fix: validate consolidated metadata listing keys and hierarchy

[barlowa124]

Summary

Second item of #4453. ConsolidatedMetadata.from_dict (and
GroupMetadata.from_dict, which delegates to it) accepted listings
the spec rules out, two of which broke reads.

Listing keys are node paths, so keys with an empty segment ("",
a//b) are now rejected with MetadataValidationError. Keys carrying
a reserved segment emit
a ZarrDeprecationWarning naming the key and advising a rename,
avoiding breakage of stores that work today.

Every non-root key also needs its ancestors present as group entries:
{"a/b": GROUP} used to surface as GroupNotFoundError on open,
making the root unopenable from one entry. It now fails with a clear
MetadataValidationError, as does a listing nested under an array.
v2 listings skip the name checks entirely. The remaining #4453 items
are untouched.

For reviewers

The reserved-name path moved from rejection to deprecation after
review, since stores written today with __-prefixed names still open
on main. It becomes a hard error once #4484 stops those names being
written. The empty-segment rule stays strict because consolidated keys
are node paths and node names cannot be empty. If #4484 lands first,
this can reuse its helper for the reserved-name part.

Author attestation

• I am a human. These are my changes. I have reviewed and understood every change and can explain why each is correct.

TODO

Done:

• Add unit tests and/or doctests in docstrings
• Add docstrings and API docs for any new/modified user-facing classes and functions
• New/modified features documented in docs/user-guide/*.md

Outstanding:

• Changes documented as a new file in changes/
• GitHub Actions have all passed
• Test coverage is 100% (Codecov passes)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.72%. Comparing base (069fd20) to head (9156127).
⚠️ Report is 15 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4485      +/-   ##
==========================================
+ Coverage   94.69%   94.72%   +0.03%     
==========================================
  Files          94       94              
  Lines       13606    13685      +79     
==========================================
+ Hits        12884    12963      +79     
  Misses        722      722              

Files with missing lines	Coverage Δ
src/zarr/core/group.py	95.77% <100.00%> (+0.09%)	⬆️

... and 3 files with indirect coverage changes

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[d-v-b]

1. Warn instead of raising when a v3 consolidated listing has a reserved node name (__-prefixed, zarr.json, ., ..). today we can write __a (create_array("__a") plus consolidate_metadata), and those stores open on main. With this PR, zarr.open_group(store) raises MetadataValidationError for the whole group, siblings included. Make it a deprecation warning that describes the listing and says to rename the node, and raise only after #4484 has stopped these names being written.
2. Don't apply the reserved-name rules to v2 listings. The v2 spec doesn't reserve these names, and v2 .zmetadata goes through the same from_dict.
3. Keep raising for a child listed without its parent and for a node listed below an array. Those listings already failed (KeyError, unopenable root), so a clear error is an improvement.
4. Use single backticks in changes/4485.bugfix.md, and say which cases warn and which raise.

[d-v-b]

we don't want to break stuff that works today, even if it violates a subtle part of the spec. so lets do this via deprecation

[barlowa124]

fc0e8cf makes the changes.

1. Reserved names in a v3 listing now emit a ZarrDeprecationWarning naming the key and advising a rename. create_array("__a") plus consolidate_metadata stores open with a warning instead of MetadataValidationError. Keys with empty path segments still raise, since no stored node can have an empty name.
2. v2 listings skip the name checks entirely.
3. Missing-parent and below-array listings still raise MetadataValidationError.
4. The changelog uses single backticks and states which cases warn and which raise.

python -m pytest tests/test_metadata/test_consolidated.py tests/test_group.py gives 1028 passed.

[barlowa124]

Done in fc0e8cf: reserved node names in a v3 consolidated listing now emit a ZarrDeprecationWarning instead of raising, so stores that write __a today keep opening while the name is flagged for rename. The raised checks that remain are the structural ones: empty path segments, a missing parent entry, a node listed under an array. Those produce stores that cannot be read back at all. 1913880 and 9156127 are format and test cleanup on top.