Saving an ILcdModel to a GeoPackage database is done by using the export method of the TLcdGeoPackageModelEncoder.

//Create a model by decoding a SHP file
ILcdModelDecoder decoder =
    new TLcdCompositeModelDecoder(TLcdServiceLoader.getInstance(ILcdModelDecoder.class));
ILcdModel model = decoder.decode("Data/Shp/Usa/city_125.shp");

//Use the model encoder to export the model to a GeoPackage file
TLcdGeoPackageModelEncoder encoder = new TLcdGeoPackageModelEncoder();
try (TLcdLockUtil.Lock readLock = TLcdLockUtil.readLock(model)) {
  encoder.export(model, outputFile);