Refactor: group file-format crates under a single top-level folder

[robinskil]

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Motivation

The workspace root currently holds ~20 beacon-* crate folders side by side. A large share of them are file-format adapters, which makes the top-level tree noisy and hard to scan. Grouping all file-format-related crates under a single parent folder would flatten the top-level directory and make the format layer easier to navigate as a cohesive unit.

Proposal

Move the file-format-related crates into a single parent folder (e.g. crates/formats/ or file-formats/) so the repository root has fewer entries and the format crates live together one level deeper.

Crates to move

Core format adapters / aggregator:

• beacon-arrow-atlas
• beacon-arrow-netcdf
• beacon-arrow-odv
• beacon-arrow-tiff
• beacon-arrow-zarr
• beacon-binary-format
• beacon-binary-format-toolbox (currently excluded from the workspace)
• beacon-formats (the aggregator that re-exports the above)

Supporting crates used by the format adapters (consider moving alongside, TBD during implementation):

• beacon-nd-array
• beacon-nd-arrow

Work required

1. Move the crate directories into the new parent folder.
2. Update members (and exclude) paths in the root Cargo.toml.
3. Fix the relative path = "../beacon-*" dependencies that point at the moved crates. Known consumers include:
   • beacon-core
   • beacon-functions
   • beacon-data-lake
   • beacon-formats (references all beacon-arrow-* + beacon-binary-format)
   • beacon-binary-format-toolbox
   • the moved crates referencing each other (beacon-nd-array, etc.)
4. Verify cargo build / cargo test across the workspace.
5. Update any Dockerfile COPY paths and CI references that hardcode crate paths.

Acceptance criteria

• All file-format crates live under one parent folder.
• Top-level directory has noticeably fewer entries.
• cargo build and cargo test pass for the whole workspace.
• Docker build still succeeds (path-sensitive COPY steps updated).
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