You cannot find any Java files under these packages in the hadoop source code repository. Java files under this packages will be generated by protoc compiler
When you execute maven install mvn install -DskipTests
protoc compiler will generate the corresponding .java files
For Setting up hadoop build environment, refer the following link
http://wiki.apache.org/hadoop/HowToContribute
Install native libraries Install protobuf etc. Refer above link for detailed information
Once you successfully execute the command mvn install -DskipTests
you can see the java files under protobuf packages