Migrate development and CI to uv and remove Upstream checks

[Billyzhang1229]

Fixes #1351.

This PR moves development and CI dependency management to uv and removes the Upstream dependency checks. These changes are split into two commits.

Changes included:

• Remove the Upstream workflow, its installation script, the README badge, and related contributor documentation.
• Replace the requirements files with dependency groups in pyproject.toml and a committed uv.lock.
• Provide test, docs, lint, and packaging groups, with an aggregate dev group for local development.
• Update contributor instructions to use uv sync and uv run.
• Use locked dependencies in standard CI, including scheduled runs, and document periodic, reviewed lockfile updates.
• Keep cd docs && make html using the shared .venv. Docs workflows install dask==2026.8.0 for task-graph rendering with NumPy 2, and the Makefile uses uv run --no-sync to preserve that override. Document local setup and restoring locked dependencies before testing.
• Migrate package builds and wheel installation checks to uv.
• Retain Cubed and Zarr compatibility testing. Limit Cubed upgrades to the experimental packages and any necessary dependency changes.

Existing runtime dependency ranges, optional extras, and Python support are preserved.

Left for follow-up PRs:

• Runtime dependency upgrades and relaxed version bounds, including newer Dask, xarray, numba and SciPy versions.
• Address any compatibility changes those upgrades require, including a previously identified tajimas_D issue.
• Remove the temporary documentation Dask override once a common version passes both tests and documentation builds.
• Upgrading the bio2zarr/Zarr stack and broader Zarr 3 support.
• Revisit the disabled GPU workflow.

Validation: local tests passed with 100% coverage; strict documentation builds and package smoke tests passed. Build, Windows, Check docs, and Cubed CI passed. The upstream-only Wheels workflow and GPU workflow were not exercised.