feat: Tight boundaries between generic spatial skeleton and catmaid; Use generic arrays over fixed x,y,z ; Update spatial skeleton metadata format

[afonsobspinto]

Closes https://metacell.atlassian.net/browse/NA-731

• The generic skeleton API defines SpatialSkeletonVector = ArrayLike<number>.
• Generic node positions use that vector type through SpatiallyIndexedSkeletonNodeBase.position.
• Bounds and spatial index chunk sizes also use the same vector representation.
• CATMAID-specific command code converts generic vectors into CATMAID x/y/z

Closes https://metacell.atlassian.net/browse/NA-741

• The generic source API now exposes fetchNodes(cellIndex: SpatialSkeletonGridCellIndex, ...).
• SpatialSkeletonGridCellIndex carries a cell vector rather than arbitrary lower/upper bounds.
• The CATMAID spatial skeleton source implements this by converting the grid cell index and chunk size into CATMAID bounds internally.

Closes https://metacell.atlassian.net/browse/NA-743

• The generic spatial skeleton metadata now has a spatial array.
• Each entry contains chunkSize, gridShape, and limit.
• CATMAID stack metadata is expected to provide metadata.spatial, with each level containing chunk_size and limit. f.e:

{"spatial": [{"limit": 500, "chunk_size": [12058882, 12058882, 12058882]}, {"limit": 500, "chunk_size": [7161485, 7161485, 7161485]}, {"limit": 2500, "chunk_size": [4253037, 4253037, 4253037]}, {"limit": 7000, "chunk_size": [2525778, 2525778, 2525778]}, {"limit": 0, "chunk_size": [1500000, 1500000, 1500000]}], "read_only": false, "cache_provider": "cached_msgpack_grid"}

Closes https://metacell.atlassian.net/browse/NA-767 and https://metacell.atlassian.net/browse/NA-766

• The generic editable source now requires command (class that implements execute, undo, redo?) factory properties keyed to explicit SpatialSkeletonActions
• Required editable operations are command factories:
  • addNodesCommand
  • deleteNodesCommand
  • moveNodesCommand
  • splitSkeletonsCommand
  • mergeSkeletonsCommand
• Optional editable operations are also command factories:
  • insertNodesCommand
  • rerootCommand
  • editNodeDescriptionCommand
  • editNodeTrueEndCommand
  • editNodeRadiusCommand
  • editNodeConfidenceCommand
• The generic flow asks for the command factory for a given action, creates a command, and runs it through generic command history.
• CATMAID owns the command implementations, including the state context creation, and the low-level CATMAID API calls.

Closes https://metacell.atlassian.net/browse/NA-725

• readOnly is part of the generic spatial skeleton source contract.
• Editable sources are explicitly typed as readOnly: false.
• CATMAID defaults to read-only.
• CATMAID stack metadata can explicitly set metadata.read_only: false to enable editing.

[afonsobspinto]

Moved to draft again as I need to re-test it after merging with latest feature/edit-mode

[seankmartin]

Generally it looks good to me and a much clearer boundary, thank you for the changes here. Most of the comments I've made are minor. The bigint/number issue I didn't spot before now, and it isn't a regression, so I'd personally be fine with us addressing it separately to this PR.

I think the the only other part I'm unsure on is what changed that we can't or at least don't use the code in spatial_chunk_sizing if there is no spatial metadata and instead reject the source

[seankmartin]

How does this work with segmentIDs being bigint? Ids in general, such as NodeIDs and parentNodeId also bigint. I think the problematic part is likely here

  getNodes(
    options: {
      segmentId?: bigint;
      lod?: number;
    } = {},
  ): SpatiallyIndexedSkeletonNode[] {
    void options.lod;
    const normalizedSegmentFilter =
      options.segmentId === undefined
        ? undefined
        : Math.round(Number(options.segmentId));

in the frontend, options.segmentId could be too large to be a number. Not sure if this has any effect on our hash map, but I think that was already designed to work with bigint