refactor: deepen GSDTools query execution seams (#3085)
* refactor: deepen gsdtools query execution seams * docs: add changeset for query seam deepening * docs: fix changeset summary text * fix: address coderabbit query seam findings * test: address remaining coderabbit findings and notes * refactor: use internal gsdtools error type import
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type: Changed
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pr: 3085
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**`GSDTools` query execution internals now use deep Module seams** — refactors runtime composition, native/subprocess adapters, and output projection behind stable public interfaces for better locality and testability.
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