Fix java_package option support

In a `.proto` file you can specify an option for a Java package name. When `protoc`, the compiler from proto files to language specific source code, is run in Java mode with this option it will inflate this package name into a directory structure. (For example, a proto file with the java_package set to `com.example.myproj` will inflate to `com/example/myproj` when compiled to Java source code)

This module did not account for this, resulting in it incorrectly reporting the target file names for some proto file inputs. This pull request fixes that and does minor clean-up (trailing whitespace and commented out code).