diff --git a/src/commands/commandUtils.ml b/src/commands/commandUtils.ml
index ba5b5b5a728..a8667491776 100644
--- a/src/commands/commandUtils.ml
+++ b/src/commands/commandUtils.ml
@@ -568,7 +568,7 @@ let file_options =
       let msg = "Could not locate flowlib files" in
       FlowExitStatus.(exit ~msg Could_not_find_flowconfig)
   in
-  let ignores_of_arg root patterns extras =
+  let ignores_of_arg root default_lib_dir patterns extras =
     let patterns = Core_list.rev_append extras patterns in
     Core_list.map
       ~f:(fun s ->
@@ -578,6 +578,8 @@ let file_options =
           |> remove_exclusion
           |> Str.split_delim Files.project_root_token
           |> String.concat root
+          |> Str.split_delim Files.flowlib_root_token
+          |> String.concat default_lib_dir
           |> Str.regexp
         in
         (s, reg))
@@ -638,17 +640,30 @@ let file_options =
   fun ~root ~no_flowlib ~temp_dir ~includes ~ignores ~libs ~untyped ~declarations flowconfig ->
     let default_lib_dir =
       let no_flowlib = no_flowlib || FlowConfig.no_flowlib flowconfig in
-      Some (default_lib_dir ~no_flowlib temp_dir)
+      default_lib_dir ~no_flowlib temp_dir
     in
-    let ignores = ignores_of_arg root (FlowConfig.ignores flowconfig) ignores in
-    let untyped = ignores_of_arg root (FlowConfig.untyped flowconfig) untyped in
-    let declarations = ignores_of_arg root (FlowConfig.declarations flowconfig) declarations in
+    let ignores = ignores_of_arg
+      root
+      (Path.to_string default_lib_dir)
+      (FlowConfig.ignores flowconfig)
+      ignores in
+    let untyped = ignores_of_arg
+      root
+      (Path.to_string default_lib_dir)
+      (FlowConfig.untyped flowconfig)
+      untyped in
+    let declarations = ignores_of_arg
+      root
+      (Path.to_string default_lib_dir)
+      (FlowConfig.declarations flowconfig)
+      declarations in
     let lib_paths = lib_paths ~root flowconfig libs in
     let includes =
       includes
       |> Core_list.rev_append (FlowConfig.includes flowconfig)
       |> includes_of_arg ~root ~lib_paths
     in
+    let default_lib_dir = Some (default_lib_dir) in
     {
       Files.default_lib_dir;
       ignores;
diff --git a/src/common/files.ml b/src/common/files.ml
index ef5816bd7f2..06c6f86493c 100644
--- a/src/common/files.ml
+++ b/src/common/files.ml
@@ -300,43 +300,6 @@ let get_all =
   in
   (fun next -> get_all_rec next SSet.empty)
 
-let init ?(flowlibs_only = false) (options : options) =
-  let node_module_filter = is_node_module options in
-  let libs =
-    if flowlibs_only then
-      []
-    else
-      options.lib_paths
-  in
-  let (libs, filter) =
-    match options.default_lib_dir with
-    | None -> (libs, is_valid_path ~options)
-    | Some root ->
-      let is_in_flowlib = is_prefix (Path.to_string root) in
-      let is_valid_path = is_valid_path ~options in
-      let filter path = is_in_flowlib path || is_valid_path path in
-      (root :: libs, filter)
-  in
-  (* preserve enumeration order *)
-  let libs =
-    if libs = [] then
-      []
-    else
-      let get_next lib =
-        let lib_str = Path.to_string lib in
-        (* TODO: better to parse json files, not ignore them *)
-        let filter' path = (path = lib_str || filter path) && not (is_json_file path) in
-        make_next_files_following_symlinks
-          ~node_module_filter
-          ~path_filter:filter'
-          ~realpath_filter:filter'
-          ~error_filter:(fun _ -> true)
-          [lib]
-      in
-      libs |> Core_list.map ~f:(fun lib -> SSet.elements (get_all (get_next lib))) |> List.flatten
-  in
-  (libs, SSet.of_list libs)
-
 (* Local reference to the module exported by a file. Like other local references
    to modules imported by the file, it is a member of Context.module_map. *)
 let module_ref file = File_key.to_string file
@@ -353,6 +316,8 @@ let absolute_path_regexp = Str.regexp "^\\(/\\|[A-Za-z]:[/\\\\]\\)"
 
 let project_root_token = Str.regexp_string "<PROJECT_ROOT>"
 
+let flowlib_root_token = Str.regexp_string "<FLOWLIB_ROOT>"
+
 let is_matching path pattern_list =
   List.fold_left
     (fun current (pattern, rx) ->
@@ -393,6 +358,37 @@ let wanted ~options lib_fileset =
 
 let watched_paths options = Path_matcher.stems options.includes
 
+let init ?(flowlibs_only=false) (options: options) =
+  let node_module_filter = is_node_module options in
+  let libs = if flowlibs_only then [] else options.lib_paths in
+  let libs, filter = match options.default_lib_dir with
+    | None -> libs, is_valid_path ~options
+    | Some root ->
+      let is_in_flowlib = is_prefix (Path.to_string root) in
+      let is_valid_path = is_valid_path ~options in
+      let filter path = (is_in_flowlib path || is_valid_path path) && (not (is_ignored options path)) in
+      root::libs, filter
+  in
+  (* preserve enumeration order *)
+  let libs = if libs = []
+    then []
+    else
+      let get_next lib =
+        let lib_str = Path.to_string lib in
+        let filter' path = path = lib_str || filter path in
+        make_next_files_following_symlinks
+          ~node_module_filter
+          ~path_filter:filter'
+          ~realpath_filter:filter'
+          ~error_filter:(fun _ -> true)
+          [lib]
+      in
+      libs
+      |> Core_list.map ~f:(fun lib -> SSet.elements (get_all (get_next lib)))
+      |> List.flatten
+  in
+  (libs, SSet.of_list libs)
+
 (**
  * Creates a "next" function (see also: `get_all`) for finding the files in a
  * given FlowConfig root. This means all the files under the root and all the
diff --git a/src/common/files.mli b/src/common/files.mli
index b38ac8ee0fa..b7f48e5283a 100644
--- a/src/common/files.mli
+++ b/src/common/files.mli
@@ -84,6 +84,8 @@ val absolute_path_regexp : Str.regexp
 
 val project_root_token : Str.regexp
 
+val flowlib_root_token : Str.regexp
+
 val watched_paths : options -> Path.t list
 
 (* given a root, make a filter for file names *)