Fix extracted metadata for IDE erased when scopes conflict, KT-44845

The root cause was that extractors for different scopes used the same
base directory, and each erased its contents. Using different base dirs
fixes the issue.

Issue #KT-44845

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/HierarchicalMppIT.kt

@@ -585,6 +585,41 @@ class HierarchicalMppIT : BaseGradleIT() {
         }
     }
 
+    @Test
+    fun testMixedScopesFilesExistKt44845() {
+        publishThirdPartyLib(withGranularMetadata = true)
+
+        transformNativeTestProjectWithPluginDsl("my-lib-foo", gradleVersion, "hierarchical-mpp-published-modules").run {
+            gradleBuildScript().appendText(
+                """
+                ${"\n"}
+                dependencies {
+                    "jvmAndJsMainImplementation"("org.jetbrains.kotlinx:kotlinx-coroutines-core:1.4.2")
+                    "jvmAndJsMainCompileOnly"("org.jetbrains.kotlinx:kotlinx-serialization-json:1.0.1")
+                }
+            """.trimIndent()
+            )
+
+            testDependencyTransformations { reports ->
+                val reportsForJvmAndJsMain = reports.filter { it.sourceSetName == "jvmAndJsMain" }
+                val thirdPartyLib = reportsForJvmAndJsMain.single {
+                    it.scope == "api" && it.groupAndModule.startsWith("com.example")
+                }
+                val coroutinesCore = reportsForJvmAndJsMain.single {
+                    it.scope == "implementation" && it.groupAndModule.contains("kotlinx-coroutines-core")
+                }
+                val serialization = reportsForJvmAndJsMain.single {
+                    it.scope == "compileOnly" && it.groupAndModule.contains("kotlinx-serialization-json")
+                }
+                listOf(thirdPartyLib, coroutinesCore, serialization).forEach { report ->
+                    assertTrue(report.newVisibleSourceSets.isNotEmpty(), "Expected visible source sets for $report")
+                    assertTrue(report.useFiles.isNotEmpty(), "Expected non-empty useFiles for $report")
+                    report.useFiles.forEach { assertTrue(it.isFile, "Expected $it to exist for $report") }
+                }
+            }
+        }
+    }
+
     private fun Project.testDependencyTransformations(
         subproject: String? = null,
         check: CompiledProject.(reports: Iterable<DependencyTransformationReport>) -> Unit

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/sources/DefaultKotlinSourceSet.kt

@@ -156,7 +156,7 @@ class DefaultKotlinSourceSet(
                 ?.associateBy { ModuleIds.fromComponent(project, it.dependency) }
                 ?: emptyMap()
 
-        val baseDir = SourceSetMetadataStorageForIde.sourceSetStorage(project, this@DefaultKotlinSourceSet.name)
+        val baseDir = SourceSetMetadataStorageForIde.sourceSetStorageWithScope(project, this@DefaultKotlinSourceSet.name, scope)
 
         if (metadataDependencyResolutionByModule.values.any { it is MetadataDependencyResolution.ChooseVisibleSourceSets }) {
             if (baseDir.isDirectory) {

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/sources/SourceSetMetadataStorageForIde.kt

@@ -39,4 +39,7 @@ object SourceSetMetadataStorageForIde {
     }
 
     fun sourceSetStorage(project: Project, sourceSetName: String) = projectStorage(project).resolve(sourceSetName)
+
+    internal fun sourceSetStorageWithScope(project: Project, sourceSetName: String, scope: KotlinDependencyScope) =
+        sourceSetStorage(project, sourceSetName).resolve(scope.scopeName)
 }