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Nix: Fix the build inputs for the shell and app.
This makes a few changes to the Nix flake to get things building on my machine. 1. On macOS, add `CoreFoundation` to the list of dependencies. 2. Remove `pkg-config`; we don't seem to need it. 3. Move `protobuf` to `nativeBuildInputs` as it's required at runtime. 4. Reuse inputs from the default package in the shell. The last point is partially undoing a change I made earlier, where the shell brought in inputs from all flake checks. This was way too broad; this narrows it a lot.
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