diff --git a/dev/x86_64/meta.h b/dev/x86_64/meta.h
index ead52f0aaf..44eb8e0748 100644
--- a/dev/x86_64/meta.h
+++ b/dev/x86_64/meta.h
@@ -31,7 +31,6 @@
 #define MLD_USE_NATIVE_POLYVECL_POINTWISE_ACC_MONTGOMERY_L7
 
 #if !defined(__ASSEMBLER__)
-#include <string.h>
 #include "../../common.h"
 #include "../api.h"
 #include "src/arith_native_x86_64.h"
diff --git a/dev/x86_64/src/arith_native_x86_64.h b/dev/x86_64/src/arith_native_x86_64.h
index 70bc00c94c..7474a9f0ad 100644
--- a/dev/x86_64/src/arith_native_x86_64.h
+++ b/dev/x86_64/src/arith_native_x86_64.h
@@ -6,7 +6,6 @@
 #ifndef MLD_NATIVE_X86_64_SRC_ARITH_NATIVE_X86_64_H
 #define MLD_NATIVE_X86_64_SRC_ARITH_NATIVE_X86_64_H
 #include "../../../common.h"
-
 #include "consts.h"
 
 #define MLD_AVX2_REJ_UNIFORM_BUFLEN \
diff --git a/mldsa/src/context.h b/mldsa/src/context.h
index f5e582d7c5..487f5a0743 100644
--- a/mldsa/src/context.h
+++ b/mldsa/src/context.h
@@ -10,6 +10,7 @@
 #if !defined(__ASSEMBLER__)
 
 #include <stdint.h>
+
 #include "cbmc.h"
 #include "sys.h"
 
diff --git a/mldsa/src/debug.c b/mldsa/src/debug.c
index 9d09231110..0f19f3bd53 100644
--- a/mldsa/src/debug.c
+++ b/mldsa/src/debug.c
@@ -15,6 +15,7 @@
 #include <inttypes.h>
 #include <stdio.h>
 #include <stdlib.h>
+
 #include "debug.h"
 
 #define MLD_DEBUG_ERROR_HEADER "[ERROR:%s:%04d] "
diff --git a/mldsa/src/fips202/fips202.h b/mldsa/src/fips202/fips202.h
index c97628e282..0664d3b704 100644
--- a/mldsa/src/fips202/fips202.h
+++ b/mldsa/src/fips202/fips202.h
@@ -6,6 +6,7 @@
 #define MLD_FIPS202_FIPS202_H
 
 #include <stddef.h>
+
 #include "../cbmc.h"
 #include "../common.h"
 
diff --git a/mldsa/src/native/x86_64/meta.h b/mldsa/src/native/x86_64/meta.h
index ead52f0aaf..44eb8e0748 100644
--- a/mldsa/src/native/x86_64/meta.h
+++ b/mldsa/src/native/x86_64/meta.h
@@ -31,7 +31,6 @@
 #define MLD_USE_NATIVE_POLYVECL_POINTWISE_ACC_MONTGOMERY_L7
 
 #if !defined(__ASSEMBLER__)
-#include <string.h>
 #include "../../common.h"
 #include "../api.h"
 #include "src/arith_native_x86_64.h"
diff --git a/mldsa/src/native/x86_64/src/arith_native_x86_64.h b/mldsa/src/native/x86_64/src/arith_native_x86_64.h
index 70bc00c94c..7474a9f0ad 100644
--- a/mldsa/src/native/x86_64/src/arith_native_x86_64.h
+++ b/mldsa/src/native/x86_64/src/arith_native_x86_64.h
@@ -6,7 +6,6 @@
 #ifndef MLD_NATIVE_X86_64_SRC_ARITH_NATIVE_X86_64_H
 #define MLD_NATIVE_X86_64_SRC_ARITH_NATIVE_X86_64_H
 #include "../../../common.h"
-
 #include "consts.h"
 
 #define MLD_AVX2_REJ_UNIFORM_BUFLEN \
diff --git a/mldsa/src/packing.c b/mldsa/src/packing.c
index 0219466f17..2165add471 100644
--- a/mldsa/src/packing.c
+++ b/mldsa/src/packing.c
@@ -3,7 +3,6 @@
  * SPDX-License-Identifier: Apache-2.0 OR ISC OR MIT
  */
 #include "packing.h"
-
 #include "common.h"
 #include "poly.h"
 #include "polyvec.h"
diff --git a/mldsa/src/poly.c b/mldsa/src/poly.c
index 4153d80b8d..46c3338c2a 100644
--- a/mldsa/src/poly.c
+++ b/mldsa/src/poly.c
@@ -19,7 +19,6 @@
  */
 
 #include "poly.h"
-
 #include "common.h"
 #include "ct.h"
 #include "debug.h"
diff --git a/mldsa/src/poly_kl.c b/mldsa/src/poly_kl.c
index 95241c08a5..868c08805a 100644
--- a/mldsa/src/poly_kl.c
+++ b/mldsa/src/poly_kl.c
@@ -19,7 +19,6 @@
  */
 
 #include "poly_kl.h"
-
 #include "ct.h"
 #include "debug.h"
 #include "rounding.h"
diff --git a/mldsa/src/polyvec.c b/mldsa/src/polyvec.c
index be13ae3f91..f56bcb2cb6 100644
--- a/mldsa/src/polyvec.c
+++ b/mldsa/src/polyvec.c
@@ -13,7 +13,6 @@
  */
 
 #include "polyvec.h"
-
 #include "debug.h"
 #include "polyvec_lazy.h"
 
diff --git a/mldsa/src/polyvec_lazy.c b/mldsa/src/polyvec_lazy.c
index dab3ce96a9..cc2c307a64 100644
--- a/mldsa/src/polyvec_lazy.c
+++ b/mldsa/src/polyvec_lazy.c
@@ -13,7 +13,6 @@
  */
 
 #include "polyvec_lazy.h"
-
 #include "debug.h"
 
 /* This namespacing is not done at the top to avoid a naming conflict
diff --git a/mldsa/src/sign.c b/mldsa/src/sign.c
index 48dac1184b..15075c562c 100644
--- a/mldsa/src/sign.c
+++ b/mldsa/src/sign.c
@@ -35,7 +35,6 @@
  */
 
 #include "sign.h"
-
 #include "cbmc.h"
 #include "ct.h"
 #include "debug.h"
diff --git a/mldsa/src/sign.h b/mldsa/src/sign.h
index dea6810ff9..6c596d93fc 100644
--- a/mldsa/src/sign.h
+++ b/mldsa/src/sign.h
@@ -16,6 +16,7 @@
 #define MLD_SIGN_H
 
 #include <stddef.h>
+
 #include "cbmc.h"
 #include "common.h"
 #include "poly.h"
diff --git a/scripts/autogen b/scripts/autogen
index 6f783c32a8..800a8ecee7 100755
--- a/scripts/autogen
+++ b/scripts/autogen
@@ -113,9 +113,12 @@ def finalize_format_batch(batch):
             # Skip files scheduled for deletion
             if content is None:
                 continue
-            with tempfile.NamedTemporaryFile(mode="w", suffix=".c", delete=False) as f:
+            # Keep the file name: clang-format uses it to identify the main
+            # include, which it sorts first.
+            temp_path = os.path.join(tempfile.mkdtemp(), os.path.basename(filename))
+            with open(temp_path, "w") as f:
                 f.write(content)
-                temp_files.append((f.name, filename))
+            temp_files.append((temp_path, filename))
 
         # Call clang-format with -i to update files in-place
         clang_format_file = os.path.join(
@@ -141,6 +144,7 @@ def finalize_format_batch(batch):
     finally:
         for temp_path, _ in temp_files:
             os.unlink(temp_path)
+            os.rmdir(os.path.dirname(temp_path))
 
 
 def finalize_file(item, dry_run):