Increase minimum Cython version to 3.1 everywhere

[Copilot]

Bumps the minimum required Cython version from 3.0 to 3.1 across all configuration and validation points.

Changes

• pyproject.toml: Update dependency to Cython>=3.1
• autowrap/__init__.py: Runtime version check now validates major.minor >= 3.1
• tests/test_cython_version.py: Test updated to verify >= 3.1
• .github/workflows/ci-autowrap.yaml: Remove Cython 3.0.0 test matrix entries

Original prompt

Increase the minimum cython version to 3.1 everywhere

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