Repro

compiler/util-klib/src/org/jetbrains/kotlin/library/ToolingResolve.kt

diff --git a/compiler/util-klib/src/org/jetbrains/kotlin/library/ToolingResolve.kt b/compiler/util-klib/src/org/jetbrains/kotlin/library/ToolingResolve.kt
index 9bf6007..b5d4b8f 100644
--- a/compiler/util-klib/src/org/jetbrains/kotlin/library/ToolingResolve.kt
+++ b/compiler/util-klib/src/org/jetbrains/kotlin/library/ToolingResolve.kt
@@ -59,19 +59,13 @@
         val extension = libraryFile.extension
 
         val wrappedAction: () -> T? = when {
-            extension == KLIB_FILE_EXTENSION -> {
-                if (!libraryFile.isFile) return null
-
-                { libraryFile.withZipFileSystem { fs -> action(fs.file("/")) } }
-            }
-
-            extension.isNotEmpty() -> return null
-
-            else -> {
-                if (!libraryFile.isDirectory) return null
-
+            libraryFile.isDirectory -> {
                 { action(libraryFile) }
             }
+            libraryFile.isFile && extension == KLIB_FILE_EXTENSION -> {
+                { libraryFile.withZipFileSystem { fs -> action(fs.file("/")) } }
+            }
+            else -> return null
         }
 
         return try {

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/compilerRunner/KotlinNativeKlibCommonizerToolRunner.kt

diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/compilerRunner/KotlinNativeKlibCommonizerToolRunner.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/compilerRunner/KotlinNativeKlibCommonizerToolRunner.kt
index 8317414..c7875ce 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/compilerRunner/KotlinNativeKlibCommonizerToolRunner.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/compilerRunner/KotlinNativeKlibCommonizerToolRunner.kt
@@ -31,4 +31,6 @@
     override val defaultMaxHeapSize: String get() = "4G"
 
     override val mustRunViaExec get() = true // because it's not enough the standard Gradle wrapper's heap size
+
+    override val systemPropertiesBlacklist: Set<String> = setOf("java.endorsed.dirs")
 }

native/commonizer/build.gradle.kts

diff --git a/native/commonizer/build.gradle.kts b/native/commonizer/build.gradle.kts
index 56d679d..195e066 100644
--- a/native/commonizer/build.gradle.kts
+++ b/native/commonizer/build.gradle.kts
@@ -35,9 +35,19 @@
     testCompile(intellijCoreDep()) { includeJars("intellij-core") }
 }
 
-val runCommonizer by tasks.registering(NoDebugJavaExec::class) {
-    classpath(sourceSets.main.get().runtimeClasspath)
+val runCommonizer by tasks.registering(JavaExec::class) {
+    classpath(sourceSets.main.get().runtimeClasspath + sourceSets.test.get().runtimeClasspath)
     main = "org.jetbrains.kotlin.descriptors.commonizer.cli.CommonizerCLI"
+
+    args = listOf(
+        "native-dist-commonize",
+        "-distribution-path",
+        "/Users/jetbrains/work/sources/kotlin-native/dist",
+        "-output-path",
+        "./ttt",
+        "-targets",
+        "ios_arm64,ios_x64"
+    )
 }
 
 sourceSets {