Employ `<required_files>` where it is missing

[kostrykin]

required_files is necessary for the tools not to fail on Pulsar: #214

List of tools that have issues with missing required_files:

• /tools/orientationpy/orientationpy.xml
• /tools/plantseg/plantseg.xml
• /tools/overlay_images/overlay_images.xml Update ip_overlay_images tool: Add required_files #214
• /tools/permutate_axis/permutate_axis.xml
• /tools/mergeneighboursinlabelimage/mergeneighboursinlabelimage.xml
• /tools/2d_histogram_equalization/histogram_equalization.xml
• /tools/binaryimage2points/binaryimage2points.xml
• /tools/split_image/split_image.xml
• /tools/split_labelmap/split_labelmap.xml
• /tools/anisotropic_diffusion/anisotropic_diffusion.xml
• /tools/ridge_filter/skimage.xml
• /tools/image_registration_affine/image_registration_affine.xml
• /tools/background_removal/background_removal.xml
• /tools/scale_image/scale_image.xml
• /tools/slice_image/slice_image.xml
• /tools/voronoi_tessellation/voronoi_tessellation.xml
• /tools/spot_detection_2d/spot_detection_2d.xml Update ip_points_association_nn, ip_curve_fitting, ip_spot_detection_2d: Employ required_files, changes output formats tsv to tabular #216
• /tools/color_deconvolution/color_deconvolution.xml
• /tools/coordinates_of_roi/coordinates_of_roi.xml
• /tools/projective_transformation/projective_transformation.xml
• /tools/curve_fitting/curve_fitting.xml Update ip_points_association_nn, ip_curve_fitting, ip_spot_detection_2d: Employ required_files, changes output formats tsv to tabular #216
• /tools/wsi_extract_top_view/wsi_extract_top_view.xml
• /tools/segmetrics/segmetrics.xml Update ip_segmetrics: Migrate from ZIP files to paired lists #213
• /tools/imagecoordinates_flipaxis/imagecoordinates_flipaxis.xml
• /tools/landmark_registration/landmark_registration.xml
• /tools/superdsm/superdsm.xml
• /tools/points2labelimage/points2label.xml
• /tools/morphological_operations/morphological_operations.xml
• /tools/labelimage2points/labelimage2points.xml
• /tools/colorize_labels/colorize_labels.xml Update colorize_labels: Add phase parameter + Zarr support #218
• /tools/highdicom/dicom2text.xml
• /tools/highdicom/dicom2tiff.xml
• /tools/count_objects/count_objects.xml
• /tools/repeat_channels/repeat_channels.xml
• /tools/projective_transformation_points/projective_transformation_points.xml
• /tools/points_association_nn/points_association_nn.xml Update ip_points_association_nn, ip_curve_fitting, ip_spot_detection_2d: Employ required_files, changes output formats tsv to tabular #216
• /tools/concat_channels/concat_channels.xml Update ip_concat_channels: Add options for spacing + Employ required_files #217
• /tools/detection_viz/detection_viz.xml
• /tools/mahotas_features/mahotas_features.xml
• /tools/crop_image/crop_image.xml
• /tools/label_to_binary/label_to_binary.xml