PY-87889: Fix module root duplication.

Apparently, the result of `createEntitySource` can't be reused.
It acts as a key in a map, so using same source for different modules breaks everything.

Test checks it, and we also need to disable external storage to store files in `.idea`


(cherry picked from commit 796b582d4d3cde9158d9fcfae910cde54886c24b)

IJ-CR-193095

GitOrigin-RevId: 8e117832070c1dff3e5ad6970908eb43208f73c4

platform/projectModel-api/src/com/intellij/openapi/project/ProjectUtilCore.kt

@@ -1,5 +1,6 @@
 // Copyright 2000-2025 JetBrains s.r.o. and contributors. Use of this source code is governed by the Apache 2.0 license.
 @file:JvmName("ProjectUtilCore")
+
 package com.intellij.openapi.project
 
 import com.intellij.ide.highlighter.ProjectFileType
@@ -18,6 +19,7 @@ import com.intellij.util.PathUtil
 import com.intellij.util.PlatformUtils
 import com.intellij.util.io.URLUtil
 import com.intellij.workspaceModel.ide.presentableName
+import org.jetbrains.annotations.ApiStatus
 import org.jetbrains.annotations.TestOnly
 
 @NlsSafe
@@ -106,6 +108,21 @@ val Project.isExternalStorageEnabled: Boolean
  */
 @TestOnly
 fun doNotEnableExternalStorageByDefaultInTests(action: () -> Unit) {
+  doNotEnableExternalStorageByDefaultInTestsImpl(action)
+}
+
+/**
+ * @see [doNotEnableExternalStorageByDefaultInTests]
+ */
+@ApiStatus.Internal
+@TestOnly
+suspend fun doNotEnableExternalStorageByDefaultInTestsSuspend(action: suspend () -> Unit) {
+  doNotEnableExternalStorageByDefaultInTestsImpl {
+    action()
+  }
+}
+
+private inline fun doNotEnableExternalStorageByDefaultInTestsImpl(action: () -> Unit) {
   enableExternalStorageByDefaultInTests = false
   try {
     action()
@@ -113,4 +130,4 @@ fun doNotEnableExternalStorageByDefaultInTests(action: () -> Unit) {
   finally {
     enableExternalStorageByDefaultInTests = true
   }
-}
+}

python/python-pyproject/src/com/intellij/python/pyproject/model/internal/workspaceBridge/workspaceTools.kt

@@ -212,9 +212,8 @@ private suspend fun createProjectModel(
 ): ImmutableEntityStorage = withContext(Dispatchers.Default) {
   val virtualFileUrlManager = project.workspaceModel.getVirtualFileUrlManager()
   val storage = MutableEntityStorage.create()
-  val entitySource = createEntitySource(project)
   for (pyProject in graph) {
-    val moduleEntity = storage addEntity ModuleEntity(pyProject.name.name, emptyList(), entitySource) {
+    val moduleEntity = storage addEntity ModuleEntity(pyProject.name.name, emptyList(), createEntitySource(project)) {
       dependencies += ModuleSourceDependency
       for (moduleName in pyProject.dependencies) {
         dependencies += ModuleDependency(ModuleId(moduleName.name), true, DependencyScope.COMPILE, false)
@@ -312,6 +311,7 @@ private class ModuleAnchor(moduleEntity: ModuleEntity) {
     (theOnlyContentRoot != null && theOnlyContentRoot.url == o.theOnlyContentRoot?.url)
 }
 
+// Warning: this entity must be unique for each model, it can't be reused
 internal fun createEntitySource(project: Project): EntitySource {
   val moduleRoot =
     project.stateStore.projectBasePath.resolve(DIRECTORY_STORE_FOLDER).toVirtualFileUrl(project.workspaceModel.getVirtualFileUrlManager())