Following is an example of the usage to fix an imported mesh that has small faults.
Running checkMesh on this geometry:
foamJob -s checkMesh -allTopology -allGeometry
generates some warnings and errors, but most important, several sets: cellZone_1, cellZone_2, concaveFaces, edgeFaces, nearPoints, nonOrthoFaces, skewFaces, undedeterminedCells, warpedFaces, wrongOrientedFaces. The next step is to collect all the cells that contain any of the concave faces, incorrect edge faces, warped faces, wrong oriented faces, or cells with a very small determinant:
foamJob -s setSet -constant Command>list Command>cellSet bubu new cellToCell underdeterminedCells any Command>list Command>cellSet bubu add faceToCell concaveFaces any Command>cellSet bubu add faceToCell edgeFaces any Command>cellSet bubu add faceToCell warpedFaces any Command>cellSet bubu add faceToCell wrongOrientedFaces any Command>cellSet bubu invert Command>cellSet bubu subset Command>quit foamJob -s subsetMesh bubu