diff --git a/java/kotlin-extractor/src/main/kotlin/ExternalClassExtractor.kt b/java/kotlin-extractor/src/main/kotlin/ExternalClassExtractor.kt
index ad50f8949b4..40a4297839f 100644
--- a/java/kotlin-extractor/src/main/kotlin/ExternalClassExtractor.kt
+++ b/java/kotlin-extractor/src/main/kotlin/ExternalClassExtractor.kt
@@ -9,7 +9,7 @@ import java.util.ArrayList
 import java.util.HashSet
 import java.util.zip.GZIPOutputStream
 
-class ExternalClassExtractor(val logger: FileLogger, val sourceFilePath: String, val primitiveTypeMapping: PrimitiveTypeMapping, val pluginContext: IrPluginContext) {
+class ExternalClassExtractor(val logger: FileLogger, val invocationTrapFile: String, val sourceFilePath: String, val primitiveTypeMapping: PrimitiveTypeMapping, val pluginContext: IrPluginContext) {
 
     val externalClassesDone = HashSet<IrClass>()
     val externalClassWorkList = ArrayList<IrClass>()
@@ -33,10 +33,17 @@ class ExternalClassExtractor(val logger: FileLogger, val sourceFilePath: String,
                             logger.info("Skipping extracting class ${irClass.name}")
                         } else {
                             GZIPOutputStream(manager.getFile().outputStream()).bufferedWriter().use { trapFileBW ->
+                                // We want our comments to be the first thing in the file,
+                                // so start off with a mere TrapWriter
+                                val tw = TrapWriter(TrapLabelManager(), trapFileBW)
+                                tw.writeComment("Generated by the CodeQL Kotlin extractor for external dependencies")
+                                tw.writeComment("Part of invocation $invocationTrapFile")
+                                // Now elevate to a SourceFileTrapWriter, and populate the
+                                // file information
                                 val binaryPath = getIrClassBinaryPath(irClass)
-                                val tw =
-                                    FileTrapWriter(TrapLabelManager(), trapFileBW, binaryPath, true)
-                                val fileExtractor = KotlinFileExtractor(logger, tw, manager, this, primitiveTypeMapping, pluginContext)
+                                val ftw = tw.makeFileTrapWriter(binaryPath, true)
+
+                                val fileExtractor = KotlinFileExtractor(logger, ftw, manager, this, primitiveTypeMapping, pluginContext)
                                 fileExtractor.extractClassSource(irClass)
                             }
                         }
diff --git a/java/kotlin-extractor/src/main/kotlin/KotlinExtractorExtension.kt b/java/kotlin-extractor/src/main/kotlin/KotlinExtractorExtension.kt
index beee3852829..a26aaac0e08 100644
--- a/java/kotlin-extractor/src/main/kotlin/KotlinExtractorExtension.kt
+++ b/java/kotlin-extractor/src/main/kotlin/KotlinExtractorExtension.kt
@@ -112,11 +112,17 @@ fun doFile(invocationTrapFile: String,
     if (checkTrapIdentical || !trapFile.exists()) {
         val trapTmpFile = File.createTempFile("$filePath.", ".trap.tmp", trapFileDir)
         trapTmpFile.bufferedWriter().use { trapFileBW ->
-            val tw = SourceFileTrapWriter(TrapLabelManager(), trapFileBW, file, true)
-            tw.writeComment("Generated by invocation $invocationTrapFile")
-            val externalClassExtractor = ExternalClassExtractor(logger, file.path, primitiveTypeMapping, pluginContext)
-            val fileExtractor = KotlinSourceFileExtractor(logger, tw, file, externalClassExtractor, primitiveTypeMapping, pluginContext)
-            fileExtractor.extractFileContents(tw.fileId)
+            // We want our comments to be the first thing in the file,
+            // so start off with a mere TrapWriter
+            val tw = TrapWriter(TrapLabelManager(), trapFileBW)
+            tw.writeComment("Generated by the CodeQL Kotlin extractor for kotlin source code")
+            tw.writeComment("Part of invocation $invocationTrapFile")
+            // Now elevate to a SourceFileTrapWriter, and populate the
+            // file information
+            val sftw = tw.makeSourceFileTrapWriter(file, true)
+            val externalClassExtractor = ExternalClassExtractor(logger, invocationTrapFile, file.path, primitiveTypeMapping, pluginContext)
+            val fileExtractor = KotlinSourceFileExtractor(logger, sftw, file, externalClassExtractor, primitiveTypeMapping, pluginContext)
+            fileExtractor.extractFileContents(sftw.fileId)
             externalClassExtractor.extractExternalClasses()
         }
         if (checkTrapIdentical && trapFile.exists()) {
diff --git a/java/kotlin-extractor/src/main/kotlin/KotlinUsesExtractor.kt b/java/kotlin-extractor/src/main/kotlin/KotlinUsesExtractor.kt
index b8fa341fe52..c3059453dad 100644
--- a/java/kotlin-extractor/src/main/kotlin/KotlinUsesExtractor.kt
+++ b/java/kotlin-extractor/src/main/kotlin/KotlinUsesExtractor.kt
@@ -73,7 +73,7 @@ open class KotlinUsesExtractor(
         val clsFile = cls.fileOrNull
 
         if (isExternalDeclaration(cls) || clsFile == null) {
-            val newTrapWriter = tw.makeFileTrapWriter(getIrClassBinaryPath(cls))
+            val newTrapWriter = tw.makeFileTrapWriter(getIrClassBinaryPath(cls), false)
             val newLogger = FileLogger(logger.logCounter, newTrapWriter)
             return KotlinFileExtractor(newLogger, newTrapWriter, dependencyCollector, externalClassExtractor, primitiveTypeMapping, pluginContext)
         }
diff --git a/java/kotlin-extractor/src/main/kotlin/TrapWriter.kt b/java/kotlin-extractor/src/main/kotlin/TrapWriter.kt
index 279223704b3..4dab36df8f3 100644
--- a/java/kotlin-extractor/src/main/kotlin/TrapWriter.kt
+++ b/java/kotlin-extractor/src/main/kotlin/TrapWriter.kt
@@ -159,8 +159,8 @@ open class TrapWriter (protected val lm: TrapLabelManager, private val bw: Buffe
      * Gets a FileTrapWriter like this one (using the same label manager,
      * writer etc), but using the given `filePath` for locations.
      */
-    fun makeFileTrapWriter(filePath: String) =
-        FileTrapWriter(lm, bw, filePath, false)
+    fun makeFileTrapWriter(filePath: String, populateFileTables: Boolean) =
+        FileTrapWriter(lm, bw, filePath, populateFileTables)
 
     /**
      * Gets a FileTrapWriter like this one (using the same label manager,