There is a "gds flatten [true| false]" option, but it is used for small cells like contacts and is mainly designed to work around the fact that the best representation for contacts in GDS is to create arrays of subcells, which is not a particularly good way to represent them in the magic database. There are ways to handle this particular problem within the "cifinput" section of the magic techfile, but it is very hard to deal with types like nwell that modify the type of device when they are in a higher-level cell. I often just read in the GDS and patch things up by hand, but it depends on the complexity and size of the GDS file.