KAPT: Fix serialization of class structure data

When serializing ClasspathEntryData, ids assigned to types were
incorrect, resulting in corrupt data when deserializing files. This
happened if there were dependencies between classes.

Fixes KT-39876
Test: ClasspathAnalyzerTest

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/kapt/incremental/ClasspathAnalyzer.kt

@@ -108,6 +108,7 @@ class ClasspathEntryData : Serializable {
 
     @Transient
     var classAbiHash = mutableMapOf<String, ByteArray>()
+
     @Transient
     var classDependencies = mutableMapOf<String, ClassDependencies>()
 
@@ -118,7 +119,9 @@ class ClasspathEntryData : Serializable {
 
         val names = LinkedHashMap<String, Int>()
         sortedClassDependencies.forEach {
-            names[it.key] = names.size
+            if (it.key !in names) {
+                names[it.key] = names.size
+            }
             it.value.abiTypes.forEach { type ->
                 if (type !in names) names[type] = names.size
             }

libraries/tools/kotlin-gradle-plugin/src/test/kotlin/org/jetbrains/kotlin/gradle/internal/kapt/incremental/ClasspathAnalyzerTest.kt

@@ -134,9 +134,34 @@ class ClasspathAnalyzerTest {
         assertTrue(data.classDependencies.isEmpty())
     }
 
-    private fun emptyClass(internalName: String): ByteArray {
+    @Test
+    fun testJarsWithDependenciesWithinClasses() {
+        val inputJar = tmp.newFile("input.jar").also { jar ->
+            ZipOutputStream(jar.outputStream()).use {
+                it.putNextEntry(ZipEntry("test/A.class"))
+                it.write(emptyClass("test/A", "test/B"))
+                it.closeEntry()
+
+                it.putNextEntry(ZipEntry("test/B.class"))
+                it.write(emptyClass("test/B"))
+                it.closeEntry()
+
+                it.putNextEntry(ZipEntry("test/C.class"))
+                it.write(emptyClass("test/C"))
+                it.closeEntry()
+            }
+        }
+        val transform = StructureArtifactTransform().also { it.outputDirectory = tmp.newFolder() }
+        val outputs = transform.transform(inputJar)
+
+        val data = ClasspathEntryData.ClasspathEntrySerializer.loadFrom(outputs.single())
+        assertEquals(setOf("test/A", "test/B", "test/C"), data.classAbiHash.keys)
+        assertEquals(setOf("test/A", "test/B", "test/C"), data.classDependencies.keys)
+    }
+
+    private fun emptyClass(internalName: String, superClass: String = "java/lang/Object"): ByteArray {
         val writer = ClassWriter(Opcodes.API_VERSION)
-        writer.visit(Opcodes.V1_8, Opcodes.ACC_PUBLIC, internalName, null, "java/lang/Object", emptyArray())
+        writer.visit(Opcodes.V1_8, Opcodes.ACC_PUBLIC, internalName, null, superClass, emptyArray())
         return writer.toByteArray()
     }
 }