[jnigen] Use `String` instead of `Uri` everywhere

[HosseinYousefi]

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[dcharkes]

@HosseinYousefi Please contribute to the discussion https://github.com/dart-lang/native/issues/1506 if you care. 👌 Then we can align the packages. (Especially, when we start using the Dart instead of YAML config and we get a hook for running code-gens. Then we don't want to be converting between File/Uri/String.)

[HosseinYousefi]

I think using strings is simplest in the move to a dart config (instead of yaml). Will do this after removing the yaml config because package:config uses Uris.