diff --git a/cpp/ql/integration-tests/header-variant-tests/clang-pch/a.c b/cpp/ql/integration-tests/header-variant-tests/clang-pch/a.c
new file mode 100644
index 000000000000..f80dfe401603
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/clang-pch/a.c
@@ -0,0 +1,2 @@
+#include "a.h"
+#define FOUR 4
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/a.h b/cpp/ql/integration-tests/header-variant-tests/clang-pch/a.h
similarity index 100%
rename from cpp/ql/test/header-variant-tests/clang-pch/a.h
rename to cpp/ql/integration-tests/header-variant-tests/clang-pch/a.h
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/b.c b/cpp/ql/integration-tests/header-variant-tests/clang-pch/b.c
similarity index 100%
rename from cpp/ql/test/header-variant-tests/clang-pch/b.c
rename to cpp/ql/integration-tests/header-variant-tests/clang-pch/b.c
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/b.h b/cpp/ql/integration-tests/header-variant-tests/clang-pch/b.h
similarity index 100%
rename from cpp/ql/test/header-variant-tests/clang-pch/b.h
rename to cpp/ql/integration-tests/header-variant-tests/clang-pch/b.h
diff --git a/cpp/ql/integration-tests/header-variant-tests/clang-pch/c.c b/cpp/ql/integration-tests/header-variant-tests/clang-pch/c.c
new file mode 100644
index 000000000000..e8c42c9c4b22
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/clang-pch/c.c
@@ -0,0 +1,3 @@
+int main() {
+  return ONE + FOUR;
+}
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/clang-pch.expected b/cpp/ql/integration-tests/header-variant-tests/clang-pch/clang-pch.expected
similarity index 100%
rename from cpp/ql/test/header-variant-tests/clang-pch/clang-pch.expected
rename to cpp/ql/integration-tests/header-variant-tests/clang-pch/clang-pch.expected
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/clang-pch.ql b/cpp/ql/integration-tests/header-variant-tests/clang-pch/clang-pch.ql
similarity index 100%
rename from cpp/ql/test/header-variant-tests/clang-pch/clang-pch.ql
rename to cpp/ql/integration-tests/header-variant-tests/clang-pch/clang-pch.ql
diff --git a/cpp/ql/integration-tests/header-variant-tests/clang-pch/d.c b/cpp/ql/integration-tests/header-variant-tests/clang-pch/d.c
new file mode 100644
index 000000000000..35e2312fd892
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/clang-pch/d.c
@@ -0,0 +1 @@
+#import "d.h"
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/d.h b/cpp/ql/integration-tests/header-variant-tests/clang-pch/d.h
similarity index 100%
rename from cpp/ql/test/header-variant-tests/clang-pch/d.h
rename to cpp/ql/integration-tests/header-variant-tests/clang-pch/d.h
diff --git a/cpp/ql/integration-tests/header-variant-tests/clang-pch/e.c b/cpp/ql/integration-tests/header-variant-tests/clang-pch/e.c
new file mode 100644
index 000000000000..571efb6f271a
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/clang-pch/e.c
@@ -0,0 +1,3 @@
+int main() {
+  return SEVENTEEN;
+}
diff --git a/cpp/ql/integration-tests/header-variant-tests/clang-pch/f.c b/cpp/ql/integration-tests/header-variant-tests/clang-pch/f.c
new file mode 100644
index 000000000000..613824dc7836
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/clang-pch/f.c
@@ -0,0 +1,5 @@
+#if 1
+#pragma hdrstop
+extern int x;
+#define SEEN_F
+#endif
diff --git a/cpp/ql/integration-tests/header-variant-tests/clang-pch/g.c b/cpp/ql/integration-tests/header-variant-tests/clang-pch/g.c
new file mode 100644
index 000000000000..bf105c29e95f
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/clang-pch/g.c
@@ -0,0 +1,5 @@
+#ifdef SEEN_F
+static int g() {
+  return 20;
+}
+#endif
diff --git a/cpp/ql/integration-tests/header-variant-tests/clang-pch/h.c b/cpp/ql/integration-tests/header-variant-tests/clang-pch/h.c
new file mode 100644
index 000000000000..6f183a7070fc
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/clang-pch/h.c
@@ -0,0 +1,4 @@
+#include "h1.h"
+#pragma hdrstop
+#include "h2.h"
+#define SEEN_H
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/h1.h b/cpp/ql/integration-tests/header-variant-tests/clang-pch/h1.h
similarity index 100%
rename from cpp/ql/test/header-variant-tests/clang-pch/h1.h
rename to cpp/ql/integration-tests/header-variant-tests/clang-pch/h1.h
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/h2.h b/cpp/ql/integration-tests/header-variant-tests/clang-pch/h2.h
similarity index 100%
rename from cpp/ql/test/header-variant-tests/clang-pch/h2.h
rename to cpp/ql/integration-tests/header-variant-tests/clang-pch/h2.h
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/i.c b/cpp/ql/integration-tests/header-variant-tests/clang-pch/i.c
similarity index 64%
rename from cpp/ql/test/header-variant-tests/clang-pch/i.c
rename to cpp/ql/integration-tests/header-variant-tests/clang-pch/i.c
index 05aa74b3047b..1274d6750001 100644
--- a/cpp/ql/test/header-variant-tests/clang-pch/i.c
+++ b/cpp/ql/integration-tests/header-variant-tests/clang-pch/i.c
@@ -13,4 +13,3 @@ static int h2() {
   return 32;
 }
 #endif
-// semmle-extractor-options: --clang -include-pch ${testdir}/clang-pch.testproj/h.pch
diff --git a/cpp/ql/integration-tests/header-variant-tests/clang-pch/test.py b/cpp/ql/integration-tests/header-variant-tests/clang-pch/test.py
new file mode 100644
index 000000000000..0a48fc3a79ce
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/clang-pch/test.py
@@ -0,0 +1,17 @@
+import os
+
+
+def test(codeql, cpp):
+    os.mkdir("pch")
+    extractor = cpp.get_tool("extractor")
+    codeql.database.create(command=[
+        f'"{extractor}" --mimic-clang -emit-pch -o pch/a.pch a.c',
+        f'"{extractor}" --mimic-clang -include-pch pch/a.pch -Iextra_dummy_path b.c',
+        f'"{extractor}" --mimic-clang -include pch/a -Iextra_dummy_path c.c',
+        f'"{extractor}" --mimic-clang -emit-pch -o pch/d.pch d.c',
+        f'"{extractor}" --mimic-clang -include-pch pch/d.pch e.c',
+        f'"{extractor}" --mimic-clang -emit-pch -o pch/f.pch f.c',
+        f'"{extractor}" --mimic-clang -include-pch pch/f.pch g.c',
+        f'"{extractor}" --mimic-clang -emit-pch -o pch/h.pch h.c',
+        f'"{extractor}" --mimic-clang -include-pch pch/h.pch i.c',
+    ])
diff --git a/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/a.c b/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/a.c
new file mode 100644
index 000000000000..2243de1baf9a
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/a.c
@@ -0,0 +1 @@
+#include "a.h"
diff --git a/cpp/ql/test/header-variant-tests/microsoft-pch/a.h b/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/a.h
similarity index 100%
rename from cpp/ql/test/header-variant-tests/microsoft-pch/a.h
rename to cpp/ql/integration-tests/header-variant-tests/microsoft-pch/a.h
diff --git a/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/b.c b/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/b.c
new file mode 100644
index 000000000000..ef8f5d3ca55d
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/b.c
@@ -0,0 +1,6 @@
+#pragma hdrstop
+#include "b.h"
+
+int b() {
+  return A;
+}
diff --git a/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/c.c b/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/c.c
new file mode 100644
index 000000000000..b270ddd64780
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/c.c
@@ -0,0 +1,6 @@
+#include "d.h"
+#include "c.h"
+
+int c() {
+  return A;
+}
diff --git a/cpp/ql/test/header-variant-tests/microsoft-pch/microsoft-pch.expected b/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/microsoft-pch.expected
similarity index 100%
rename from cpp/ql/test/header-variant-tests/microsoft-pch/microsoft-pch.expected
rename to cpp/ql/integration-tests/header-variant-tests/microsoft-pch/microsoft-pch.expected
diff --git a/cpp/ql/test/header-variant-tests/microsoft-pch/microsoft-pch.ql b/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/microsoft-pch.ql
similarity index 100%
rename from cpp/ql/test/header-variant-tests/microsoft-pch/microsoft-pch.ql
rename to cpp/ql/integration-tests/header-variant-tests/microsoft-pch/microsoft-pch.ql
diff --git a/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/test.py b/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/test.py
new file mode 100644
index 000000000000..89bceec397e8
--- /dev/null
+++ b/cpp/ql/integration-tests/header-variant-tests/microsoft-pch/test.py
@@ -0,0 +1,11 @@
+import os
+
+
+def test(codeql, cpp):
+    os.mkdir("pch")
+    extractor = cpp.get_tool("extractor")
+    codeql.database.create(command=[
+        f'"{extractor}" --mimic-cl /Yca.h /Fppch/a.pch a.c',
+        f'"{extractor}" --mimic-cl /Yub.h /Fppch/a.pch b.c',
+        f'"{extractor}" --mimic-cl /Yuc.h /Fppch/a.pch c.c',
+    ])
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/_.c b/cpp/ql/test/header-variant-tests/clang-pch/_.c
deleted file mode 100644
index 6186edd586f7..000000000000
--- a/cpp/ql/test/header-variant-tests/clang-pch/_.c
+++ /dev/null
@@ -1,3 +0,0 @@
-// This file exists to ensure that the output subdirectory exists prior to
-// a.c being indexed, as said directory needs to exist for the PCH file to
-// be created, and will be created by running the extractor.
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/a.c b/cpp/ql/test/header-variant-tests/clang-pch/a.c
deleted file mode 100644
index 9164cdc19a58..000000000000
--- a/cpp/ql/test/header-variant-tests/clang-pch/a.c
+++ /dev/null
@@ -1,3 +0,0 @@
-#include "a.h"
-#define FOUR 4
-// semmle-extractor-options: --clang -emit-pch -o ${testdir}/clang-pch.testproj/a.pch
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/c.c b/cpp/ql/test/header-variant-tests/clang-pch/c.c
deleted file mode 100644
index 0a8b97667137..000000000000
--- a/cpp/ql/test/header-variant-tests/clang-pch/c.c
+++ /dev/null
@@ -1,4 +0,0 @@
-int main() {
-  return ONE + FOUR;
-}
-// semmle-extractor-options: --clang -include ${testdir}/clang-pch.testproj/a -Iextra_dummy_path
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/d.c b/cpp/ql/test/header-variant-tests/clang-pch/d.c
deleted file mode 100644
index f81af3d1b63c..000000000000
--- a/cpp/ql/test/header-variant-tests/clang-pch/d.c
+++ /dev/null
@@ -1,2 +0,0 @@
-#import "d.h"
-// semmle-extractor-options: --clang -emit-pch -o ${testdir}/clang-pch.testproj/d.pch
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/e.c b/cpp/ql/test/header-variant-tests/clang-pch/e.c
deleted file mode 100644
index abdb59002009..000000000000
--- a/cpp/ql/test/header-variant-tests/clang-pch/e.c
+++ /dev/null
@@ -1,4 +0,0 @@
-int main() {
-  return SEVENTEEN;
-}
-// semmle-extractor-options: --clang -include-pch ${testdir}/clang-pch.testproj/d.pch
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/f.c b/cpp/ql/test/header-variant-tests/clang-pch/f.c
deleted file mode 100644
index cca56931acd5..000000000000
--- a/cpp/ql/test/header-variant-tests/clang-pch/f.c
+++ /dev/null
@@ -1,6 +0,0 @@
-#if 1
-#pragma hdrstop
-extern int x;
-#define SEEN_F
-#endif
-// semmle-extractor-options: --clang -emit-pch -o ${testdir}/clang-pch.testproj/f.pch
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/g.c b/cpp/ql/test/header-variant-tests/clang-pch/g.c
deleted file mode 100644
index b16ca33ab369..000000000000
--- a/cpp/ql/test/header-variant-tests/clang-pch/g.c
+++ /dev/null
@@ -1,6 +0,0 @@
-#ifdef SEEN_F
-static int g() {
-  return 20;
-}
-#endif
-// semmle-extractor-options: --clang -include-pch ${testdir}/clang-pch.testproj/f.pch
diff --git a/cpp/ql/test/header-variant-tests/clang-pch/h.c b/cpp/ql/test/header-variant-tests/clang-pch/h.c
deleted file mode 100644
index 7ffc9b6133c1..000000000000
--- a/cpp/ql/test/header-variant-tests/clang-pch/h.c
+++ /dev/null
@@ -1,5 +0,0 @@
-#include "h1.h"
-#pragma hdrstop
-#include "h2.h"
-#define SEEN_H
-// semmle-extractor-options: --clang -emit-pch -o ${testdir}/clang-pch.testproj/h.pch
diff --git a/cpp/ql/test/header-variant-tests/microsoft-pch/_.c b/cpp/ql/test/header-variant-tests/microsoft-pch/_.c
deleted file mode 100644
index 6186edd586f7..000000000000
--- a/cpp/ql/test/header-variant-tests/microsoft-pch/_.c
+++ /dev/null
@@ -1,3 +0,0 @@
-// This file exists to ensure that the output subdirectory exists prior to
-// a.c being indexed, as said directory needs to exist for the PCH file to
-// be created, and will be created by running the extractor.
diff --git a/cpp/ql/test/header-variant-tests/microsoft-pch/a.c b/cpp/ql/test/header-variant-tests/microsoft-pch/a.c
deleted file mode 100644
index ba41bafcaade..000000000000
--- a/cpp/ql/test/header-variant-tests/microsoft-pch/a.c
+++ /dev/null
@@ -1,2 +0,0 @@
-#include "a.h"
-// semmle-extractor-options: --microsoft /Yca.h /Fp${testdir}/microsoft-pch.testproj/a.pch
diff --git a/cpp/ql/test/header-variant-tests/microsoft-pch/b.c b/cpp/ql/test/header-variant-tests/microsoft-pch/b.c
deleted file mode 100644
index b6ea5085fd1f..000000000000
--- a/cpp/ql/test/header-variant-tests/microsoft-pch/b.c
+++ /dev/null
@@ -1,7 +0,0 @@
-#pragma hdrstop
-#include "b.h"
-
-int b() {
-  return A;
-}
-// semmle-extractor-options: --microsoft /Yub.h /Fp${testdir}/microsoft-pch.testproj/a.pch
diff --git a/cpp/ql/test/header-variant-tests/microsoft-pch/c.c b/cpp/ql/test/header-variant-tests/microsoft-pch/c.c
deleted file mode 100644
index aaddbae8688d..000000000000
--- a/cpp/ql/test/header-variant-tests/microsoft-pch/c.c
+++ /dev/null
@@ -1,7 +0,0 @@
-#include "d.h"
-#include "c.h"
-
-int c() {
-  return A;
-}
-// semmle-extractor-options: --microsoft /Yuc.h /Fp${testdir}/microsoft-pch.testproj/a.pch