DM: Now extrusion is like DMRefine() and implemented through DMPlexTransform - DMExtrude() replaces DMPlexExtrude() - Added an extrusion transformation - Added DMPlexTransformSetDimensions() and setd

DM: Now extrusion is like DMRefine() and implemented through DMPlexTransform - DMExtrude() replaces DMPlexExtrude() - Added an extrusion transformation - Added DMPlexTransformSetDimensions() and setdimensions function - DMPlexTransformMapCoordinates() and DMPlexSnapToGeomModel() now take the coordinate dimension - -dm_extrude replaces -dm_plex_extrude_layers

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Fix manpages: more errors reported by doctext

Fix manpages: mismatching number of parameters

Fix manpages: Input/Output Parameter --> Parameters

Plex: DMPlexTransform is now the way to manipulate a Plex
- Replace DMPlexCellRefiner with DMPlexTransform
- Replace CellRefinerInCellTest_Internal() with DMPolytopeInCellTest()
- Replace DMPlexCe

Plex: DMPlexTransform is now the way to manipulate a Plex
- Replace DMPlexCellRefiner with DMPlexTransform
- Replace CellRefinerInCellTest_Internal() with DMPolytopeInCellTest()
- Replace DMPlexCellRefinerGetAffineTransforms() with
DMPlexRefineRegularGetAffineTransforms()

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