diff --git a/usr/lib/akshara/utils/gen_rootfs.py b/usr/lib/akshara/utils/gen_rootfs.py
index 289c7e1..918eef5 100644
--- a/usr/lib/akshara/utils/gen_rootfs.py
+++ b/usr/lib/akshara/utils/gen_rootfs.py
@@ -61,4 +61,24 @@ def gen_rootfs(system_config: dict, rootfs_path: str) -> RootFS:
         json.dump(system_config, system_json_file, ensure_ascii=False)
         pass
 
+    with open(
+        os.path.join(str(rootfs), "usr/immutable.list"), "w"
+    ) as immutable_list_file:
+        immutable_set = set(
+            [
+                override["path"]
+                for override in system_config["override"]
+                if isinstance(override.get("immutable"), bool) and override["immutable"]
+            ]
+            if isinstance(system_config.get("override"), list)
+            else {}
+        )
+
+        immutable_set.add("/usr")
+
+        immutable_list_file.write("\n".join(list(immutable_set)))
+
+    subprocess.run(["cp", "-ax", f"{rootfs}/etc", f"{rootfs}/usr/etc"])
+    subprocess.run(["cp", "-ax", f"{rootfs}/var", f"{rootfs}/usr/var"])
+
     return rootfs
diff --git a/usr/lib/akshara/utils/update.py b/usr/lib/akshara/utils/update.py
index 3737ae4..70f668d 100644
--- a/usr/lib/akshara/utils/update.py
+++ b/usr/lib/akshara/utils/update.py
@@ -47,8 +47,6 @@ def merge_etc(new_rootfs: RootFS, overrides_keep_new: dict) -> None:
         new_rootfs: New RootFS instance.
         overrides_keep_new: Dictionary comprising overrides and whether to keep new.
     """
-    subprocess.run(["cp", "-ax", f"{new_rootfs}/etc", f"{new_rootfs}/usr/etc"])
-
     if not os.path.isdir("/usr/etc"):
         subprocess.run(["rm", "-rf", "/usr/etc"])
         subprocess.run(["cp", "-ax", "/etc", "/usr/etc"])
@@ -102,7 +100,6 @@ def merge_var(new_rootfs: RootFS, overrides_keep_new: dict) -> None:
         new_rootfs: Path to rootfs.
         overrides_keep_new: Dictionary comprising overrides and whether to keep new.
     """
-    subprocess.run(["cp", "-ax", f"{new_rootfs}/var", f"{new_rootfs}/usr/var"])
     subprocess.run(["rm", "-rf", f"{new_rootfs}/var/lib"])
     subprocess.run(["cp", "-ax", "/var/lib", f"{new_rootfs}/var/lib"])
 
@@ -329,23 +326,6 @@ def update() -> None:
     output.info("merging /var...")
     merge_var(new_rootfs, overrides_keep_new)
 
-    with open(
-        os.path.join(str(new_rootfs), "usr/immutable.list"), "w"
-    ) as immutable_list_file:
-        immutable_set = set(
-            [
-                override["path"]
-                for override in system_config["override"]
-                if isinstance(override.get("immutable"), bool) and override["immutable"]
-            ]
-            if isinstance(system_config.get("override"), list)
-            else {}
-        )
-
-        immutable_set.add("/usr")
-
-        immutable_list_file.write("\n".join(list(immutable_set)))
-
     subprocess.run(["cp", "-ax", str(new_rootfs), "/.update_rootfs"])
 
     handle_boot(new_rootfs, system_config["boot"])