Upgrade protobuf plugin from 0.8.19 to 0.9.4 (#3101)

https://github.com/google/protobuf-gradle-plugin/releases

> - Significantly improve support for task configuration avoidance.
README.md has not yet been updated to encourage using configureEach
instead of each within generateProtoTasks {}, but it is beneficial as
long as you are not using any IDE plugins
> - Added generated code to java SourceSet instead of only adding it to
JavaCompile and related tasks. This should cause tasks like sourcesJar
and javadoc to now include the generated code. You may need to exclude
the generated code from linters

I skimmed through the differences in the generated java files in
protogen, and AFAICT the only change is that `Builder`s now have
`@SuppressWarnings("deprecation")` on them.

---------

Co-authored-by: Alec Grieser <[email protected]>

Author: ScottDugas

fdb-record-layer-jmh/fdb-record-layer-jmh.gradle

@@ -23,16 +23,6 @@ plugins {
 }
 
 apply from: rootProject.file('gradle/proto.gradle')
-sourceSets {
-    jmh {
-        proto {
-            srcDir "src/jmh/proto"
-        }
-        java {
-            srcDir 'protogen/jmh/java'
-        }
-    }
-}
 
 def coreProject = ":${ext.coreProjectName}"
 dependencies {

fdb-relational-grpc/fdb-relational-grpc.gradle

@@ -40,15 +40,6 @@ protobuf {
     }
 }
 
-sourceSets {
-    main {
-        java {
-            // Add these two dirs to the default src/main/java.
-            srcDir("${projectDir}/protogen/main/grpc")
-        }
-    }
-}
-
 dependencies {
     // Have grpc depend on fdb-relational-api. Anyone that uses grpc will also use api.
     // Having grpc depend on api makes it so we can add utility here shared by

gradle/libs.versions.toml

@@ -155,7 +155,7 @@ download = { id = "de.undercouch.download", version = "5.6.0" }
 gitversion = { id = "com.palantir.git-version", version = "3.1.0" }
 jmh = { id = "me.champeau.jmh", version = "0.7.2" }
 nexus = { id = "io.github.gradle-nexus.publish-plugin", version = "2.0.0" }
-protobuf = { id = "com.google.protobuf", version = "0.8.19" }
+protobuf = { id = "com.google.protobuf", version = "0.9.4" }
 serviceloader = { id = "com.github.harbby.gradle.serviceloader", version = "1.1.8" }
 shadow = { id = "com.github.johnrengelman.shadow", version = "7.1.2" }
 spotbugs = { id = "com.github.spotbugs", version = "6.1.3" }

gradle/proto.gradle

@@ -20,19 +20,6 @@
 
 apply plugin: 'com.google.protobuf'
 
-sourceSets {
-    main {
-        java {
-            srcDir 'protogen/main/java'
-        }
-    }
-    test {
-        java {
-            srcDir 'protogen/test/java'
-        }
-    }
-}
-
 configurations {
     compileProtoPath {
         // The default generated by com.google.protobuf.gradle.ProtobufPlugin.createCompileProtoPathConfiguration