Update dependencies for xarray, zarr-python, icechunk, kerchunk

[TomNicholas]

Currently to use icechunk with virtualizarr you need multiple special branches of various packages. Once those get released we need to update the (optional or required) dependencies of virtualizarr and the upstream-dev CI environment dependencies.

Tracking:

• Xarray - Compatibility for zarr-python 3.x pydata/xarray#9552
• Kerchunk - zarr-python v3 compatibility fsspec/kerchunk#516
• Zarr-Python - we want beta to become main
• Icechunk - conda-forge receipe for icechunk-python earth-mover/icechunk#252

[TomNicholas]

Closed by everything that allowed v1.3.0