diff --git a/bin/main.ml b/bin/main.ml
index 7e5d872b..07c9479f 100644
--- a/bin/main.ml
+++ b/bin/main.ml
@@ -804,7 +804,7 @@ let clean =
     begin
       set_common common ~targets:[];
       Build_system.files_in_source_tree_to_delete ()
-      |> List.iter ~f:Path.unlink_no_err;
+      |> Path.Set.iter ~f:Path.unlink_no_err;
       Path.rm_rf Path.build_dir
     end
   in
diff --git a/src/build_system.ml b/src/build_system.ml
index 6950811d..edceb4c2 100644
--- a/src/build_system.ml
+++ b/src/build_system.ml
@@ -11,25 +11,24 @@ let misc_dir = Path.(relative build_dir) ".misc"
 
 module Promoted_to_delete = struct
   module P = Utils.Persistent(struct
-      type t = Path.t list
+      type t = Path.Set.t
       let name = "PROMOTED-TO-DELETE"
       let version = 1
     end)
-  let db = ref []
+
+  let db = ref Path.Set.empty
 
   let fn = Path.relative Path.build_dir ".to-delete-in-source-tree"
 
-  let add p = db := p :: !db
+  let add p = db := Path.Set.add !db p
 
   let load () =
-    Option.value ~default:[] (P.load fn)
+    Option.value ~default:Path.Set.empty (P.load fn)
 
   let dump () =
     if Path.build_dir_exists () then
       load ()
-      |> Path.Set.of_list
-      |> Path.Set.union (Path.Set.of_list !db)
-      |> Path.Set.to_list
+      |> Path.Set.union !db
       |> P.dump fn
 end
 
diff --git a/src/build_system.mli b/src/build_system.mli
index 4abbcd2b..631122ee 100644
--- a/src/build_system.mli
+++ b/src/build_system.mli
@@ -204,11 +204,11 @@ val all_lib_deps_by_context
 (** List of all buildable targets *)
 val all_targets : t -> Path.t list
 
-(** Return the list of files that were created in the source tree and
+(** Return the set of files that were created in the source tree and
     needs to be deleted *)
 val files_in_source_tree_to_delete
   :  unit
-  -> Path.t list
+  -> Path.Set.t
 
 (** {2 Build rules} *)