diff --git a/internal/fourslash/baselineutil.go b/internal/fourslash/baselineutil.go
index b233a86e68..03eb2210ff 100644
--- a/internal/fourslash/baselineutil.go
+++ b/internal/fourslash/baselineutil.go
@@ -58,8 +58,13 @@ func getBaselineExtension(command string) string {
 	}
 }
 
-func getBaselineOptions(command string) baseline.Options {
+func getBaselineOptions(command string, testPath string) baseline.Options {
 	subfolder := "fourslash/" + normalizeCommandName(command)
+	if !isSubmoduleTest(testPath) {
+		return baseline.Options{
+			Subfolder: subfolder,
+		}
+	}
 	switch command {
 	case "Smart Selection":
 		return baseline.Options{
@@ -229,6 +234,10 @@ func getBaselineOptions(command string) baseline.Options {
 	}
 }
 
+func isSubmoduleTest(testPath string) bool {
+	return strings.Contains(testPath, "fourslash/tests/gen") || strings.Contains(testPath, "fourslash/tests/manual")
+}
+
 func normalizeCommandName(command string) string {
 	words := strings.Fields(command)
 	command = strings.Join(words, "")
diff --git a/internal/fourslash/fourslash.go b/internal/fourslash/fourslash.go
index 6edbbf1be6..0665e58a24 100644
--- a/internal/fourslash/fourslash.go
+++ b/internal/fourslash/fourslash.go
@@ -5,6 +5,7 @@ import (
 	"fmt"
 	"io"
 	"maps"
+	"runtime"
 	"slices"
 	"strings"
 	"testing"
@@ -203,9 +204,10 @@ func NewFourslash(t *testing.T, capabilities *lsproto.ClientCapabilities, conten
 	}
 	f.activeFilename = f.testData.Files[0].fileName
 
+	_, testPath, _, _ := runtime.Caller(1)
 	t.Cleanup(func() {
 		inputWriter.Close()
-		f.verifyBaselines(t)
+		f.verifyBaselines(t, testPath)
 	})
 	return f
 }
@@ -2243,9 +2245,9 @@ func (f *FourslashTest) getRangeText(r *RangeMarker) string {
 	return script.content[r.Range.Pos():r.Range.End()]
 }
 
-func (f *FourslashTest) verifyBaselines(t *testing.T) {
+func (f *FourslashTest) verifyBaselines(t *testing.T, testPath string) {
 	for command, content := range f.baselines {
-		baseline.Run(t, getBaselineFileName(t, command), content.String(), getBaselineOptions(command))
+		baseline.Run(t, getBaselineFileName(t, command), content.String(), getBaselineOptions(command, testPath))
 	}
 }
 
diff --git a/testdata/baselines/reference/submodule/fourslash/inlayHints/inlayHintsTupleTypeCrash.baseline b/testdata/baselines/reference/fourslash/inlayHints/inlayHintsTupleTypeCrash.baseline
similarity index 100%
rename from testdata/baselines/reference/submodule/fourslash/inlayHints/inlayHintsTupleTypeCrash.baseline
rename to testdata/baselines/reference/fourslash/inlayHints/inlayHintsTupleTypeCrash.baseline
diff --git a/testdata/baselines/reference/submodule/fourslash/inlayHints/inlayHintsTupleTypeCrash.baseline.diff b/testdata/baselines/reference/submodule/fourslash/inlayHints/inlayHintsTupleTypeCrash.baseline.diff
deleted file mode 100644
index 4b68d3baf3..0000000000
--- a/testdata/baselines/reference/submodule/fourslash/inlayHints/inlayHintsTupleTypeCrash.baseline.diff
+++ /dev/null
@@ -1,24 +0,0 @@
---- old.inlayHintsTupleTypeCrash.baseline
-+++ new.inlayHintsTupleTypeCrash.baseline
-@@= skipped --1, +0 lines =@@
-+// === Inlay Hints ===
-+  tuples.forEach((l) => {})
-+                   ^
-+{
-+  "label": [
-+    {
-+      "value": ": "
-+    },
-+    {
-+      "value": "["
-+    },
-+    {
-+      "value": "string"
-+    },
-+    {
-+      "value": "]"
-+    }
-+  ],
-+  "kind": 1,
-+  "paddingLeft": true
-+}
\ No newline at end of file