chore: reorganize design issues as subissues under #53

Moved design refinement issues to be subissues under #53:
- #68: Redesign ndarrayShimUri for multiple array storage methods
- #69: Review optional metadata fields in sampleSchema
- #70: Remove redundant previousVersion/migrationLens fields
- #71: Refactor jsonSchema to flexible schema field

Closed original issues #64-67 with superseded notes.

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Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>