there is a new addon v.clean.ogr that imports a single OGR layer with
polygons, cleans the polygons, and exports the polygons again. Any overlaps
are exported as a separate OGR layer.
This tool should only be used with polygons that are not supposed to
overlap. For example, administrative boundaries in NUTS 2013  correctly
overlap in layer UTS_RG_60M_2013_3035 because this layer contains several
levels at once. A particular level can be selected during import or with
v.clean.ogr with the where option, e.g. where='LEVL_CODE = 0' selects
country borders which are not supposed to overlap.
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