Just to add, as also discussed in another recent thread, I believe that the option to use nccopy to convert netCDF-4 compressed files back to netCDF files using the classic data model hinges upon whether your netCDF installation (which nccopy is a part of, just like ncdump and ncgen) was built with netCDF4 support or not.
Put differently, to use these files, at a minimum you will need to have a netCDF installation with netCDF4 support to be able to use nccopy. Once you have that installation, you could then also opt to use that installation to build the I/O API libraries used in building CCTM in which case CCTM should be able to read these netCDF4 files directly without having to convert them with nccopy first.
Full disclaimer: I do not have a netCDF installation without netCDF4 support, so I did not verify that nccopy from such an installation would fail in converting the netCDF4-compressed files to netCDF classic, but conceptually that’s what I would expect to happen. I’d be glad to be wrong here, and I very well might be wrong, but I just thought I’d spell out these considerations since these netCDF4-compressed files are becoming more common, including in our own work.