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The imported fields do not seem to be assigned to the correct fieldgroups.
When I look into the database, at the display_settings field, I see that it has the 'parent' field set correctly -- it just doesn't seem to actually show up correctly in the UI.
I suspected that this was because fieldgroup wasn't allowed to insert its hooks, so I made sure I was running alternate_content_copy_import_content with $require_hooks_execution set to true. But this does not seem to work.