Hot fix: root attributes

Summary

This hotfix improves AnnData on-disk schema compliance and subset-output interoperability, especially for downstream tools that validate element metadata.

Highlights

1) Root AnnData metadata enforcement

• Enforced root attributes on writable store operations:
  • encoding-type: "anndata"
  • encoding-version: "0.1.0"
• Added non-fatal read-time warning when these root attributes are missing.
• Applied enforcement consistently through store copy/convert paths.

2) Subset output schema hardening

• subset now guarantees presence of optional AnnData mapping groups when absent in source:
  • layers, obsm, obsp, varm, varp
• These mapping groups now carry mapping metadata for compatibility with this codebase’s documented schema:
  • encoding-type: "dict"
  • encoding-version: "0.1.0"

3) Documentation updates

• Updated element specification docs for HDF5 and Zarr to align with latest requirements and preserve explicit legacy compatibility notes.
• Clarified handling of historical mapping metadata (dict v0.1.0) for backward compatibility.

Test Coverage Added/Updated

• Added tests for root AnnData attribute enforcement and warning behavior.
• Added/updated subset integration tests to validate optional group creation and mapping metadata.

Impact

• No intended breaking CLI changes.
• Improves compatibility with schema-aware downstream readers.
• Reduces risk of malformed subset outputs due to missing mapping metadata.

Notes for users

• Some anndata versions (notably <= 0.12.0) may still fail in experimental.concat_on_disk(..., merge='same') when var contains columns due to upstream behavior. This is version-specific to anndata, not specific to this hotfix.

Included changes (since 0.3.1 baseline)

• Source: storage metadata enforcement and subset schema fixes
• Docs: element specification updates (HDF5/Zarr)
• Tests: new/expanded coverage for storage/subset behavior
• Lockfile: updated uv.lock