diff --git a/scip-java/src/main/kotlin/org/scip_code/scip_java/ScipJava.kt b/scip-java/src/main/kotlin/org/scip_code/scip_java/ScipJava.kt
index 2e6ddbde6..a970e5056 100644
--- a/scip-java/src/main/kotlin/org/scip_code/scip_java/ScipJava.kt
+++ b/scip-java/src/main/kotlin/org/scip_code/scip_java/ScipJava.kt
@@ -18,7 +18,7 @@ object ScipJava {
     @JvmStatic
     fun main(args: Array<String>) {
         app.runAndExitIfNonZero(args.toList())
-        // The Analysis API indexer leaves non-daemon threads behind; exit explicitly.
+        // IntelliJ's application thread pool keeps the JVM alive (see KotlinAnalysisIndexer).
         exitProcess(0)
     }
 
diff --git a/scip-kotlin-analysis/src/main/kotlin/org/scip_code/scip_java/kotlin_analysis/KotlinAnalysisIndexer.kt b/scip-kotlin-analysis/src/main/kotlin/org/scip_code/scip_java/kotlin_analysis/KotlinAnalysisIndexer.kt
index 1c1dd00e4..8f1aadee4 100644
--- a/scip-kotlin-analysis/src/main/kotlin/org/scip_code/scip_java/kotlin_analysis/KotlinAnalysisIndexer.kt
+++ b/scip-kotlin-analysis/src/main/kotlin/org/scip_code/scip_java/kotlin_analysis/KotlinAnalysisIndexer.kt
@@ -81,6 +81,10 @@ import org.scip_code.scip_java.shared.ScipShardWriter
  * One SCIP shard is written per source file under
  * `<targetroot>/META-INF/scip/<relative-source-path>.scip`, the layout produced by the scip-javac
  * compiler plugin.
+ *
+ * The JVM does not exit on its own after [run]. The Analysis API starts IntelliJ's process-wide
+ * application thread pool, which keeps a non-daemon thread alive and cannot be shut down without
+ * breaking later runs in the same process. Command-line callers must call `exitProcess` when done.
  */
 class KotlinAnalysisIndexer(
     private val sourceroot: Path,
diff --git a/scip-kotlin-analysis/src/main/kotlin/org/scip_code/scip_java/kotlin_analysis/Main.kt b/scip-kotlin-analysis/src/main/kotlin/org/scip_code/scip_java/kotlin_analysis/Main.kt
index ee447f4fc..99d1e6502 100644
--- a/scip-kotlin-analysis/src/main/kotlin/org/scip_code/scip_java/kotlin_analysis/Main.kt
+++ b/scip-kotlin-analysis/src/main/kotlin/org/scip_code/scip_java/kotlin_analysis/Main.kt
@@ -37,8 +37,8 @@ fun main(args: Array<String>) {
     require(sourceroot != null) { "missing required flag: --sourceroot" }
     require(targetroot != null) { "missing required flag: --targetroot" }
     require(sourceRoots.isNotEmpty()) { "missing source files or directories" }
-    // The Analysis API environment leaves non-daemon threads behind; exit
-    // explicitly, also on failure, so callers are not left waiting on them.
+    // IntelliJ's application thread pool keeps the JVM alive (see KotlinAnalysisIndexer);
+    // exit explicitly, also on failure, so callers are not left waiting on it.
     try {
         KotlinAnalysisIndexer(
                 sourceroot = sourceroot,