Gradle protobuf plugin still uses Configuration.setVisible()

Since Gradle 9.0.0, the `Configuration.setVisible()` no longer has a meaningful effect. We will be deprecating this method in Gradle 9.8.0 with eventual removal in Gradle 11.0.0.

The protobuf plugin calls this method [here](https://github.com/google/protobuf-gradle-plugin/blob/master/src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy#L166) and [here](https://github.com/google/protobuf-gradle-plugin/blob/master/src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy#L187).

Since this method has no effect any more, the correct resolution here would be to simply remove the method call.

Open src/main/groovy/com/google/protobuf/gradle/ProtobufPlugin.groovy and inspect the calls at lines 166 and 187. Remove both Configuration.setVisible() calls; the work is done when the plugin no longer invokes this deprecated, ineffective method.

Written by the indexing model from the issue text.