Adopt copick 2.0.0-alpha.1 and metadata-based Zarr reads

[uermel]

Parent Epic: #39
Implementation: #45

Goal

Adopt the published copick 2.0 alpha runtime and replace metadata-blind Zarr reads with one explicitly read-only accessor.

Scope

• Require Python >=3.11, NumPy >=2.0.2, copick >=2.0.0a1,<3, copick-shared-ui >=2.0.0a1,<3, and Zarr >=3.1.6,<4.
• Remove unused napari-ome-zarr and regenerate the compatible lock.
• Open entity stores with zarr.open_group(store=..., mode="r").
• Resolve ordered datasets through get_multiscales() and get_level_path().
• Preserve non-negative high-level clamping; reject negative levels and invalid metadata clearly.
• Use the accessor for tomograms, segmentations, and level-zero target-shape discovery.
• Derive (z, y, x) viewer scale from OME transforms relative to entity voxel size.
• Preserve full NumPy materialization and existing worker result contracts.
• Update classifiers, repository URLs, CI versions, and README accuracy.

Acceptance criteria

• OME-Zarr 0.4/v2 and 0.5/v3 numeric and non-numeric paths return exact selected data.
• Segmentation reads request read-only access.
• One-level clamping and malformed-store errors behave clearly.
• Non-power-of-two transforms produce the expected layer scale.
• The locked source behavior suite passes.

No dedicated dependency tests, structural source scans, or AST parsing are required.