Chunk-aligned indexing on ManifestArray

[TomNicholas]

Summary

Implements chunk-aligned integer and slice indexing on ManifestArray, making xarray.Dataset.isel work end-to-end on virtual datasets for any chunk-aligned selection.

• Slice indexers preserve the axis. Multi-chunk slices, mixed integer + slice, and selections that end on a partial final chunk all work.
• Integer indexers drop the indexed axis (numpy / array-API semantics). Only legal when chunk_size == 1 along that axis; picking a single element of a larger chunk is sub-chunk indexing and raises.
• Misaligned selections raise the new SubChunkIndexingError — a ValueError subclass, not NotImplementedError, because splitting compressed chunks without loading bytes is a permanent constraint of a virtual array.
• Previously slice misalignment silently no-op'd while integer indexing unconditionally raised NotImplementedError. Both paths are now real.

Implementation lives in virtualizarr/manifests/indexing.py: each 1D indexer is translated into a chunk-grid selector (int when the array axis is dropped, slice otherwise), the manifest's _paths / _offsets / _lengths arrays are subset in one shot via numpy fancy indexing, the inlined-chunk dict is filtered and re-keyed, and the metadata is rebuilt with the kept axes' shape, chunks, and dimension_names.

Documents the headline use case in docs/scaling.md under "Tips for success": parse one massive Zarr store with ZarrParser, then write to Icechunk in chunk-aligned .isel slices to stay under the 50M-chunk-refs-per-commit limit.

Supersedes #499 (the old branch had diverged 151 files from main and the indexing framework on main is a clean rewrite from #734 / #730, so I picked up the goal of #499 on a fresh branch rather than rebasing).

Test plan

• virtualizarr/tests/test_manifests/test_array.py::TestIndexing — 49 cases covering chunk-aligned int/slice, multi-dim, mixed, partial final chunk, axis dropping, and misalignment errors
• virtualizarr/tests/test_xarray.py::TestIsel — 6 cases routing through xarray's .isel: slice along chunk boundary, length-1-slice (keeps axis), integer (drops axis), integer misaligned (raises), slice misaligned (raises), iterative chunk-aligned append simulation
• No regressions across test_manifests/, test_xarray.py, test_integration.py, test_writers/ (333 tests pass)
• Pre-commit hooks clean

Acceptance criteria

• Closes Support indexing by slicing along chunk boundaries? #51
• Tests added
• Tests passing
• Full type hint coverage
• Changes are documented in docs/releases.md
• New functionality has documentation (docs/scaling.md, docs/data_structures.md, docs/faq.md, and the __getitem__ docstring)

[codecov]

Codecov Report

❌ Patch coverage is 90.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.98%. Comparing base (8d7c33a) to head (34ff775).

Files with missing lines	Patch %	Lines
virtualizarr/manifests/indexing.py	90.00%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #994   +/-   ##
=======================================
  Coverage   89.97%   89.98%           
=======================================
  Files          33       33           
  Lines        2064     2066    +2     
=======================================
+ Hits         1857     1859    +2     
  Misses        207      207           

Files with missing lines	Coverage Δ
virtualizarr/manifests/array.py	85.00% <ø> (ø)
virtualizarr/manifests/indexing.py	93.33% <90.00%> (+0.47%)	⬆️

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