diff --git a/src/jbuild_load.ml b/src/jbuild_load.ml
index 97641448..b31b8c8a 100644
--- a/src/jbuild_load.ml
+++ b/src/jbuild_load.ml
@@ -146,10 +146,10 @@ let load ~dir ~visible_packages ~closest_packages =
       ; closest_packages
       }
 
-let load () =
+let load ?(extra_ignored_subtrees=Path.Set.empty) () =
   let ftree = File_tree.load Path.root in
   let packages, ignored_subtrees =
-    File_tree.fold ftree ~init:([], Path.Set.empty) ~f:(fun dir (pkgs, ignored) ->
+    File_tree.fold ftree ~init:([], extra_ignored_subtrees) ~f:(fun dir (pkgs, ignored) ->
       let path = File_tree.Dir.path dir in
       let files = File_tree.Dir.files dir in
       let pkgs =
@@ -220,18 +220,14 @@ let load () =
       else
         jbuilds
     in
-    let sub_dirs =
-      if String_set.mem "jbuild-ignore" files then
-        String_map.filter sub_dirs ~f:(fun _ dir ->
-          not (Path.Set.mem (File_tree.Dir.path dir) ignored_subtrees))
-      else
-        sub_dirs
-    in
     let children, jbuilds =
       String_map.fold sub_dirs ~init:([], jbuilds)
         ~f:(fun ~key:_ ~data:dir (children, jbuilds) ->
-          let child, jbuilds = walk dir jbuilds visible_packages closest_packages in
-          (child :: children, jbuilds))
+          if Path.Set.mem (File_tree.Dir.path dir) ignored_subtrees then
+            (children, jbuilds)
+          else
+            let child, jbuilds = walk dir jbuilds visible_packages closest_packages in
+            (child :: children, jbuilds))
     in
     (Alias.Node (path, children), jbuilds)
   in
diff --git a/src/jbuild_load.mli b/src/jbuild_load.mli
index 80633e7b..f2b2290c 100644
--- a/src/jbuild_load.mli
+++ b/src/jbuild_load.mli
@@ -13,4 +13,4 @@ type conf =
   ; packages  : Package.t String_map.t
   }
 
-val load : unit -> conf
+val load : ?extra_ignored_subtrees:Path.Set.t -> unit -> conf
diff --git a/src/main.ml b/src/main.ml
index 01405300..b11a371a 100644
--- a/src/main.ml
+++ b/src/main.ml
@@ -16,8 +16,10 @@ let package_install_file { packages; _ } pkg =
 let setup ?(log=Log.no_log) ?filter_out_optional_stanzas_with_missing_deps
       ?workspace ?(workspace_file="jbuild-workspace")
       ?(use_findlib=true)
-      ?only_packages () =
-  let conf = Jbuild_load.load () in
+      ?only_packages
+      ?extra_ignored_subtrees
+      () =
+  let conf = Jbuild_load.load ?extra_ignored_subtrees () in
   Option.iter only_packages ~f:(fun set ->
     String_set.iter set ~f:(fun pkg ->
       if not (String_map.mem pkg conf.packages) then
@@ -131,6 +133,13 @@ let report_error ?map_fname ppf exn =
     let backtrace = Printexc.get_raw_backtrace () in
     report_error ?map_fname ppf exn ~backtrace
 
+let ignored_during_bootstrap =
+  Path.Set.of_list
+    (List.map ~f:Path.of_string
+       [ "test"
+       ; "example"
+       ])
+
 (* Called by the script generated by ../build.ml *)
 let bootstrap () =
   Ansi_color.setup_err_formatter_colors ();
@@ -146,7 +155,9 @@ let bootstrap () =
     let log = Log.create () in
     Future.Scheduler.go ~log
       (setup ~log ~workspace:{ merlin_context = Some "default"; contexts = [Default] }
-         ~use_findlib:false ()
+         ~use_findlib:false
+         ~extra_ignored_subtrees:ignored_during_bootstrap
+         ()
        >>= fun { build_system = bs; _ } ->
        Build_system.do_build_exn bs [Path.(relative root) (pkg ^ ".install")])
   in
@@ -156,4 +167,4 @@ let bootstrap () =
     Format.eprintf "%a@?" (report_error ?map_fname:None) exn;
     exit 1
 
-let setup = setup ~use_findlib:true
+let setup = setup ~use_findlib:true ~extra_ignored_subtrees:Path.Set.empty