IDEA-383444 Keep existing dependencies in sync contributors

plugins/gradle/plugin-resources/META-INF/plugin.xml

@@ -71,6 +71,7 @@
     <syncContributor implementation="org.jetbrains.plugins.gradle.service.syncAction.impl.contributors.GradleContentRootSyncContributor"/>
     <syncContributor implementation="org.jetbrains.plugins.gradle.service.syncAction.impl.contributors.GradleVersionCatalogSyncContributor"/>
     <syncExtension implementation="org.jetbrains.plugins.gradle.service.syncAction.impl.extensions.GradleJpsSyncExtension"/>
+    <syncExtension implementation="org.jetbrains.plugins.gradle.service.syncAction.impl.extensions.GradleDependencySyncExtension"/>
     <syncExtension implementation="org.jetbrains.plugins.gradle.service.syncAction.impl.extensions.GradleBaseSyncExtension"/>
     <syncExtension implementation="org.jetbrains.plugins.gradle.service.syncAction.impl.extensions.GradleDependencySubstitutionSyncExtension"/>
 

plugins/gradle/src/org/jetbrains/plugins/gradle/service/syncAction/impl/extensions/GradleDependencySyncExtension.kt

@@ -0,0 +1,47 @@
+// Copyright 2000-2025 JetBrains s.r.o. and contributors. Use of this source code is governed by the Apache 2.0 license.
+package org.jetbrains.plugins.gradle.service.syncAction.impl.extensions
+
+import com.intellij.openapi.externalSystem.util.Order
+import com.intellij.platform.workspace.jps.entities.InheritedSdkDependency
+import com.intellij.platform.workspace.jps.entities.ModuleEntity
+import com.intellij.platform.workspace.jps.entities.SdkDependency
+import com.intellij.platform.workspace.jps.entities.modifyModuleEntity
+import com.intellij.platform.workspace.storage.MutableEntityStorage
+import org.jetbrains.plugins.gradle.service.project.ProjectResolverContext
+import org.jetbrains.plugins.gradle.service.syncAction.GradleSyncExtension
+import org.jetbrains.plugins.gradle.service.syncAction.GradleSyncPhase
+
+/**
+ * Since dependencies are not expressed as entities, they are kept manually by this sync extension.
+ *
+ * By nature, this only preserves the already existing dependencies, and doesn't allow any cleanup of dependencies the entity source for
+ * each dependency is not known. Cleanup is expected to be done by data services instead.
+ */
+@Order(GradleDependencySyncExtension.ORDER)
+class GradleDependencySyncExtension : GradleSyncExtension {
+  override fun updateProjectModel(
+    context: ProjectResolverContext,
+    syncStorage: MutableEntityStorage,
+    projectStorage: MutableEntityStorage,
+    phase: GradleSyncPhase,
+  ) {
+    syncStorage.entitiesToReplace<ModuleEntity>(context, phase).forEach { moduleEntity ->
+      val existingDependencies = projectStorage.resolve(moduleEntity.symbolicId)?.dependencies ?: return@forEach
+      val syncDependencies = moduleEntity.dependencies.toHashSet()
+      val explicitSdk = moduleEntity.dependencies.find { it is SdkDependency }
+
+      syncStorage.modifyModuleEntity(moduleEntity) {
+        // Clean up all existing SDKs and set the explicitly set SDK if known already in the sync storage,
+        // otherwise use the project's explicit SDK, and otherwise inherit.
+        dependencies.removeAll { it is InheritedSdkDependency || it is SdkDependency }
+        dependencies.add(explicitSdk ?: existingDependencies.find { it is SdkDependency } ?: InheritedSdkDependency)
+        dependencies.addAll(existingDependencies.filterNot { syncDependencies.contains(it) || it is SdkDependency || it is InheritedSdkDependency })
+      }
+    }
+  }
+
+  companion object {
+
+    const val ORDER: Int = GradleBaseSyncExtension.ORDER - 500
+  }
+}