diff --git a/src/rebar_ct.erl b/src/rebar_ct.erl
index f3ed29f..c075e8c 100644
--- a/src/rebar_ct.erl
+++ b/src/rebar_ct.erl
@@ -210,7 +210,7 @@ make_cmd(TestDir, RawLogDir, Config) ->
     CodeDirs = [io_lib:format("\"~s\"", [Dir]) ||
                    Dir <- [EbinDir|NonLibCodeDirs]],
     CodePathString = string:join(CodeDirs, " "),
-    Cmd = case get_ct_specs(Cwd) of
+    Cmd = case get_ct_specs(Config, Cwd) of
               undefined ->
                   ?FMT("~s"
                        " -pa ~s"
@@ -260,8 +260,8 @@ build_name(Config) ->
 get_extra_params(Config) ->
     rebar_config:get_local(Config, ct_extra_params, "").
 
-get_ct_specs(Cwd) ->
-    case collect_glob(Cwd, ".*\.test\.spec\$") of
+get_ct_specs(Config, Cwd) ->
+    case collect_glob(Config, Cwd, ".*\.test\.spec\$") of
         [] -> undefined;
         [Spec] ->
             " -spec " ++ Spec;
@@ -275,31 +275,38 @@ get_cover_config(Config, Cwd) ->
         false ->
             "";
         true ->
-            case collect_glob(Cwd, ".*cover\.spec\$") of
+            case collect_glob(Config, Cwd, ".*cover\.spec\$") of
                 [] ->
                     ?DEBUG("No cover spec found: ~s~n", [Cwd]),
                     "";
                 [Spec] ->
-                    ?DEBUG("Found cover file ~w~n", [Spec]),
+                    ?DEBUG("Found cover file ~s~n", [Spec]),
                     " -cover " ++ Spec;
                 Specs ->
                     ?ABORT("Multiple cover specs found: ~p~n", [Specs])
             end
     end.
 
-collect_glob(Cwd, Glob) ->
-    filelib:fold_files(Cwd, Glob, true, fun collect_files/2, []).
+collect_glob(Config, Cwd, Glob) ->
+    {true, Deps} = rebar_deps:get_deps_dir(Config),
+    CwdParts = filename:split(Cwd),
+    filelib:fold_files(Cwd, Glob, true, fun(F, Acc) ->
+        %% Ignore any specs under the deps/ directory. Do this pulling
+        %% the dirname off the F and then splitting it into a list.
+        Parts = filename:split(filename:dirname(F)),
+        Parts2 = remove_common_prefix(Parts, CwdParts),
+        case lists:member(Deps, Parts2) of
+            true ->
+                Acc;                % There is a directory named "deps" in path
+            false ->
+                [F | Acc]           % No "deps" directory in path
+        end
+    end, []).
 
-collect_files(F, Acc) ->
-    %% Ignore any specs under the deps/ directory. Do this pulling
-    %% the dirname off the the F and then splitting it into a list.
-    Parts = filename:split(filename:dirname(F)),
-    case lists:member("deps", Parts) of
-        true ->
-            Acc;                % There is a directory named "deps" in path
-        false ->
-            [F | Acc]           % No "deps" directory in path
-    end.
+remove_common_prefix([H1|T1], [H1|T2]) ->
+    remove_common_prefix(T1, T2);
+remove_common_prefix(L1, _) ->
+    L1.
 
 get_ct_config_file(TestDir) ->
     Config = filename:join(TestDir, "test.config"),
diff --git a/src/rebar_deps.erl b/src/rebar_deps.erl
index 392882c..bd94921 100644
--- a/src/rebar_deps.erl
+++ b/src/rebar_deps.erl
@@ -40,6 +40,7 @@
 
 %% for internal use only
 -export([info/2]).
+-export([get_deps_dir/1]).
 
 -record(dep, { dir,
                app,