We need to remove empty modules (except for pom.xml) when transport changes.

For example, in googleapis/googleapis@de97a5f, the transport changed from grpc+rest to rest and the source code in the grpc module is removed. However, the pom.xml in the module is not removed and cause test failure in graalvm build:

09:13:06:345 [ERROR] Failed to execute goal org.graalvm.buildtools:native-maven-plugin:0.10.3:test (test-native) on project google-cloud-connectgateway: Missing jar-file for com.google.api.grpc:grpc-google-cloud-connectgateway-v1:jar:0.6.0:test. Ensure that native-maven-plugin runs in package phase. -> [Help 1]

We should either

1. Remove the pom.xml from a module if there's no source code
2. Do not generate pom.xml if there's no source code (this is preferable)

part of b/372713264