea before triangulating