Remove Kerchunk from dependencies where possible

[TomNicholas]

Now that the Kerchunk package is officially deprecated, we should remove any dependencies on Kerchunk we can.

We still want to keep the ability to read and write refs from the Kerchunk JSON/Parquet formats (since file formats are eternal), but for that we only need to keep the Kerchunk parsers / writer, and neither of those need to actually import the Kerchunk package.

Specifically, we should:

• Remove kerchunk from test deps, in favour of all tests using ManifestStore where possible,
• Rewrite all parsers that still use Kerchunk to be standalone, which I think are now just:
  • NetCDF3 (started in Re-implement netCDF3 parser without Kerchunk #1086)
  • FITS (started in Reimplement the FITS parser natively, without kerchunk #1090)