docs: streamline agent guidance and standardize rustdoc links
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## Main entry points
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- [`core_builtin_tools`](src/lib.rs) / [`routed_builtin_tools`](src/lib.rs): registration by provider capability and connection resolution.
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- [`checkout`](src/checkout.rs): shared handling for route-bound native operations and regular Tools.
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- [`tracker`](src/tracker.rs): read hashes and change tracking per connection generation.
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- [`view_image`](src/view_image.rs): bounded byte retrieval and image detection.
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- [`core_builtin_tools`] / [`routed_builtin_tools`]: registration by provider capability and connection resolution.
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- [`checkout`]: shared handling for route-bound native operations and regular Tools.
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- [`tracker`]: read hashes and change tracking per connection generation.
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- [`view_image`]: bounded byte retrieval and image detection.
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