Include root-level Java files in source set

Uncommented and updated the configuration to include all .java files at the project root in the source set. This ensures that Java files located directly in the project directory are recognized and compiled.

Author: Stefterv

java/gradle/src/main/kotlin/ProcessingPlugin.kt

@@ -165,9 +165,9 @@ class ProcessingPlugin @Inject constructor(private val objectFactory: ObjectFact
                 srcDir("$workingDir/unsaved")
             }
             sourceSet.allSource.source(pdeSourceSet)
-//            sourceSet.java.srcDir(project.layout.projectDirectory).apply {
-//                include("*.java")
-//            }
+            sourceSet.java.srcDir(project.layout.projectDirectory).apply {
+                include("/*.java")
+            }
 
             val librariesTaskName = sourceSet.getTaskName("scanLibraries", "PDE")
             val librariesScan = project.tasks.register(librariesTaskName, LibrariesTask::class.java) { task ->