Fix 'default messager has already been registered' warning

- Remove duplicate plugin application in samples-azure-functions/build.gradle
- Remove duplicate plugin application in endtoendtests/build.gradle
- Move 'java' plugin to plugins block
- Upgrade azure-functions plugin from 1.11.1 to 1.16.1

Co-authored-by: torosent <17064840+torosent@users.noreply.github.com>

Author: Copilot

endtoendtests/build.gradle

@@ -1,8 +1,7 @@
 plugins {
-    id "com.microsoft.azure.azurefunctions" version "1.11.1"
+    id 'java'
+    id "com.microsoft.azure.azurefunctions" version "1.16.1"
 }
-apply plugin: 'java'
-apply plugin: "com.microsoft.azure.azurefunctions"
 
 group 'com.durabletask.endtoend'
 version '0.0.0-SNAPSHOT'

samples-azure-functions/build.gradle

@@ -1,8 +1,7 @@
 plugins {
-    id "com.microsoft.azure.azurefunctions" version "1.11.1"
+    id 'java'
+    id "com.microsoft.azure.azurefunctions" version "1.16.1"
 }
-apply plugin: 'java'
-apply plugin: "com.microsoft.azure.azurefunctions"
 
 group 'com.functions'
 version '0.1.0-SNAPSHOT'