CommandLineModules allow the module writer to specify the type of images/geometry file formats to transmit to the module. Slicer will write image/model nodes to the specified format before executing the module. If the file format is a type that produces several files, for instance, a mhd file which produces a small ascii header file and a separate bulk data file, then the CommandLineModule looses track of the bulk data file and does not delete it when the module completes.

Meta, Analyze, Nrrd (header), DICOM can all produce multiple files when they are written to disk. The IO mechansism will properly load these multiple file images/geometries. However, the cleanup code does not know to remove the secondary or dependent files.

We should suggest that module writers only use file formats that use a single file. Or we need to build a mapping from master file to dependent files. Some of these are not too bad, mhd->raw, hdr->img, etc. However, some header files can reference many many dependent files (where each slice in a series results in a separate file).