Implement option to transpose neighbor lists of PrecomputedNeighborhoodSearch

[efaulhaber]

This PR implements the "transposed NL" optimization mentioned in trixi-framework/TrixiParticles.jl#968. See this PR for benchmark results.

[Copilot]

Pull request overview

This PR implements an option to transpose the neighbor lists data structure in PrecomputedNeighborhoodSearch to optimize GPU performance through coalesced memory access patterns. When transpose_backend = true, the first neighbors of all points are stored contiguously in memory rather than all neighbors of each point, which can provide up to 3x speedup on GPUs.

• Added transpose_backend parameter to PrecomputedNeighborhoodSearch and related functions
• Implemented transposed memory layout using PermutedDimsArray wrapper in DynamicVectorOfVectors
• Added comprehensive tests to verify both regular and transposed backend behavior
• Updated documentation to explain when to use transposed backend (GPU vs CPU optimization)

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
test/unittest.jl	Added inclusion of new test file for precomputed neighborhood search
test/nhs_precomputed.jl	New test file verifying both regular and transposed backend memory layouts
src/vector_of_vectors.jl	Extended DynamicVectorOfVectors constructor to support transpose option and added helper functions to check backend type
src/nhs_precomputed.jl	Added transpose_backend parameter with detailed documentation about CPU vs GPU optimization trade-offs
src/nhs_grid.jl	Added documentation note about search_radius type determining distance computation type
src/nhs_trivial.jl	Added documentation note about search_radius type determining distance computation type
src/cell_lists/cell_lists.jl	Updated construct_backend functions to accept and propagate transpose_backend parameter with validation
src/PointNeighbors.jl	Exported DynamicVectorOfVectors for public API access

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[codecov]

Codecov Report

❌ Patch coverage is 93.75000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 84.82%. Comparing base (d8b0de2) to head (14bf102).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/cell_lists/cell_lists.jl	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #137      +/-   ##
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+ Coverage   84.75%   84.82%   +0.07%     
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  Files          15       15              
  Lines         715      725      +10     
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+ Hits          606      615       +9     
- Misses        109      110       +1     

Flag	Coverage Δ
unit	84.82% <93.75%> (+0.07%)	⬆️

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