diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt
index 96ff84af8b7..f29b88ab748 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt
@@ -117,6 +117,28 @@ class KotlinCoreEnvironment private constructor(
         override fun preregisterServices() {
             registerProjectExtensionPoints(Extensions.getArea(project))
         }
+
+        override fun registerJavaPsiFacade() {
+            with (project) {
+                registerService(CoreJavaFileManager::class.java, ServiceManager.getService(this, JavaFileManager::class.java) as CoreJavaFileManager)
+
+                val cliLightClassGenerationSupport = CliLightClassGenerationSupport(this)
+                registerService(LightClassGenerationSupport::class.java, cliLightClassGenerationSupport)
+                registerService(CliLightClassGenerationSupport::class.java, cliLightClassGenerationSupport)
+                registerService(CodeAnalyzerInitializer::class.java, cliLightClassGenerationSupport)
+
+                registerService(ExternalAnnotationsManager::class.java, MockExternalAnnotationsManager())
+                registerService(InferredAnnotationsManager::class.java, MockInferredAnnotationsManager())
+
+                val area = Extensions.getArea(this)
+
+                area.getExtensionPoint(PsiElementFinder.EP_NAME).registerExtension(JavaElementFinder(this, cliLightClassGenerationSupport))
+                area.getExtensionPoint(PsiElementFinder.EP_NAME).registerExtension(
+                        PsiElementFinderImpl(this, ServiceManager.getService(this, JavaFileManager::class.java)))
+            }
+
+            super.registerJavaPsiFacade()
+        }
     }
     private val sourceFiles = ArrayList<KtFile>()
     private val rootsIndex: JvmDependenciesDynamicCompoundIndex
@@ -469,23 +491,11 @@ class KotlinCoreEnvironment private constructor(
         }
 
         private fun registerProjectServicesForCLI(projectEnvironment: JavaCoreProjectEnvironment) {
-            with (projectEnvironment.project) {
-                registerService(CoreJavaFileManager::class.java, ServiceManager.getService(this, JavaFileManager::class.java) as CoreJavaFileManager)
+            /**
+             * Note that Kapt may restart code analysis process, and CLI services should be aware of that.
+             * Use PsiManager.getModificationTracker() to ensure that all the data you cached is still valid.
+             */
 
-                val cliLightClassGenerationSupport = CliLightClassGenerationSupport(this)
-                registerService(LightClassGenerationSupport::class.java, cliLightClassGenerationSupport)
-                registerService(CliLightClassGenerationSupport::class.java, cliLightClassGenerationSupport)
-                registerService(CodeAnalyzerInitializer::class.java, cliLightClassGenerationSupport)
-
-                registerService(ExternalAnnotationsManager::class.java, MockExternalAnnotationsManager())
-                registerService(InferredAnnotationsManager::class.java, MockInferredAnnotationsManager())
-
-                val area = Extensions.getArea(this)
-
-                area.getExtensionPoint(PsiElementFinder.EP_NAME).registerExtension(JavaElementFinder(this, cliLightClassGenerationSupport))
-                area.getExtensionPoint(PsiElementFinder.EP_NAME).registerExtension(
-                        PsiElementFinderImpl(this, ServiceManager.getService(this, JavaFileManager::class.java)))
-            }
         }
     }
 }