Remove references to non-existent Zarr chunk manifest format

[TomNicholas]

When this package was started Icechunk did not exist. The plan at that time was to generalize Zarr with a ZEP to add manifest.json files to the spec. There are methods in the code and docs that experimentally write to and read from this format, even though it is not currently supported anywhere else (including in Zarr-python itself).

These references are arguably now vestigial, and confusing. They should be removed until such a time as someone actually implements a Zarr store that uses the manifest.json format on-disk (but they probably never will, because they would now be better off just using Icechunk's format instead).