diff --git a/bootstrap b/bootstrap
index 37f2146..c68bcab 100755
--- a/bootstrap
+++ b/bootstrap
@@ -56,13 +56,13 @@ main(Args) ->
     %% Run rebar to do proper .app validation and such
     rebar:main(["compile"] ++ Args),
 
-    %% Read the contents of the files in ebin and templates; note that we
-    %% place all the beam files at the top level of the code archive so
-    %% that code loading works properly.
-    Files = load_files("*", "ebin") ++ load_files("priv/templates/*", "."),
+    TempDir = make_temp_dir(),
+    ok = copy_files(TempDir), %% Copy the ebin and priv/templates
+    {ok, Dirs} = file:list_dir(TempDir),
 
-    case zip:create("mem", Files, [memory]) of
+    case zip:create("mem", Dirs, [memory, {cwd, TempDir}]) of
         {ok, {"mem", ZipBin}} ->
+            ok = rebar_file_utils:rm_rf(TempDir),
             %% Archive was successfully created. Prefix that binary with our
             %% header and write to "rebar" file.
             %% Without -noshell -noinput escript consumes all input that would
@@ -78,6 +78,7 @@ main(Args) ->
                     halt(1)
             end;
         {error, ZipError} ->
+            ok = rebar_file_utils:rm_rf(TempDir),
             io:format("Failed to construct rebar script archive: ~p\n",
                       [ZipError]),
             halt(1)
@@ -103,6 +104,37 @@ main(Args) ->
               "Place this script anywhere in your path\n"
               "and you can use rebar to build OTP-compliant apps.\n").
 
+make_temp_dir() ->
+    case temp_name("rebar.") of
+        {ok, TempDir} ->
+            case file:make_dir(TempDir) of
+                ok ->
+                    TempDir;
+                Error ->
+                    io:format("Failed to create temporary directory: ~p~n",
+                              [Error]),
+                    halt(1),
+                    Error
+            end;
+        Error ->
+            io:format("Failed to create temporary directory: ~p~n",
+                      [Error]),
+            halt(1)
+    end.
+
+temp_name(Prefix) ->
+    temp_name(Prefix, 5).
+
+temp_name(_Prefix, 0) ->
+    {error, eexist};
+temp_name(Prefix, N) ->
+    Hash = erlang:phash2(make_ref()),
+    Name = Prefix ++ integer_to_list(Hash),
+    case filelib:is_file(Name) of
+        false -> {ok, Name};
+        true  -> temp_name(Prefix, N-1)
+    end.
+
 rm(Path) ->
     NativePath = filename:nativename(Path),
     Cmd = case os:type() of
@@ -117,13 +149,25 @@ build_time() ->
     lists:flatten(io_lib:format("~4..0w~2..0w~2..0w_~2..0w~2..0w~2..0w",
                                 [Y, M, D, H, Min, S])).
 
+copy_files(Temp) ->
+    BaseEbinDir = filename:join("rebar", "ebin"),
+    BaseTemplatesDir = filename:join("priv", "templates"),
+    EbinDir = filename:join(Temp, BaseEbinDir),
+    TemplatesDir = filename:join(Temp, BaseTemplatesDir),
 
-load_files(Wildcard, Dir) ->
-    [read_file(Filename, Dir) || Filename <- filelib:wildcard(Wildcard, Dir)].
+    %% prepare directory structure
+    lists:foreach(
+      fun(Dir) ->
+              ok = filelib:ensure_dir(filename:join(Dir, "dummy"))
+      end, [EbinDir, TemplatesDir]),
 
-read_file(Filename, Dir) ->
-    {ok, Bin} = file:read_file(filename:join(Dir, Filename)),
-    {Filename, Bin}.
+    %% copy content of ebin
+    EbinSrc = filename:join(["ebin", "*"]),
+    ok = rebar_file_utils:cp_r([EbinSrc], EbinDir),
+
+    %% copy content of priv/templates
+    TemplatesSrc = filename:join(BaseTemplatesDir, "*"),
+    ok = rebar_file_utils:cp_r([TemplatesSrc], TemplatesDir).
 
 vcs_info([]) ->
     "No VCS info available.";