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[native_assets_builder] Use ` package:file`s `FileSystem` abstraction (#1825)

The main motivation for this change is to make `package:native_assets_builder` cleanly usable in flutter tools. Right now flutter tools operates on a `FileSystem` and checks whether `.dart_tool/package_config.json` exists using that `FileSystem` but then reads the file with this packagag's code which uses `dart:io`.

This inconsistency causes issues in flutter tools. Using `package:file` should solve this and would also
allow injecting mocks. To be fully mockable the implementation would also need to make process invocations
mockable via `package:process`. That's a future task.

See also https://github.com/dart-lang/native/issues/90

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