refactor `rebar_erlc_compiler`

* modify compiler interface to work on either application objects or
  directories containing source files
* compile all sources in `src_dirs` to the application `ebin` dir and
  all sources in `extra_src_dirs` to a directory mirroring it's
  position in the app's `_build` directory. for example, `apps/foo/more`
  would compile to `_build/default/lib/foo/more`
  for `extra_src_dirs` in the root of a project with multiple
  applications (so orphan directories that don't "belong" to an
  application) compile to `_build/default/extras/more`
* copy directories specified in `extra_src_dirs` into the `_build`
  directory so tools like `ct` and `xref` that expect source to be
  in a particular location still work
* clean compiled artifacts from all `extra_src_dirs`
* alter `eunit`, `ct` and `cover` to work with the new directory
  structure
* billions of new tests

15 files changed, 1107 insertions, 303 deletions

diff --git a/rebar.config b/rebar.config
index deff2cc..6eed68f 100644
--- a/rebar.config
+++ b/rebar.config
@@ -18,6 +18,7 @@
                       {"rebar/priv/templates/*", "_build/default/lib/"}]}.
 
 {erl_opts, [{platform_define, "^[0-9]+", namespaced_types},
+            {platform_define, "^R1[4|5]", no_list_dir_all},
             no_debug_info,
             warnings_as_errors]}.
 
diff --git a/src/rebar_erlc_compiler.erl b/src/rebar_erlc_compiler.erl
index 06d09bd..5075f0f 100644
--- a/src/rebar_erlc_compiler.erl
+++ b/src/rebar_erlc_compiler.erl
@@ -26,8 +26,9 @@
 %% -------------------------------------------------------------------
 -module(rebar_erlc_compiler).
 
--export([compile/1,
-         compile/3,
+-export([compile/1, compile/2, compile/3,
+         compile_dir/3, compile_dir/4,
+         compile_dirs/5,
          clean/1]).
 
 -include("rebar.hrl").
@@ -38,14 +39,22 @@
 -type erlc_info_v() :: {digraph:vertex(), term()} | 'false'.
 -type erlc_info_e() :: {digraph:vertex(), digraph:vertex()}.
 -type erlc_info() :: {list(erlc_info_v()), list(erlc_info_e()), list(string())}.
--record(erlcinfo,
-        {
-          vsn = ?ERLCINFO_VSN :: pos_integer(),
-          info = {[], [], []} :: erlc_info()
-        }).
+-record(erlcinfo, {
+    vsn = ?ERLCINFO_VSN :: pos_integer(),
+    info = {[], [], []} :: erlc_info()
+}).
 
+-type compile_opts() :: [compile_opt()].
+-type compile_opt() :: {recursive, boolean()}.
+
+-record(compile_opts, {
+    recursive = true
+}).
+
+-define(DEFAULT_OUTDIR, "ebin").
 -define(RE_PREFIX, "^[^._]").
 
+
 %% ===================================================================
 %% Public API
 %% ===================================================================
@@ -80,106 +89,189 @@
 %%                           'old_inets'}]}.
 %%
 
--spec compile(rebar_app_info:t()) -> 'ok'.
-compile(AppInfo) ->
+%% @equiv compile(AppInfo, []).
+
+-spec compile(rebar_app_info:t()) -> ok.
+compile(AppInfo) when is_tuple(AppInfo), element(1, AppInfo) == app_info_t ->
+    compile(AppInfo, []).
+
+%% @doc compile an individual application.
+
+-spec compile(rebar_app_info:t(), compile_opts()) -> ok.
+compile(AppInfo, CompileOpts) when is_tuple(AppInfo), element(1, AppInfo) == app_info_t ->
     Dir = ec_cnv:to_list(rebar_app_info:out_dir(AppInfo)),
-    compile(rebar_app_info:opts(AppInfo), Dir, filename:join([Dir, "ebin"])).
+    RebarOpts = rebar_app_info:opts(AppInfo),
 
--spec compile(rebar_dict(), file:name(), file:name()) -> 'ok'.
-compile(Opts, Dir, OutDir) ->
-    rebar_base_compiler:run(Opts,
+    rebar_base_compiler:run(RebarOpts,
                             check_files([filename:join(Dir, File)
-                                         || File <- rebar_opts:get(Opts, xrl_first_files, [])]),
+                                         || File <- rebar_opts:get(RebarOpts, xrl_first_files, [])]),
                             filename:join(Dir, "src"), ".xrl", filename:join(Dir, "src"), ".erl",
                             fun compile_xrl/3),
-    rebar_base_compiler:run(Opts,
+    rebar_base_compiler:run(RebarOpts,
                             check_files([filename:join(Dir, File)
-                                         || File <- rebar_opts:get(Opts, yrl_first_files, [])]),
+                                         || File <- rebar_opts:get(RebarOpts, yrl_first_files, [])]),
                             filename:join(Dir, "src"), ".yrl", filename:join(Dir, "src"), ".erl",
                             fun compile_yrl/3),
-    rebar_base_compiler:run(Opts,
+    rebar_base_compiler:run(RebarOpts,
                             check_files([filename:join(Dir, File)
-                                         || File <- rebar_opts:get(Opts, mib_first_files, [])]),
+                                         || File <- rebar_opts:get(RebarOpts, mib_first_files, [])]),
                             filename:join(Dir, "mibs"), ".mib", filename:join([Dir, "priv", "mibs"]), ".bin",
                             fun compile_mib/3),
-    doterl_compile(Opts, Dir, OutDir).
 
--spec clean(file:filename()) -> 'ok'.
-clean(AppDir) ->
-    MibFiles = rebar_utils:find_files(filename:join(AppDir, "mibs"), ?RE_PREFIX".*\\.mib\$"),
+    SrcDirs = lists:map(fun(SrcDir) -> filename:join(Dir, SrcDir) end,
+                        rebar_dir:src_dirs(RebarOpts, ["src"])),
+    OutDir = filename:join(Dir, outdir(RebarOpts)),
+    compile_dirs(RebarOpts, Dir, SrcDirs, OutDir, CompileOpts),
+
+    ExtraDirs = rebar_dir:extra_src_dirs(RebarOpts),
+    F = fun(D) ->
+        case ec_file:is_dir(filename:join([Dir, D])) of
+            true  -> compile_dirs(RebarOpts, Dir, [D], D, CompileOpts);
+            false -> ok
+        end
+    end,
+    lists:foreach(F, lists:map(fun(SrcDir) -> filename:join(Dir, SrcDir) end, ExtraDirs)).
+
+%% @hidden
+%% these are kept for backwards compatibility but they're bad functions with
+%% bad interfaces you probably shouldn't use
+%% State/RebarOpts have to have src_dirs set and BaseDir must be the parent
+%% directory of those src_dirs
+
+-spec compile(rebar_dict() | rebar_state:t(), file:name(), file:name()) -> ok.
+compile(State, BaseDir, OutDir) when is_tuple(State), element(1, State) == state_t ->
+    compile(rebar_state:opts(State), BaseDir, OutDir, [{recursive, false}]);
+compile(RebarOpts, BaseDir, OutDir) ->
+    compile(RebarOpts, BaseDir, OutDir, [{recursive, false}]).
+
+%% @hidden
+
+-spec compile(rebar_dict() | rebar_state:t(), file:name(), file:name(), compile_opts()) -> ok.
+compile(State, BaseDir, OutDir, CompileOpts) when is_tuple(State), element(1, State) == state_t ->
+    compile(rebar_state:opts(State), BaseDir, OutDir, CompileOpts);
+compile(RebarOpts, BaseDir, OutDir, CompileOpts) ->
+    SrcDirs = lists:map(fun(SrcDir) -> filename:join(BaseDir, SrcDir) end,
+                        rebar_dir:src_dirs(RebarOpts, ["src"])),
+    compile_dirs(RebarOpts, BaseDir, SrcDirs, OutDir, CompileOpts),
+
+    ExtraDirs = rebar_dir:extra_src_dirs(RebarOpts),
+    F = fun(D) ->
+        case ec_file:is_dir(filename:join([BaseDir, D])) of
+            true  -> compile_dirs(RebarOpts, BaseDir, [D], D, CompileOpts);
+            false -> ok
+        end
+    end,
+    lists:foreach(F, lists:map(fun(SrcDir) -> filename:join(BaseDir, SrcDir) end, ExtraDirs)).
+
+%% @equiv compile_dirs(Context, BaseDir, [Dir], Dir, [{recursive, false}]).
+
+-spec compile_dir(rebar_dict() | rebar_state:t(), file:name(), file:name()) -> ok.
+compile_dir(State, BaseDir, Dir) when is_tuple(State), element(1, State) == state_t ->
+    compile_dir(rebar_state:opts(State), BaseDir, Dir, [{recursive, false}]);
+compile_dir(RebarOpts, BaseDir, Dir) ->
+    compile_dir(RebarOpts, BaseDir, Dir, [{recursive, false}]).
+
+%% @equiv compile_dirs(Context, BaseDir, [Dir], Dir, Opts).
+
+-spec compile_dir(rebar_dict() | rebar_state:t(), file:name(), file:name(), compile_opts()) -> ok.
+compile_dir(State, BaseDir, Dir, Opts) when is_tuple(State), element(1, State) == state_t ->
+    compile_dirs(rebar_state:opts(State), BaseDir, [Dir], Dir, Opts);
+compile_dir(RebarOpts, BaseDir, Dir, Opts) ->
+    compile_dirs(RebarOpts, BaseDir, [Dir], Dir, Opts).
+
+%% @doc compile a list of directories with the given opts.
+
+-spec compile_dirs(rebar_dict() | rebar_state:t(),
+                   file:filename(),
+                   [file:filename()],
+                   file:filename(),
+                   compile_opts()) -> ok.
+compile_dirs(State, BaseDir, Dirs, OutDir, CompileOpts) when is_tuple(State), element(1, State) == state_t ->
+    compile_dirs(rebar_state:opts(State), BaseDir, Dirs, OutDir, CompileOpts);
+compile_dirs(RebarOpts, BaseDir, SrcDirs, OutDir, Opts) ->
+    CompileOpts = parse_opts(Opts),
+  
+    ErlOpts = rebar_opts:erl_opts(RebarOpts),
+    Recursive = CompileOpts#compile_opts.recursive,
+    AllErlFiles = gather_src(SrcDirs, Recursive),
+
+    %% Make sure that outdir is on the path
+    ok = filelib:ensure_dir(filename:join(OutDir, "dummy.beam")),
+    true = code:add_patha(filename:absname(OutDir)),
+
+    G = init_erlcinfo(proplists:get_all_values(i, ErlOpts), AllErlFiles, BaseDir, OutDir),
+
+    NeededErlFiles = needed_files(G, ErlOpts, BaseDir, OutDir, AllErlFiles),
+    {ErlFirstFiles, ErlOptsFirst} = erl_first_files(RebarOpts, ErlOpts, BaseDir, NeededErlFiles),
+    {DepErls, OtherErls} = lists:partition(
+                             fun(Source) -> digraph:in_degree(G, Source) > 0 end,
+                             [File || File <- NeededErlFiles, not lists:member(File, ErlFirstFiles)]),
+    SubGraph = digraph_utils:subgraph(G, DepErls),
+    DepErlsOrdered = digraph_utils:topsort(SubGraph),
+    FirstErls = ErlFirstFiles ++ lists:reverse(DepErlsOrdered),
+    try
+        rebar_base_compiler:run(
+            RebarOpts, FirstErls, OtherErls,
+            fun(S, C) ->
+                    ErlOpts1 = case lists:member(S, ErlFirstFiles) of
+                                   true -> ErlOptsFirst;
+                                   false -> ErlOpts
+                               end,
+                    internal_erl_compile(C, BaseDir, S, OutDir, ErlOpts1)
+            end)
+    after
+        true = digraph:delete(SubGraph),
+        true = digraph:delete(G)
+    end,
+    ok.
+
+%% @doc remove compiled artifacts from an AppDir.
+
+-spec clean(rebar_app_info:t()) -> 'ok'.
+clean(AppInfo) ->
+    AppDir = rebar_app_info:out_dir(AppInfo),
+
+    MibFiles = rebar_utils:find_files(filename:join([AppDir, "mibs"]), ?RE_PREFIX".*\\.mib\$"),
     MIBs = [filename:rootname(filename:basename(MIB)) || MIB <- MibFiles],
     rebar_file_utils:delete_each(
       [filename:join([AppDir, "include",MIB++".hrl"]) || MIB <- MIBs]),
-    lists:foreach(fun(F) -> ok = rebar_file_utils:rm_rf(F) end,
-                  [filename:join(AppDir, "ebin/*.beam"), filename:join(AppDir, "priv/mibs/*.bin")]),
+    ok = rebar_file_utils:rm_rf(filename:join([AppDir, "priv/mibs/*.bin"])),
 
-    YrlFiles = rebar_utils:find_files(filename:join(AppDir, "src"), ?RE_PREFIX".*\\.[x|y]rl\$"),
+    YrlFiles = rebar_utils:find_files(filename:join([AppDir, "src"]), ?RE_PREFIX".*\\.[x|y]rl\$"),
     rebar_file_utils:delete_each(
       [ binary_to_list(iolist_to_binary(re:replace(F, "\\.[x|y]rl$", ".erl")))
         || F <- YrlFiles ]),
 
+    BinDirs = ["ebin"|rebar_dir:extra_src_dirs(rebar_app_info:opts(AppInfo))],
+    ok = clean_dirs(AppDir, BinDirs),
+
     %% Delete the build graph, if any
-    rebar_file_utils:rm_rf(erlcinfo_file(AppDir)),
+    rebar_file_utils:rm_rf(erlcinfo_file(AppDir)).
 
+clean_dirs(_AppDir, []) -> ok;
+clean_dirs(AppDir, [Dir|Rest]) ->
+    ok = rebar_file_utils:rm_rf(filename:join([AppDir, Dir, "*.beam"])),
     %% Erlang compilation is recursive, so it's possible that we have a nested
     %% directory structure in ebin with .beam files within. As such, we want
-    %% to scan whatever is left in the ebin/ directory for sub-dirs which
+    %% to scan whatever is left in the app's out_dir directory for sub-dirs which
     %% satisfy our criteria.
-    BeamFiles = rebar_utils:find_files(filename:join(AppDir, "ebin"), ?RE_PREFIX".*\\.beam\$"),
+    BeamFiles = rebar_utils:find_files(filename:join([AppDir, Dir]), ?RE_PREFIX".*\\.beam\$"),
     rebar_file_utils:delete_each(BeamFiles),
-    lists:foreach(fun(Dir) -> delete_dir(Dir, dirs(Dir)) end, dirs(filename:join(AppDir, "ebin"))),
-    ok.
+    lists:foreach(fun(D) -> delete_dir(D, dirs(D)) end, dirs(filename:join([AppDir, Dir]))),
+    clean_dirs(AppDir, Rest).
+
 
 %% ===================================================================
 %% Internal functions
 %% ===================================================================
 
--spec doterl_compile(rebar_dict(), file:filename(), file:filename()) -> ok.
-doterl_compile(Opts, Dir, ODir) ->
-    ErlOpts = rebar_opts:erl_opts(Opts),
-    doterl_compile(Opts, Dir, ODir, [], ErlOpts).
-
-doterl_compile(Opts, Dir, OutDir, MoreSources, ErlOpts) ->
-    ?DEBUG("erl_opts ~p", [ErlOpts]),
-    %% Support the src_dirs option allowing multiple directories to
-    %% contain erlang source. This might be used, for example, should
-    %% eunit tests be separated from the core application source.
-    SrcDirs = [filename:join(Dir, X) || X <- rebar_dir:all_src_dirs(Opts, ["src"], [])],
-    AllErlFiles = gather_src(SrcDirs, []) ++ MoreSources,
-
-    %% Make sure that ebin/ exists and is on the path
-    ok = filelib:ensure_dir(filename:join(OutDir, "dummy.beam")),
-    true = code:add_patha(filename:absname(OutDir)),
-
-    OutDir1 = proplists:get_value(outdir, ErlOpts, OutDir),
-
-    G = init_erlcinfo(proplists:get_all_values(i, ErlOpts), AllErlFiles, Dir, OutDir),
-
-    NeededErlFiles = needed_files(G, ErlOpts, Dir, OutDir1, AllErlFiles),
-    {ErlFirstFiles, ErlOptsFirst} = erl_first_files(Opts, ErlOpts, Dir, NeededErlFiles),
-    {DepErls, OtherErls} = lists:partition(
-                             fun(Source) -> digraph:in_degree(G, Source) > 0 end,
-                             [File || File <- NeededErlFiles, not lists:member(File, ErlFirstFiles)]),
-    SubGraph = digraph_utils:subgraph(G, DepErls),
-    DepErlsOrdered = digraph_utils:topsort(SubGraph),
-    FirstErls = ErlFirstFiles ++ lists:reverse(DepErlsOrdered),
-    ?DEBUG("Files to compile first: ~p", [FirstErls]),
-    try
-        rebar_base_compiler:run(
-          Opts, FirstErls, OtherErls,
-          fun(S, C) ->
-                  ErlOpts1 = case lists:member(S, ErlFirstFiles) of
-                                 true -> ErlOptsFirst;
-                                 false -> ErlOpts
-                             end,
-                  internal_erl_compile(C, Dir, S, OutDir1, ErlOpts1)
-          end)
-    after
-        true = digraph:delete(SubGraph),
-        true = digraph:delete(G)
-    end,
-    ok.
+gather_src(Dirs, Recursive) ->
+    gather_src(Dirs, [], Recursive).
 
+gather_src([], Srcs, _Recursive) -> Srcs;
+gather_src([Dir|Rest], Srcs, Recursive) ->
+    gather_src(Rest, Srcs ++ rebar_utils:find_files(Dir, ?RE_PREFIX".*\\.erl\$", Recursive), Recursive).
+    
 %% Get files which need to be compiled first, i.e. those specified in erl_first_files
 %% and parse_transform options.  Also produce specific erl_opts for these first
 %% files, so that yet to be compiled parse transformations are excluded from it.
@@ -487,11 +579,7 @@ compile_xrl_yrl(_Opts, Source, Target, AllOpts, Mod) ->
 needs_compile(Source, Target) ->
     filelib:last_modified(Source) > filelib:last_modified(Target).
 
-gather_src([], Srcs) ->
-    Srcs;
-gather_src([Dir|Rest], Srcs) ->
-    gather_src(
-      Rest, Srcs ++ rebar_utils:find_files(Dir, ?RE_PREFIX".*\\.erl\$")).
+
 
 -spec dirs(file:filename()) -> [file:filename()].
 dirs(Dir) ->
@@ -620,3 +708,13 @@ check_file(File) ->
         false -> ?ABORT("File ~p is missing, aborting\n", [File]);
         true -> File
     end.
+
+outdir(RebarOpts) ->
+    ErlOpts = rebar_opts:erl_opts(RebarOpts),
+    proplists:get_value(outdir, ErlOpts, ?DEFAULT_OUTDIR).
+
+parse_opts(Opts) -> parse_opts(Opts, #compile_opts{}).
+
+parse_opts([], CompileOpts) -> CompileOpts;
+parse_opts([{recursive, Recursive}|Rest], CompileOpts) when Recursive == true; Recursive == false ->
+    parse_opts(Rest, CompileOpts#compile_opts{recursive = Recursive}).
diff --git a/src/rebar_prv_clean.erl b/src/rebar_prv_clean.erl
index a2b537a..6694dc0 100644
--- a/src/rebar_prv_clean.erl
+++ b/src/rebar_prv_clean.erl
@@ -49,6 +49,7 @@ do(State) ->
     Cwd = rebar_dir:get_cwd(),
     rebar_hooks:run_all_hooks(Cwd, pre, ?PROVIDER, Providers, State),
     clean_apps(State, Providers, ProjectApps),
+    clean_extras(State),
     rebar_hooks:run_all_hooks(Cwd, post, ?PROVIDER, Providers, State),
 
     {ok, State}.
@@ -66,10 +67,14 @@ clean_apps(State, Providers, Apps) ->
          ?INFO("Cleaning out ~s...", [rebar_app_info:name(AppInfo)]),
          AppDir = rebar_app_info:dir(AppInfo),
          AppInfo1 = rebar_hooks:run_all_hooks(AppDir, pre, ?PROVIDER, Providers, AppInfo, State),
-         rebar_erlc_compiler:clean(rebar_app_info:out_dir(AppInfo1)),
+         rebar_erlc_compiler:clean(AppInfo1),
          rebar_hooks:run_all_hooks(AppDir, post, ?PROVIDER, Providers, AppInfo1, State)
      end || AppInfo <- Apps].
 
+clean_extras(State) ->
+    BaseDir = rebar_dir:base_dir(State),
+    rebar_file_utils:rm_rf(filename:join([BaseDir, "extras"])).
+
 handle_args(State) ->
     {Args, _} = rebar_state:command_parsed_args(State),
     All = proplists:get_value(all, Args, false),
diff --git a/src/rebar_prv_common_test.erl b/src/rebar_prv_common_test.erl
index 9155d3b..1f4c02d 100644
--- a/src/rebar_prv_common_test.erl
+++ b/src/rebar_prv_common_test.erl
@@ -285,26 +285,7 @@ find_suite_dirs(Suites) ->
 
 copy(State, Dir) ->
     From = reduce_path(Dir),
-    case From == rebar_state:dir(State) of
-        true  -> throw({error, suite_at_project_root});
-        false -> ok
-    end,
-    case retarget_path(State, From) of
-        %% directory lies outside of our project's file structure so
-        %%  don't copy it
-        From   -> From;
-        Target ->
-            %% recursively delete any symlinks in the target directory
-            %%  if it exists so we don't smash files in the linked dirs
-            case ec_file:is_dir(Target) of
-                true  -> remove_links(Target);
-                false -> ok
-            end,
-            case rebar_file_utils:symlink_or_copy(From, Target) of
-               exists -> Target;
-               ok     -> Target
-            end
-    end.
+    retarget_path(State, From).
 
 compile_dir(State, Dir) ->
     NewState = replace_src_dirs(State, [filename:absname(Dir)]),
@@ -350,29 +331,6 @@ reduce_path([_|Acc], [".."|Rest])  -> reduce_path(Acc, Rest);
 reduce_path([], [".."|Rest])       -> reduce_path([], Rest);
 reduce_path(Acc, [Component|Rest]) -> reduce_path([Component|Acc], Rest).
 
-
-remove_links(Path) ->
-    IsDir = ec_file:is_dir(Path),
-    case ec_file:is_symlink(Path) of
-        true when IsDir ->
-            delete_dir_link(Path);
-        false when IsDir ->
-                lists:foreach(fun(ChildPath) ->
-                                      remove_links(ChildPath)
-                              end, dir_entries(Path));
-        _ -> file:delete(Path)
-    end.
-
-delete_dir_link(Path) ->
-    case os:type() of
-        {unix, _} -> file:delete(Path);
-        {win32, _} -> file:del_dir(Path)
-    end.
-
-dir_entries(Path) ->
-    {ok, SubDirs} = file:list_dir(Path),
-    [filename:join(Path, SubDir) || SubDir <- SubDirs].
-
 replace_src_dirs(State, Dirs) ->
     %% replace any `src_dirs` with the test dirs
     ErlOpts = rebar_state:get(State, erl_opts, []),
diff --git a/src/rebar_prv_compile.erl b/src/rebar_prv_compile.erl
index 9811de9..2996aee 100644
--- a/src/rebar_prv_compile.erl
+++ b/src/rebar_prv_compile.erl
@@ -52,8 +52,10 @@ do(State) ->
     ProjectApps2 = build_apps(State, Providers, ProjectApps1),
     State2 = rebar_state:project_apps(State, ProjectApps2),
 
-    ProjAppsPaths = [filename:join(rebar_app_info:out_dir(X), "ebin") || X <- ProjectApps2],
-    State3 = rebar_state:code_paths(State2, all_deps, DepsPaths ++ ProjAppsPaths),
+    %% projects with structures like /apps/foo,/apps/bar,/test
+    build_extra_dirs(State, ProjectApps2),
+
+    State3 = update_code_paths(State2, ProjectApps2, DepsPaths),
 
     rebar_hooks:run_all_hooks(Cwd, post, ?PROVIDER, Providers, State2),
     case rebar_state:has_all_artifacts(State3) of
@@ -82,6 +84,30 @@ build_app(State, Providers, AppInfo) ->
     copy_app_dirs(AppInfo, AppDir, OutDir),
     compile(State, Providers, AppInfo).
 
+build_extra_dirs(State, Apps) ->
+    BaseDir = rebar_state:dir(State),
+    F = fun(App) -> rebar_app_info:dir(App) == BaseDir end,
+    %% check that this app hasn't already been dealt with
+    case lists:any(F, Apps) of
+        false ->
+            ProjOpts = rebar_state:opts(State),
+            Extras = rebar_dir:extra_src_dirs(ProjOpts, []),
+            [build_extra_dir(State, Dir) || Dir <- Extras];
+        true  -> ok
+    end.
+
+build_extra_dir(_State, []) -> ok;
+build_extra_dir(State, Dir) ->
+    case ec_file:is_dir(filename:join([rebar_state:dir(State), Dir])) of
+        true ->
+            BaseDir = filename:join([rebar_dir:base_dir(State), "extras"]),
+            OutDir = filename:join([BaseDir, Dir]),
+            filelib:ensure_dir(filename:join([OutDir, "dummy.beam"])),
+            copy(rebar_state:dir(State), BaseDir, Dir),
+            rebar_erlc_compiler:compile_dir(State, BaseDir, OutDir);
+        false -> ok
+    end.
+
 compile(State, AppInfo) ->
     compile(State, rebar_state:providers(State), AppInfo).
 
@@ -104,6 +130,33 @@ compile(State, Providers, AppInfo) ->
 %% Internal functions
 %% ===================================================================
 
+update_code_paths(State, ProjectApps, DepsPaths) ->
+    ProjAppsPaths = paths_for_apps(ProjectApps),
+    ExtrasPaths = paths_for_extras(State, ProjectApps),
+    rebar_state:code_paths(State, all_deps, DepsPaths ++ ProjAppsPaths ++ ExtrasPaths).
+
+paths_for_apps(Apps) -> paths_for_apps(Apps, []).
+
+paths_for_apps([], Acc) -> Acc;
+paths_for_apps([App|Rest], Acc) ->
+    {_SrcDirs, ExtraDirs} = resolve_src_dirs(rebar_app_info:opts(App)),
+    Paths = [filename:join([rebar_app_info:out_dir(App), Dir]) || Dir <- ["ebin"|ExtraDirs]],
+    FilteredPaths = lists:filter(fun ec_file:is_dir/1, Paths),
+    paths_for_apps(Rest, Acc ++ FilteredPaths).
+    
+paths_for_extras(State, Apps) ->
+    F = fun(App) -> rebar_app_info:dir(App) == rebar_state:dir(State) end,
+    %% check that this app hasn't already been dealt with
+    case lists:any(F, Apps) of
+        false -> paths_for_extras(State);
+        true  -> []
+    end.
+
+paths_for_extras(State) ->
+    {_SrcDirs, ExtraDirs} = resolve_src_dirs(rebar_state:opts(State)),
+    Paths = [filename:join([rebar_dir:base_dir(State), "extras", Dir]) || Dir <- ExtraDirs],
+    lists:filter(fun ec_file:is_dir/1, Paths).
+
 has_all_artifacts(AppInfo1) ->
     case rebar_app_info:has_all_artifacts(AppInfo1) of
         {false, File} ->
@@ -120,17 +173,17 @@ copy_app_dirs(AppInfo, OldAppDir, AppDir) ->
             %% copy all files from ebin if it exists
             case filelib:is_dir(EbinDir) of
                 true ->
-                    OutEbin = filename:join(AppDir, "ebin"),
-                    filelib:ensure_dir(filename:join(OutEbin, "dummy.beam")),
-                    rebar_file_utils:cp_r(filelib:wildcard(filename:join(EbinDir, "*")), OutEbin);
+                    OutEbin = filename:join([AppDir, "ebin"]),
+                    filelib:ensure_dir(filename:join([OutEbin, "dummy.beam"])),
+                    rebar_file_utils:cp_r(filelib:wildcard(filename:join([EbinDir, "*"])), OutEbin);
                 false ->
                     ok
             end,
 
-            filelib:ensure_dir(filename:join(AppDir, "dummy")),
+            filelib:ensure_dir(filename:join([AppDir, "dummy"])),
 
             %% link or copy mibs if it exists
-            case filelib:is_dir(filename:join(OldAppDir, "mibs")) of
+            case filelib:is_dir(filename:join([OldAppDir, "mibs"])) of
                 true ->
                     %% If mibs exist it means we must ensure priv exists.
                     %% mibs files are compiled to priv/mibs/
@@ -139,15 +192,57 @@ copy_app_dirs(AppInfo, OldAppDir, AppDir) ->
                 false ->
                     ok
             end,
-
+            {SrcDirs, ExtraDirs} = resolve_src_dirs(rebar_app_info:opts(AppInfo)),
             %% link to src_dirs to be adjacent to ebin is needed for R15 use of cover/xref
-            SrcDirs = rebar_dir:all_src_dirs(rebar_app_info:opts(AppInfo), ["src"], []),
-            [symlink_or_copy(OldAppDir, AppDir, Dir) || Dir <- ["priv", "include"] ++ SrcDirs];
+            [symlink_or_copy(OldAppDir, AppDir, Dir) || Dir <- ["priv", "include"] ++ SrcDirs],
+            %% copy all extra_src_dirs as they build into themselves and linking means they
+            %% are shared across profiles
+            [copy(OldAppDir, AppDir, Dir) || Dir <- ExtraDirs];
         false ->
             ok
     end.
 
 symlink_or_copy(OldAppDir, AppDir, Dir) ->
-    Source = filename:join(OldAppDir, Dir),
-    Target = filename:join(AppDir, Dir),
+    Source = filename:join([OldAppDir, Dir]),
+    Target = filename:join([AppDir, Dir]),
     rebar_file_utils:symlink_or_copy(Source, Target).
+
+copy(OldAppDir, AppDir, Dir) ->
+    Source = filename:join([OldAppDir, Dir]),
+    Target = filename:join([AppDir, Dir]),
+    case ec_file:is_dir(Source) of
+        true  -> copy(Source, Target);
+        false -> ok
+    end.
+
+%% TODO: use ec_file:copy/2 to do this, it preserves timestamps and
+%% may prevent recompilation of files in extra dirs
+copy(Source, Target) ->
+    %% important to do this so no files are copied onto themselves
+    %% which truncates them to zero length on some platforms
+    ok = delete_if_symlink(Target),
+    ok = filelib:ensure_dir(filename:join([Target, "dummy.beam"])),
+    {ok, Files} = rebar_utils:list_dir(Source),
+    case [filename:join([Source, F]) || F <- Files] of
+        []    -> ok;
+        Paths -> rebar_file_utils:cp_r(Paths, Target)
+    end.
+
+delete_if_symlink(Path) ->
+    case ec_file:is_symlink(Path) of
+        true  -> file:delete(Path);
+        false -> ok
+    end.
+
+resolve_src_dirs(Opts) ->
+    SrcDirs = rebar_dir:src_dirs(Opts, ["src"]),
+    ExtraDirs = rebar_dir:extra_src_dirs(Opts, []),
+    normalize_src_dirs(SrcDirs, ExtraDirs).
+
+%% remove duplicates and make sure no directories that exist
+%% in src_dirs also exist in extra_src_dirs
+normalize_src_dirs(SrcDirs, ExtraDirs) ->
+    S = lists:usort(SrcDirs),
+    E = lists:usort(ExtraDirs),
+    {S, lists:subtract(E, S)}.
+
diff --git a/src/rebar_prv_cover.erl b/src/rebar_prv_cover.erl
index fc7457e..0b9b9bb 100644
--- a/src/rebar_prv_cover.erl
+++ b/src/rebar_prv_cover.erl
@@ -103,7 +103,7 @@ analyze(State) ->
 
 get_all_coverdata(CoverDir) ->
     ok = filelib:ensure_dir(filename:join([CoverDir, "dummy.log"])),
-    {ok, Files} = file:list_dir(CoverDir),
+    {ok, Files} = rebar_utils:list_dir(CoverDir),
     rebar_utils:filtermap(fun(FileName) ->
         case filename:extension(FileName) == ".coverdata" of
             true  -> {true, filename:join([CoverDir, FileName])};
@@ -277,8 +277,9 @@ strip_coverdir(File) ->
 
 cover_compile(State, apps) ->
     Apps = filter_checkouts(rebar_state:project_apps(State)),
-    AppDirs = app_ebin_dirs(Apps, []),
-    cover_compile(State, AppDirs);
+    AppDirs = app_dirs(Apps),
+    ExtraDirs = extra_src_dirs(State, Apps),
+    cover_compile(State, AppDirs ++ ExtraDirs);
 cover_compile(State, Dirs) ->
     %% start the cover server if necessary
     {ok, CoverPid} = start_cover(),
@@ -290,9 +291,30 @@ cover_compile(State, Dirs) ->
 
 compile([], Acc) -> lists:reverse(Acc);
 compile([Dir|Rest], Acc) ->
+    ?INFO("covering ~p", [Dir]),
     Result = cover:compile_beam_directory(Dir),
     compile(Rest, [Result|Acc]).
 
+app_dirs(Apps) ->
+    lists:foldl(fun app_ebin_dirs/2, [], Apps).
+
+app_ebin_dirs(App, Acc) ->
+    AppDir = rebar_app_info:ebin_dir(App),
+    ExtraDirs = rebar_dir:extra_src_dirs(rebar_app_info:opts(App), []),
+    OutDir = rebar_app_info:out_dir(App),
+    [filename:join([OutDir, D]) || D <- [AppDir|ExtraDirs]] ++ Acc.
+
+extra_src_dirs(State, Apps) ->
+    BaseDir = rebar_state:dir(State),
+    F = fun(App) -> rebar_app_info:dir(App) == BaseDir end,
+    %% check that this app hasn't already been dealt with
+    Extras = case lists:any(F, Apps) of
+        false -> rebar_dir:extra_src_dirs(rebar_state:opts(State), []);
+        true  -> []
+    end,
+    OutDir = rebar_dir:base_dir(State),
+    [filename:join([OutDir, "extras", D]) || D <- Extras].
+
 filter_checkouts(Apps) -> filter_checkouts(Apps, []).
 
 filter_checkouts([], Acc) -> lists:reverse(Acc);
@@ -302,10 +324,6 @@ filter_checkouts([App|Rest], Acc) ->
         false -> filter_checkouts(Rest, [App|Acc])
     end.
 
-app_ebin_dirs([], Acc) -> Acc;
-app_ebin_dirs([App|Rest], Acc) ->
-    app_ebin_dirs(Rest, [rebar_app_info:ebin_dir(App)|Acc]).
-
 start_cover() ->
     case cover:start() of
         {ok, Pid}                       -> {ok, Pid};
diff --git a/src/rebar_prv_eunit.erl b/src/rebar_prv_eunit.erl
index 959be3f..71a1063 100644
--- a/src/rebar_prv_eunit.erl
+++ b/src/rebar_prv_eunit.erl
@@ -9,7 +9,7 @@
          do/1,
          format_error/1]).
 %% exported solely for tests
--export([compile/1, prepare_tests/1, eunit_opts/1]).
+-export([compile/2, prepare_tests/1, eunit_opts/1]).
 
 -include("rebar.hrl").
 -include_lib("providers/include/providers.hrl").
@@ -39,14 +39,15 @@ init(State) ->
 
 -spec do(rebar_state:t()) -> {ok, rebar_state:t()} | {error, string()}.
 do(State) ->
-    case compile(State) of
+    Tests = prepare_tests(State),
+    case compile(State, Tests) of
         %% successfully compiled apps
-        {ok, S} -> do_tests(S);
+        {ok, S} -> do(S, Tests);
         %% this should look like a compiler error, not an eunit error
         Error   -> Error
     end.
 
-do_tests(State) ->
+do(State, Tests) ->
     ?INFO("Performing EUnit tests...", []),
 
     rebar_utils:update_code(rebar_state:code_paths(State, all_deps)),
@@ -56,9 +57,9 @@ do_tests(State) ->
     Cwd = rebar_dir:get_cwd(),
     rebar_hooks:run_all_hooks(Cwd, pre, ?PROVIDER, Providers, State),
 
-    case prepare_tests(State) of
-        {ok, Tests} ->
-            case do_tests(State, Tests) of
+    case Tests of
+        {ok, T} ->
+            case run_tests(State, T) of
                 {ok, State1} ->
                     %% Run eunit provider posthooks
                     rebar_hooks:run_all_hooks(Cwd, post, ?PROVIDER, Providers, State1),
@@ -73,11 +74,12 @@ do_tests(State) ->
             Error
     end.
 
-do_tests(State, Tests) ->
+run_tests(State, Tests) ->
+    T = translate_paths(State, Tests),
     EUnitOpts = resolve_eunit_opts(State),
-    ?DEBUG("eunit_tests ~p", [Tests]),
-    ?DEBUG("eunit_opts  ~p", [EUnitOpts]),
-    Result = eunit:test(Tests, EUnitOpts),
+    ?INFO("eunit_tests ~p", [T]),
+    ?INFO("eunit_opts  ~p", [EUnitOpts]),
+    Result = eunit:test(T, EUnitOpts),
     ok = maybe_write_coverdata(State),
     case handle_results(Result) of
         {error, Reason} ->
@@ -114,38 +116,80 @@ safe_define_test_macro(Opts) ->
        false -> [{d, 'TEST'}] ++ Opts
     end.
 
-compile(State) ->
-    %% inject `eunit_first_files` and `eunit_compile_opts` into the applications to be compiled
-    NewState = inject_eunit_state(State),
+compile(State, {ok, Tests}) ->
+    %% inject `eunit_first_files`, `eunit_compile_opts` and any
+    %% directories required by tests into the applications
+    NewState = inject_eunit_state(State, Tests),
 
     case rebar_prv_compile:do(NewState) of
         %% successfully compiled apps
         {ok, S} ->
             ok = maybe_cover_compile(S),
-            ok = maybe_compile_bare_testdir(S),
             {ok, S};
         %% this should look like a compiler error, not an eunit error
         Error   -> Error
-    end.
+    end;
+%% maybe compile even in the face of errors?
+compile(_State, Error) -> Error.
 
-inject_eunit_state(State) ->
+inject_eunit_state(State, Tests) ->
     Apps = project_apps(State),
-    ModdedApps = lists:map(fun(App) -> inject(State, App) end, Apps),
-    rebar_state:project_apps(State, ModdedApps).
-
-inject(State, App) ->
+    ModdedApps = lists:map(fun(App) ->
+        NewOpts = inject(rebar_app_info:opts(App), State),
+        rebar_app_info:opts(App, NewOpts)
+    end, Apps),
+    NewOpts = inject(rebar_state:opts(State), State),
+    NewState = rebar_state:opts(State, NewOpts),
+    test_dirs(NewState, ModdedApps, Tests).
+
+inject(Opts, State) ->
     %% append `eunit_compile_opts` to app defined `erl_opts`
-    ErlOpts = rebar_app_info:get(App, erl_opts, []),
+    ErlOpts = rebar_opts:get(Opts, erl_opts, []),
     EUnitOpts = rebar_state:get(State, eunit_compile_opts, []),
-    NewOpts = EUnitOpts ++ ErlOpts,
+    NewErlOpts = EUnitOpts ++ ErlOpts,
     %% append `eunit_first_files` to app defined `erl_first_files`
-    FirstFiles = rebar_app_info:get(App, erl_first_files, []),
+    FirstFiles = rebar_opts:get(Opts, erl_first_files, []),
     EUnitFirstFiles = rebar_state:get(State, eunit_first_files, []),
     NewFirstFiles = EUnitFirstFiles ++ FirstFiles,
-    %% insert the new keys into the app
-    lists:foldl(fun({K, V}, NewApp) -> rebar_app_info:set(NewApp, K, V) end,
-                App,
-                [{erl_opts, NewOpts}, {erl_first_files, NewFirstFiles}]).
+    %% insert the new keys into the opts
+    lists:foldl(fun({K, V}, NewOpts) -> rebar_opts:set(NewOpts, K, V) end,
+                Opts,
+                [{erl_opts, NewErlOpts}, {erl_first_files, NewFirstFiles}]).
+
+test_dirs(State, Apps, []) -> rebar_state:project_apps(State, Apps);
+test_dirs(State, Apps, [{dir, Dir}|Rest]) ->
+    %% insert `Dir` into an app if relative, or the base state if not
+    %% app relative but relative to the root or not at all if outside
+    %% project scope
+    {NewState, NewApps} = maybe_inject_test_dir(State, [], Apps, Dir),
+    test_dirs(NewState, NewApps, Rest);
+test_dirs(State, Apps, [{file, File}|Rest]) ->
+    Dir = filename:dirname(File),
+    {NewState, NewApps} = maybe_inject_test_dir(State, [], Apps, Dir),
+    test_dirs(NewState, NewApps, Rest);
+test_dirs(State, Apps, [_|Rest]) -> test_dirs(State, Apps, Rest).
+
+maybe_inject_test_dir(State, AppAcc, [App|Rest], Dir) ->
+    case rebar_file_utils:path_from_ancestor(Dir, rebar_app_info:dir(App)) of
+        {ok, Path} ->
+            Opts = inject_test_dir(rebar_app_info:opts(App), Path),
+            {State, AppAcc ++ [rebar_app_info:opts(App, Opts)] ++ Rest};
+        {error, badparent} ->
+            maybe_inject_test_dir(State, AppAcc ++ [App], Rest, Dir)
+    end;
+maybe_inject_test_dir(State, AppAcc, [], Dir) ->
+    case rebar_file_utils:path_from_ancestor(Dir, rebar_state:dir(State)) of
+        {ok, Path} ->
+            Opts = inject_test_dir(rebar_state:opts(State), Path),
+            {rebar_state:opts(State, Opts), AppAcc};
+        {error, badparent} ->
+            {State, AppAcc}
+    end.
+
+inject_test_dir(Opts, Dir) ->
+    %% append specified test targets to app defined `extra_src_dirs`
+    ExtraSrcDirs = rebar_opts:get(Opts, extra_src_dirs, []),
+    rebar_opts:set(Opts, extra_src_dirs, ExtraSrcDirs ++ [Dir]).
 
 test_defined([{d, 'TEST'}|_]) -> true;
 test_defined([{d, 'TEST', true}|_]) -> true;
@@ -212,7 +256,7 @@ default_tests(State, Apps) ->
         %%  included or `test` does not exist
         false -> lists:reverse(Tests);
         %% need to add `test` dir at root to dirs to be included
-        true  -> lists:reverse([{dir, filename:join([rebar_dir:base_dir(State), "test"])}|Tests])
+        true  -> lists:reverse([{dir, BareTest}|Tests])
     end.
 
 set_apps([], Acc) -> Acc;
@@ -268,14 +312,14 @@ validate_app(State, [App|Rest], AppName) ->
         false -> validate_app(State, Rest, AppName)
     end.
 
-validate_dir(_State, Dir) ->
-    case ec_file:is_dir(Dir) of
+validate_dir(State, Dir) ->
+    case ec_file:is_dir(filename:join([rebar_state:dir(State), Dir])) of
         true  -> ok;
         false -> {error, lists:concat(["Directory `", Dir, "' not found."])}
     end.
 
-validate_file(_State, File) ->
-    case ec_file:exists(File) of
+validate_file(State, File) ->
+    case ec_file:exists(filename:join([rebar_state:dir(State), File])) of
         true  -> ok;
         false -> {error, lists:concat(["File `", File, "' not found."])}
     end.
@@ -302,6 +346,31 @@ set_verbose(Opts) ->
         false -> [verbose] ++ Opts
     end.
 
+translate_paths(State, Tests) -> translate_paths(State, Tests, []).
+
+translate_paths(_State, [], Acc) -> lists:reverse(Acc);
+translate_paths(State, [{dir, Dir}|Rest], Acc) ->
+    Apps = project_apps(State),
+    translate_paths(State, Rest, [translate(State, Apps, Dir)|Acc]);
+translate_paths(State, [{file, File}|Rest], Acc) ->
+    Dir = filename:dirname(File),
+    Apps = project_apps(State),
+    translate_paths(State, Rest, [translate(State, Apps, Dir)|Acc]);
+translate_paths(State, [Test|Rest], Acc) ->
+    translate_paths(State, Rest, [Test|Acc]).
+
+translate(State, [App|Rest], Dir) ->
+    case rebar_file_utils:path_from_ancestor(Dir, rebar_app_info:dir(App)) of
+        {ok, Path}         -> {dir, filename:join([rebar_app_info:out_dir(App), Path])};
+        {error, badparent} -> translate(State, Rest, Dir)
+    end;
+translate(State, [], Dir) ->
+    case rebar_file_utils:path_from_ancestor(Dir, rebar_state:dir(State)) of
+        {ok, Path}         -> {dir, filename:join([rebar_dir:base_dir(State), "extras", Path])};
+        %% not relative, leave as is
+        {error, badparent} -> {dir, Dir}
+    end.
+
 maybe_cover_compile(State) ->
     {RawOpts, _} = rebar_state:command_parsed_args(State),
     State1 = case proplists:get_value(cover, RawOpts, false) of
@@ -310,14 +379,6 @@ maybe_cover_compile(State) ->
     end,
     rebar_prv_cover:maybe_cover_compile(State1).
 
-maybe_cover_compile(State, Dir) ->
-    {RawOpts, _} = rebar_state:command_parsed_args(State),
-    State1 = case proplists:get_value(cover, RawOpts, false) of
-        true  -> rebar_state:set(State, cover_enabled, true);
-        false -> State
-    end,
-    rebar_prv_cover:maybe_cover_compile(State1, [Dir]).
-
 maybe_write_coverdata(State) ->
     {RawOpts, _} = rebar_state:command_parsed_args(State),
     State1 = case proplists:get_value(cover, RawOpts, false) of
@@ -326,30 +387,6 @@ maybe_write_coverdata(State) ->
     end,
     rebar_prv_cover:maybe_write_coverdata(State1, ?PROVIDER).
 
-maybe_compile_bare_testdir(State) ->
-    Apps = project_apps(State),
-    BareTest = filename:join([rebar_state:dir(State), "test"]),
-    F = fun(App) -> rebar_app_info:dir(App) == rebar_state:dir(State) end,
-    case ec_file:is_dir(BareTest) andalso not lists:any(F, Apps) of
-        true ->
-            ErlOpts = rebar_state:get(State, erl_opts, []),
-            EUnitOpts = rebar_state:get(State, eunit_compile_opts, []),
-            NewErlOpts = safe_define_test_macro(EUnitOpts ++ ErlOpts),
-            %% append `eunit_first_files` to app defined `erl_first_files`
-            FirstFiles = rebar_state:get(State, erl_first_files, []),
-            EUnitFirstFiles = rebar_state:get(State, eunit_first_files, []),
-            NewFirstFiles = EUnitFirstFiles ++ FirstFiles,
-            Opts = rebar_state:opts(State),
-            NewOpts = lists:foldl(fun({K, V}, Dict) -> rebar_opts:set(Dict, K, V) end,
-                                  Opts,
-                                  [{erl_opts, NewErlOpts}, {erl_first_files, NewFirstFiles}, {src_dirs, ["test"]}]),
-            OutDir = filename:join([rebar_dir:base_dir(State), "test"]),
-            filelib:ensure_dir(filename:join([OutDir, "dummy.beam"])),
-            rebar_erlc_compiler:compile(NewOpts, rebar_state:dir(State), OutDir),
-            maybe_cover_compile(State, [OutDir]);
-        false -> ok
-    end.
-
 handle_results(ok) -> ok;
 handle_results(error) ->
     {error, unknown_error};
diff --git a/src/rebar_utils.erl b/src/rebar_utils.erl
index ccdf960..4fd4bd1 100644
--- a/src/rebar_utils.erl
+++ b/src/rebar_utils.erl
@@ -65,7 +65,8 @@
          escape_double_quotes_weak/1,
          check_min_otp_version/1,
          check_blacklisted_otp_versions/1,
-         info_useless/2]).
+         info_useless/2,
+         list_dir/1]).
 
 %% for internal use only
 -export([otp_release/0]).
@@ -774,3 +775,9 @@ info_useless(Old, New) ->
      || Name <- Old,
         not lists:member(Name, New)],
     ok.
+
+-ifdef(no_list_dir_all).
+list_dir(Dir) -> file:list_dir(Dir).
+-else.
+list_dir(Dir) -> file:list_dir_all(Dir).
+-endif.
diff --git a/test/rebar_compile_SUITE.erl b/test/rebar_compile_SUITE.erl
index cc37441..1c2c527 100644
--- a/test/rebar_compile_SUITE.erl
+++ b/test/rebar_compile_SUITE.erl
@@ -5,12 +5,23 @@
          end_per_suite/1,
          init_per_testcase/2,
          end_per_testcase/2,
+         init_per_group/2,
+         end_per_group/2,
          all/0,
-         build_basic_app/1,
-         build_release_apps/1,
-         build_checkout_apps/1,
-         build_checkout_deps/1,
-         build_all_srcdirs/1,
+         groups/0,
+         build_basic_app/1, paths_basic_app/1, clean_basic_app/1,
+         build_release_apps/1, paths_release_apps/1, clean_release_apps/1,
+         build_checkout_apps/1, paths_checkout_apps/1,
+         build_checkout_deps/1, paths_checkout_deps/1,
+         build_basic_srcdirs/1, paths_basic_srcdirs/1,
+         build_release_srcdirs/1, paths_release_srcdirs/1,
+         build_unbalanced_srcdirs/1, paths_unbalanced_srcdirs/1,
+         build_basic_extra_dirs/1, paths_basic_extra_dirs/1, clean_basic_extra_dirs/1,
+         build_release_extra_dirs/1, paths_release_extra_dirs/1, clean_release_extra_dirs/1,
+         build_unbalanced_extra_dirs/1, paths_unbalanced_extra_dirs/1,
+         build_extra_dirs_in_project_root/1,
+         paths_extra_dirs_in_project_root/1,
+         clean_extra_dirs_in_project_root/1,
          recompile_when_hrl_changes/1,
          recompile_when_opts_change/1,
          dont_recompile_when_opts_dont_change/1,
@@ -35,116 +46,590 @@
 suite() ->
     [].
 
-init_per_suite(Config) ->
-    Config.
-
-end_per_suite(_Config) ->
-    ok.
-
-init_per_testcase(_, Config) ->
-    rebar_test_utils:init_rebar_state(Config).
-
-end_per_testcase(_, _Config) ->
-    catch meck:unload().
-
 all() ->
-    [build_basic_app, build_release_apps,
-     build_checkout_apps, build_checkout_deps,
-     build_all_srcdirs, recompile_when_hrl_changes,
-     recompile_when_opts_change, dont_recompile_when_opts_dont_change,
-     dont_recompile_yrl_or_xrl, delete_beam_if_source_deleted,
+    [{group, basic_app}, {group, release_apps},
+     {group, checkout_apps}, {group, checkout_deps},
+     {group, basic_srcdirs}, {group, release_srcdirs}, {group, unbalanced_srcdirs},
+     {group, basic_extras}, {group, release_extras}, {group, unbalanced_extras},
+     {group, root_extras},
+     recompile_when_hrl_changes, recompile_when_opts_change,
+     dont_recompile_when_opts_dont_change, dont_recompile_yrl_or_xrl,
+     delete_beam_if_source_deleted,
      deps_in_path, checkout_priority, highest_version_of_pkg_dep,
      parse_transform_test, erl_first_files_test, mib_test,
      umbrella_mib_first_test, only_default_transitive_deps,
-     clean_all, override_deps, profile_override_deps, build_more_sources].
-
-build_basic_app(Config) ->
-    AppDir = ?config(apps, Config),
-
-    Name = rebar_test_utils:create_random_name("app1_"),
+     clean_all, override_deps, profile_override_deps].
+
+groups() ->
+    [{basic_app, [], [build_basic_app, paths_basic_app, clean_basic_app]},
+     {release_apps, [], [build_release_apps, paths_release_apps, clean_release_apps]},
+     {checkout_apps, [], [build_checkout_apps, paths_checkout_apps]},
+     {checkout_deps, [], [build_checkout_deps, paths_checkout_deps]},
+     {basic_srcdirs, [], [build_basic_srcdirs, paths_basic_srcdirs]},
+     {release_srcdirs, [], [build_release_srcdirs,
+                            paths_release_srcdirs]},
+     {unbalanced_srcdirs, [], [build_unbalanced_srcdirs,
+                               paths_unbalanced_srcdirs]},
+     {basic_extras, [], [build_basic_extra_dirs,
+                         paths_basic_extra_dirs,
+                         clean_basic_extra_dirs]},
+     {release_extras, [], [build_release_extra_dirs,
+                           paths_release_extra_dirs,
+                           clean_release_extra_dirs]},
+     {unbalanced_extras, [], [build_unbalanced_extra_dirs,
+                              paths_unbalanced_extra_dirs]},
+     {root_extras, [], [build_extra_dirs_in_project_root,
+                        paths_extra_dirs_in_project_root,
+                        clean_extra_dirs_in_project_root]}].
+
+init_per_group(basic_app, Config) ->
+    NewConfig = rebar_test_utils:init_rebar_state(Config, "basic_app_"),
+    AppDir = ?config(apps, NewConfig),
+
+    Name = rebar_test_utils:create_random_name("app1"),
     Vsn = rebar_test_utils:create_random_vsn(),
     rebar_test_utils:create_app(AppDir, Name, Vsn, [kernel, stdlib]),
+    
+    [{app_names, [Name]}, {vsns, [Vsn]}|NewConfig];
 
-    rebar_test_utils:run_and_check(Config, [], ["compile"], {ok, [{app, Name}]}).
-
-build_release_apps(Config) ->
-    AppDir = ?config(apps, Config),
+init_per_group(release_apps, Config) ->
+    NewConfig = rebar_test_utils:init_rebar_state(Config, "release_apps_"),
+    AppDir = ?config(apps, NewConfig),
 
     Name1 = rebar_test_utils:create_random_name("relapp1_"),
     Vsn1 = rebar_test_utils:create_random_vsn(),
     rebar_test_utils:create_app(filename:join([AppDir,"apps",Name1]), Name1, Vsn1, [kernel, stdlib]),
+
     Name2 = rebar_test_utils:create_random_name("relapp2_"),
     Vsn2 = rebar_test_utils:create_random_vsn(),
     rebar_test_utils:create_app(filename:join([AppDir,"apps",Name2]), Name2, Vsn2, [kernel, stdlib]),
+    
+    [{app_names, [Name1, Name2]}, {vsns, [Vsn1, Vsn2]}|NewConfig];
 
-    rebar_test_utils:run_and_check(
-        Config, [], ["compile"],
-        {ok, [{app, Name1}, {app, Name2}]}
-    ).
+init_per_group(checkout_apps, Config) ->
+    NewConfig = rebar_test_utils:init_rebar_state(Config, "checkout_apps_"),
+    AppDir = ?config(apps, NewConfig),
+    CheckoutsDir = ?config(checkouts, NewConfig),
 
-build_checkout_apps(Config) ->
-    AppDir = ?config(apps, Config),
-    CheckoutsDir = ?config(checkouts, Config),
     Name1 = rebar_test_utils:create_random_name("checkapp1_"),
     Vsn1 = rebar_test_utils:create_random_vsn(),
     rebar_test_utils:create_app(AppDir, Name1, Vsn1, [kernel, stdlib]),
+
     Name2 = rebar_test_utils:create_random_name("checkapp2_"),
     Vsn2 = rebar_test_utils:create_random_vsn(),
     rebar_test_utils:create_app(filename:join([CheckoutsDir,Name2]), Name2, Vsn2, [kernel, stdlib]),
 
-    rebar_test_utils:run_and_check(
-        Config, [], ["compile"],
-        {ok, [{app, Name1}, {checkout, Name2}]}
-    ).
+    [{app_names, [Name1, Name2]}, {vsns, [Vsn1, Vsn2]}|NewConfig];
 
-build_checkout_deps(Config) ->
-    AppDir = ?config(apps, Config),
-    CheckoutsDir = ?config(checkouts, Config),
+init_per_group(checkout_deps, Config) ->
+    NewConfig = rebar_test_utils:init_rebar_state(Config, "checkout_deps_"),
+    AppDir = ?config(apps, NewConfig),
+    CheckoutsDir = ?config(checkouts, NewConfig),
     DepsDir = filename:join([AppDir, "_build", "default", "lib"]),
+
     Name1 = rebar_test_utils:create_random_name("checkapp1_"),
     Vsn1 = rebar_test_utils:create_random_vsn(),
     rebar_test_utils:create_app(AppDir, Name1, Vsn1, [kernel, stdlib]),
+
     Name2 = rebar_test_utils:create_random_name("checkapp2_"),
     Vsn2 = rebar_test_utils:create_random_vsn(),
     rebar_test_utils:create_app(filename:join([CheckoutsDir,Name2]), Name2, Vsn2, [kernel, stdlib]),
+
     rebar_test_utils:create_app(filename:join([DepsDir,Name2]), Name2, Vsn1, [kernel, stdlib]),
 
+    [{app_names, [Name1, Name2]}, {vsns, [Vsn1, Vsn2]}|NewConfig];
+
+init_per_group(Group, Config) when Group == basic_srcdirs; Group == basic_extras ->
+    NewConfig = rebar_test_utils:init_rebar_state(Config, "basic_srcdirs_"),
+    AppDir = ?config(apps, NewConfig),
+
+    Name = rebar_test_utils:create_random_name("app1_"),
+    Vsn = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_app(AppDir, Name, Vsn, [kernel, stdlib]),
+
+    ExtraSrc = io_lib:format("-module(~ts_extra).\n-export([ok/0]).\nok() -> ok.\n", [Name]),
+
+    ok = filelib:ensure_dir(filename:join([AppDir, "extra", "dummy"])),
+    ok = file:write_file(filename:join([AppDir, "extra", io_lib:format("~ts_extra.erl", [Name])]),
+                         ExtraSrc),
+
+    [{app_names, [Name]}, {vsns, [Vsn]}|NewConfig];
+
+init_per_group(Group, Config) when Group == release_srcdirs; Group == release_extras ->
+    NewConfig = rebar_test_utils:init_rebar_state(Config, "release_srcdirs_"),
+    AppDir = ?config(apps, NewConfig),
+
+    Name1 = rebar_test_utils:create_random_name("relapp1_"),
+    Vsn1 = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_app(filename:join([AppDir, "apps", Name1]), Name1, Vsn1, [kernel, stdlib]),
+
+    Name2 = rebar_test_utils:create_random_name("relapp2_"),
+    Vsn2 = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_app(filename:join([AppDir, "apps", Name2]), Name2, Vsn2, [kernel, stdlib]),
+
+    ExtraOne = io_lib:format("-module(~ts_extra).\n-export([ok/0]).\nok() -> ok.\n", [Name1]),
+
+    ok = filelib:ensure_dir(filename:join([AppDir, "apps", Name1, "extra", "dummy"])),
+    ok = file:write_file(filename:join([AppDir, "apps", Name1, "extra",
+                                        io_lib:format("~ts_extra.erl", [Name1])]),
+                         ExtraOne),
+
+    ExtraTwo = io_lib:format("-module(~ts_extra).\n-export([ok/0]).\nok() -> ok.\n", [Name2]),
+
+    ok = filelib:ensure_dir(filename:join([AppDir, "apps", Name2, "extra", "dummy"])),
+    ok = file:write_file(filename:join([AppDir, "apps", Name2, "extra",
+                                        io_lib:format("~ts_extra.erl", [Name2])]),
+                         ExtraTwo),
+
+    [{app_names, [Name1, Name2]}, {vsns, [Vsn1, Vsn2]}|NewConfig];
+
+init_per_group(Group, Config) when Group == unbalanced_srcdirs; Group == unbalanced_extras ->
+    NewConfig = rebar_test_utils:init_rebar_state(Config, "unbalanced_srcdirs_"),
+    AppDir = ?config(apps, NewConfig),
+
+    Name1 = rebar_test_utils:create_random_name("relapp1_"),
+    Vsn1 = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_app(filename:join([AppDir, "apps", Name1]), Name1, Vsn1, [kernel, stdlib]),
+
+    Name2 = rebar_test_utils:create_random_name("relapp2_"),
+    Vsn2 = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_app(filename:join([AppDir, "apps", Name2]), Name2, Vsn2, [kernel, stdlib]),
+
+    ExtraOne = io_lib:format("-module(~ts_extra).\n-export([ok/0]).\nok() -> ok.\n", [Name1]),
+
+    ok = filelib:ensure_dir(filename:join([AppDir, "apps", Name1, "extra", "dummy"])),
+    ok = file:write_file(filename:join([AppDir, "apps", Name1, "extra",
+                                        io_lib:format("~ts_extra.erl", [Name1])]),
+                         ExtraOne),
+
+    [{app_names, [Name1, Name2]}, {vsns, [Vsn1, Vsn2]}|NewConfig];
+
+init_per_group(root_extras, Config) ->
+    NewConfig = rebar_test_utils:init_rebar_state(Config, "root_extras_"),
+    AppDir = ?config(apps, NewConfig),
+
+    Name1 = rebar_test_utils:create_random_name("relapp1_"),
+    Vsn1 = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_app(filename:join([AppDir, "apps", Name1]), Name1, Vsn1, [kernel, stdlib]),
+
+    Name2 = rebar_test_utils:create_random_name("relapp2_"),
+    Vsn2 = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_app(filename:join([AppDir, "apps", Name2]), Name2, Vsn2, [kernel, stdlib]),
+
+    Extra = <<"-module(extra).\n-export([ok/0]).\nok() -> ok.\n">>,
+
+    ok = filelib:ensure_dir(filename:join([AppDir, "extra", "dummy"])),
+    ok = file:write_file(filename:join([AppDir, "extra", "extra.erl"]), Extra),
+
+    [{app_names, [Name1, Name2]}, {vsns, [Vsn1, Vsn2]}|NewConfig].
+
+end_per_group(_Group, _Config) ->
+    ok.
+
+init_per_suite(Config) ->
+    Config.
+
+end_per_suite(_Config) ->
+    ok.
+
+init_per_testcase(_, Config) ->
+    case ?config(apps, Config) of
+        undefined -> rebar_test_utils:init_rebar_state(Config);
+        _         -> Config
+    end.
+
+end_per_testcase(_, _Config) ->
+    catch meck:unload().
+
+
+
+%% test cases
+
+build_basic_app(Config) ->
+    [Name] = ?config(app_names, Config),
+    rebar_test_utils:run_and_check(Config, [], ["compile"], {ok, [{app, Name}]}).
+
+build_release_apps(Config) ->
+    [Name1, Name2] = ?config(app_names, Config),
+    rebar_test_utils:run_and_check(
+        Config, [], ["compile"],
+        {ok, [{app, Name1}, {app, Name2}]}
+    ).
+
+build_checkout_apps(Config) ->
+    [Name1, Name2] = ?config(app_names, Config),
+    rebar_test_utils:run_and_check(
+        Config, [], ["compile"],
+        {ok, [{app, Name1}, {checkout, Name2}]}
+    ).
+
+build_checkout_deps(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
+    [_, Vsn2] = ?config(vsns, Config),
+
     Deps = [{list_to_atom(Name2), Vsn2, {git, "", ""}}],
     {ok, RebarConfig} = file:consult(rebar_test_utils:create_config(AppDir, [{deps, Deps}])),
 
-    {ok, State} = rebar_test_utils:run_and_check(
+    rebar_test_utils:run_and_check(
         Config, RebarConfig, ["compile"],
         {ok, [{app, Name1}, {checkout, Name2}]}
+    ).
+
+build_basic_srcdirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name] = ?config(app_names, Config),
+
+    RebarConfig = [{erl_opts, [{src_dirs, ["src", "extra"]}]}],
+
+    %% check a beam corresponding to the src in the extra src_dir exists
+    ExtraBeam = filename:join([AppDir, "_build", "default", "lib", Name, "ebin",
+                               io_lib:format("~ts_extra.beam", [Name])]),
+    %% check the extra src_dir was copied/linked into the _build dir
+    ExtraDir = filename:join([AppDir, "_build", "default", "lib", Name, "extra"]),
+
+    rebar_test_utils:run_and_check(
+        Config, RebarConfig, ["compile"],
+        {ok, [{app, Name}, {file, ExtraBeam}, {dir, ExtraDir}]}
+    ).
+
+build_release_srcdirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
+
+    RebarConfig = [{erl_opts, [{src_dirs, ["src", "extra"]}]}],
+
+    %% check a beam corresponding to the src in the extra src_dir exists
+    Extra1Beam = filename:join([AppDir, "_build", "default", "lib", Name1, "ebin",
+                                io_lib:format("~ts_extra.beam", [Name1])]),
+    Extra2Beam = filename:join([AppDir, "_build", "default", "lib", Name2, "ebin",
+                                io_lib:format("~ts_extra.beam", [Name2])]),
+
+    %% check the extra src_dir was copied/linked into the _build dir
+    Extra1Dir = filename:join([AppDir, "_build", "default", "lib", Name1, "extra"]),
+    Extra2Dir = filename:join([AppDir, "_build", "default", "lib", Name2, "extra"]),
+
+    rebar_test_utils:run_and_check(
+        Config, RebarConfig, ["compile"],
+        {ok, [{app, Name1}, {app, Name2},
+              {file, Extra1Beam}, {file, Extra2Beam},
+              {dir, Extra1Dir}, {dir, Extra2Dir}]}
+    ).
+
+build_unbalanced_srcdirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
+
+    RebarConfig = [{erl_opts, [{src_dirs, ["src", "extra"]}]}],
+
+    %% check a beam corresponding to the src in the extra src_dir exists
+    Extra1Beam = filename:join([AppDir, "_build", "default", "lib", Name1, "ebin",
+                                io_lib:format("~ts_extra.beam", [Name1])]),
+
+    %% check the extra src_dir was copied/linked into the _build dir
+    Extra1Dir = filename:join([AppDir, "_build", "default", "lib", Name1, "extra"]),
+
+    rebar_test_utils:run_and_check(
+        Config, RebarConfig, ["compile"],
+        {ok, [{app, Name1}, {app, Name2}, {file, Extra1Beam}, {dir, Extra1Dir}]}
+    ),
+
+    %% check no extra src_dir were copied/linked into the _build dir
+    Extra2Dir = filename:join([AppDir, "_build", "default", "lib", Name2, "extra"]),
+    false = filelib:is_dir(Extra2Dir),
+    %% check only expected beams are in the ebin dir
+    {ok, Files} = rebar_utils:list_dir(filename:join([AppDir, "_build", "default", "lib", Name2, "ebin"])),
+    lists:all(fun(Beam) -> lists:member(Beam, [Name2 ++ ".app", "not_a_real_src_" ++ Name2 ++ ".beam"]) end,
+              Files).
+
+build_basic_extra_dirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name] = ?config(app_names, Config),
+
+    RebarConfig = [{erl_opts, [{extra_src_dirs, ["extra"]}]}],
+
+    %% check a beam corresponding to the src in the extra src_dir exists
+    ExtraBeam = filename:join([AppDir, "_build", "default", "lib", Name, "extra",
+                               io_lib:format("~ts_extra.beam", [Name])]),
+
+    rebar_test_utils:run_and_check(
+        Config, RebarConfig, ["compile"],
+        {ok, [{app, Name}, {file, ExtraBeam}]}
+    ).
+
+build_release_extra_dirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
+
+    RebarConfig = [{erl_opts, [{extra_src_dirs, ["extra"]}]}],
+
+    %% check a beam corresponding to the src in the extra src_dir exists
+    Extra1Beam = filename:join([AppDir, "_build", "default", "lib", Name1, "extra",
+                                io_lib:format("~ts_extra.beam", [Name1])]),
+    Extra2Beam = filename:join([AppDir, "_build", "default", "lib", Name2, "extra",
+                                io_lib:format("~ts_extra.beam", [Name2])]),
+
+    rebar_test_utils:run_and_check(
+        Config, RebarConfig, ["compile"],
+        {ok, [{app, Name1}, {app, Name2}, {file, Extra1Beam}, {file, Extra2Beam}]}
+    ).
+
+build_unbalanced_extra_dirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
+
+    RebarConfig = [{erl_opts, [{extra_src_dirs, ["extra"]}]}],
+
+    %% check a beam corresponding to the src in the extra src_dir exists
+    Extra1Beam = filename:join([AppDir, "_build", "default", "lib", Name1, "extra",
+                                io_lib:format("~ts_extra.beam", [Name1])]),
+
+    rebar_test_utils:run_and_check(
+        Config, RebarConfig, ["compile"],
+        {ok, [{app, Name1}, {app, Name2}, {file, Extra1Beam}]}
     ),
+
+    %% check no extra src_dir were copied/linked into the _build dir
+    false = filelib:is_dir(filename:join([AppDir, "_build", "default", "lib", Name2, "extra"])),
+    %% check only expected beams are in the ebin dir
+    {ok, Files} = rebar_utils:list_dir(filename:join([AppDir, "_build", "default", "lib", Name2, "ebin"])),
+    lists:all(fun(Beam) -> lists:member(Beam, [Name2 ++ ".app", "not_a_real_src_" ++ Name2 ++ ".beam"]) end,
+              Files).
+
+build_extra_dirs_in_project_root(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
+
+    RebarConfig = [{erl_opts, [{extra_src_dirs, ["extra"]}]}],
+
+    %% check a beam corresponding to the src in the extra src_dir exists
+    ExtraBeam = filename:join([AppDir, "_build", "default", "extras", "extra", "extra.beam"]),
+
+    rebar_test_utils:run_and_check(
+        Config, RebarConfig, ["compile"],
+        {ok, [{app, Name1}, {app, Name2}, {file, ExtraBeam}]}
+    ).
+
+paths_basic_app(Config) ->
+    [Name] = ?config(app_names, Config),
+    [Vsn] = ?config(vsns, Config),
+
+    {ok, State} = rebar_test_utils:run_and_check(Config, [], ["compile"], return),
+    
+    code:add_paths(rebar_state:code_paths(State, all_deps)),
+    ok = application:load(list_to_atom(Name)),
+    Loaded = application:loaded_applications(),
+    {_, _, Vsn} = lists:keyfind(list_to_atom(Name), 1, Loaded).
+
+paths_release_apps(Config) ->
+    [Name1, Name2] = ?config(app_names, Config),
+    [Vsn1, Vsn2] = ?config(vsns, Config),
+
+    {ok, State} = rebar_test_utils:run_and_check(Config, [], ["compile"], return),
+
     code:add_paths(rebar_state:code_paths(State, all_deps)),
+    ok = application:load(list_to_atom(Name1)),
     ok = application:load(list_to_atom(Name2)),
     Loaded = application:loaded_applications(),
+    {_, _, Vsn1} = lists:keyfind(list_to_atom(Name1), 1, Loaded),
     {_, _, Vsn2} = lists:keyfind(list_to_atom(Name2), 1, Loaded).
 
-build_all_srcdirs(Config) ->
+paths_checkout_apps(Config) ->
+    [Name1, _Name2] = ?config(app_names, Config),
+    [Vsn1, _Vsn2] = ?config(vsns, Config),
+
+    {ok, State} = rebar_test_utils:run_and_check(Config, [], ["compile"], return),
+
+    code:add_paths(rebar_state:code_paths(State, all_deps)),
+    ok = application:load(list_to_atom(Name1)),
+    Loaded = application:loaded_applications(),
+    {_, _, Vsn1} = lists:keyfind(list_to_atom(Name1), 1, Loaded).
+
+paths_checkout_deps(Config) ->
     AppDir = ?config(apps, Config),
+    [_Name1, Name2] = ?config(app_names, Config),
+    [_Vsn1, Vsn2] = ?config(vsns, Config),
+
+    %% rebar_test_utils:init_rebar_state/1,2 uses rebar_state:new/3 which
+    %% maybe incorrectly sets deps to [] (based on `rebar.lock`) instead of
+    %% to the checkapps
+    %% until that is sorted out the lock file has to be removed before
+    %% this test will pass
+    file:delete(filename:join([AppDir, "rebar.lock"])),
+
+    {ok, RebarConfig} = file:consult(filename:join([AppDir, "rebar.config"])),
+
+    {ok, State} = rebar_test_utils:run_and_check(Config, RebarConfig, ["compile"], return),
+
+    code:add_paths(rebar_state:code_paths(State, all_deps)),
+    ok = application:load(list_to_atom(Name2)),
+    Loaded = application:loaded_applications(),
+    {_, _, Vsn2} = lists:keyfind(list_to_atom(Name2), 1, Loaded).
+
+paths_basic_srcdirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name] = ?config(app_names, Config),
 
     RebarConfig = [{erl_opts, [{src_dirs, ["src", "extra"]}]}],
 
-    Name = rebar_test_utils:create_random_name("app1_"),
-    Vsn = rebar_test_utils:create_random_vsn(),
-    rebar_test_utils:create_app(AppDir, Name, Vsn, [kernel, stdlib]),
+    {ok, State} = rebar_test_utils:run_and_check(Config, RebarConfig, ["compile"], return),
 
-    ExtraSrc = <<"-module(extra_src).\n"
-        "-export([ok/0]).\n"
-        "ok() -> ok.\n">>,
+    code:add_paths(rebar_state:code_paths(State, all_deps)),
+    Mod = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name]))),
+    {module, Mod} = code:ensure_loaded(Mod),
 
-    ok = filelib:ensure_dir(filename:join([AppDir, "extra", "dummy"])),
-    ok = file:write_file(filename:join([AppDir, "extra", "extra_src.erl"]), ExtraSrc),
+    Expect = filename:join([AppDir, "_build", "default", "lib", Name, "ebin",
+                            io_lib:format("~ts_extra.beam", [Name])]),
+    Expect = code:which(Mod).
 
-    rebar_test_utils:run_and_check(Config, RebarConfig, ["compile"], {ok, [{app, Name}]}),
+paths_release_srcdirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
 
-    %% check a beam corresponding to the src in the extra src_dir exists in ebin
-    EbinDir = filename:join([AppDir, "_build", "default", "lib", Name, "ebin"]),
-    true = filelib:is_file(filename:join([EbinDir, "extra_src.beam"])),
+    RebarConfig = [{erl_opts, [{src_dirs, ["src", "extra"]}]}],
 
-    %% check the extra src_dir was linked into the _build dir
-    true = filelib:is_dir(filename:join([AppDir, "_build", "default", "lib", Name, "extra"])).
+    {ok, State} = rebar_test_utils:run_and_check(Config, RebarConfig, ["compile"], return),
+
+    code:add_paths(rebar_state:code_paths(State, all_deps)),
+    Mod1 = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name1]))),
+    {module, Mod1} = code:ensure_loaded(Mod1),
+    Mod2 = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name2]))),
+    {module, Mod2} = code:ensure_loaded(Mod2),
+
+    ExpectOne = filename:join([AppDir, "_build", "default", "lib", Name1, "ebin",
+                               io_lib:format("~ts_extra.beam", [Name1])]),
+    ExpectOne = code:which(Mod1),
+    ExpectTwo = filename:join([AppDir, "_build", "default", "lib", Name2, "ebin",
+                               io_lib:format("~ts_extra.beam", [Name2])]),
+    ExpectTwo = code:which(Mod2).
+
+paths_unbalanced_srcdirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
+
+    RebarConfig = [{erl_opts, [{src_dirs, ["src", "extra"]}]}],
+
+    {ok, State} = rebar_test_utils:run_and_check(Config, RebarConfig, ["compile"], return),
+
+    code:add_paths(rebar_state:code_paths(State, all_deps)),
+    Mod1 = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name1]))),
+    {module, Mod1} = code:ensure_loaded(Mod1),
+    Mod2 = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name2]))),
+    {error, nofile} = code:ensure_loaded(Mod2),
+
+    ExpectOne = filename:join([AppDir, "_build", "default", "lib", Name1, "ebin",
+                               io_lib:format("~ts_extra.beam", [Name1])]),
+    ExpectOne = code:which(Mod1).
+
+paths_basic_extra_dirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name] = ?config(app_names, Config),
+
+    RebarConfig = [{erl_opts, [{extra_src_dirs, ["extra"]}]}],
+
+    {ok, State} = rebar_test_utils:run_and_check(Config, RebarConfig, ["compile"], return),
+
+    code:add_paths(rebar_state:code_paths(State, all_deps)),
+    Mod = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name]))),
+    {module, Mod} = code:ensure_loaded(Mod),
+
+    Expect = filename:join([AppDir, "_build", "default", "lib", Name, "extra",
+                            io_lib:format("~ts_extra.beam", [Name])]),
+    Expect = code:which(Mod).
+
+paths_release_extra_dirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
+
+    RebarConfig = [{erl_opts, [{extra_src_dirs, ["extra"]}]}],
+
+    {ok, State} = rebar_test_utils:run_and_check(Config, RebarConfig, ["compile"], return),
+
+    code:add_paths(rebar_state:code_paths(State, all_deps)),
+    Mod1 = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name1]))),
+    {module, Mod1} = code:ensure_loaded(Mod1),
+    Mod2 = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name2]))),
+    {module, Mod2} = code:ensure_loaded(Mod2),
+
+    ExpectOne = filename:join([AppDir, "_build", "default", "lib", Name1, "extra",
+                               io_lib:format("~ts_extra.beam", [Name1])]),
+    ExpectOne = code:which(Mod1),
+    ExpectTwo = filename:join([AppDir, "_build", "default", "lib", Name2, "extra",
+                               io_lib:format("~ts_extra.beam", [Name2])]),
+    ExpectTwo = code:which(Mod2).
+
+
+paths_unbalanced_extra_dirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
+
+    RebarConfig = [{erl_opts, [{extra_src_dirs, ["extra"]}]}],
+
+    {ok, State} = rebar_test_utils:run_and_check(Config, RebarConfig, ["compile"], return),
+
+    code:add_paths(rebar_state:code_paths(State, all_deps)),
+    Mod1 = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name1]))),
+    {module, Mod1} = code:ensure_loaded(Mod1),
+    Mod2 = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name2]))),
+    {error, nofile} = code:ensure_loaded(Mod2),
+
+    ExpectOne = filename:join([AppDir, "_build", "default", "lib", Name1, "extra",
+                               io_lib:format("~ts_extra.beam", [Name1])]),
+    ExpectOne = code:which(Mod1).
+
+paths_extra_dirs_in_project_root(Config) ->
+    AppDir = ?config(apps, Config),
+
+    RebarConfig = [{erl_opts, [{extra_src_dirs, ["extra"]}]}],
+
+    {ok, State} = rebar_test_utils:run_and_check(Config, RebarConfig, ["compile"], return),
+
+    code:add_paths(rebar_state:code_paths(State, all_deps)),
+    {module, extra} = code:ensure_loaded(extra),
+
+    Expect = filename:join([AppDir, "_build", "default", "extras", "extra", "extra.beam"]),
+    Expect = code:which(extra).
+
+clean_basic_app(Config) ->
+    [Name] = ?config(app_names, Config),
+
+    rebar_test_utils:run_and_check(Config, [], ["clean"], {ok, [{app, Name, invalid}]}).
+
+clean_release_apps(Config) ->
+    [Name1, Name2] = ?config(app_names, Config),
+
+    rebar_test_utils:run_and_check(Config, [], ["clean"],
+                                   {ok, [{app, Name1, invalid}, {app, Name2, invalid}]}).
+
+clean_basic_extra_dirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name] = ?config(app_names, Config),
+
+    rebar_test_utils:run_and_check(Config, [], ["clean"], {ok, [{app, Name, invalid}]}),
+
+    Beam = lists:flatten(io_lib:format("~ts_extra", [Name])),
+    false = ec_file:exists(filename:join([AppDir, "_build", "default", "lib", Name, "extras", Beam])).
+
+clean_release_extra_dirs(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
+
+    rebar_test_utils:run_and_check(Config, [], ["clean"],
+                                   {ok, [{app, Name1, invalid}, {app, Name2, invalid}]}),
+
+    Beam1 = lists:flatten(io_lib:format("~ts_extra", [Name1])),
+    false = ec_file:exists(filename:join([AppDir, "_build", "default", "lib", Name1, "extras", Beam1])),
+    Beam2 = lists:flatten(io_lib:format("~ts_extra", [Name2])),
+    false = ec_file:exists(filename:join([AppDir, "_build", "default", "lib", Name2, "extras", Beam2])).
+
+clean_extra_dirs_in_project_root(Config) ->
+    AppDir = ?config(apps, Config),
+    [Name1, Name2] = ?config(app_names, Config),
+
+    rebar_test_utils:run_and_check(Config, [], ["clean"],
+                                   {ok, [{app, Name1, invalid}, {app, Name2, invalid}]}),
+
+    false = ec_file:exists(filename:join([AppDir, "_build", "default", "extras"])).
 
 recompile_when_hrl_changes(Config) ->
     AppDir = ?config(apps, Config),
@@ -167,7 +652,7 @@ recompile_when_hrl_changes(Config) ->
     rebar_test_utils:run_and_check(Config, [], ["compile"], {ok, [{app, Name}]}),
 
     EbinDir = filename:join([AppDir, "_build", "default", "lib", Name, "ebin"]),
-    {ok, Files} = file:list_dir(EbinDir),
+    {ok, Files} = rebar_utils:list_dir(EbinDir),
     ModTime = [filelib:last_modified(filename:join([EbinDir, F]))
                || F <- Files, filename:extension(F) == ".beam"],
 
@@ -178,7 +663,7 @@ recompile_when_hrl_changes(Config) ->
 
     rebar_test_utils:run_and_check(Config, [], ["compile"], {ok, [{app, Name}]}),
 
-    {ok, NewFiles} = file:list_dir(EbinDir),
+    {ok, NewFiles} = rebar_utils:list_dir(EbinDir),
     NewModTime = [filelib:last_modified(filename:join([EbinDir, F]))
                   || F <- NewFiles, filename:extension(F) == ".beam"],
 
@@ -194,7 +679,7 @@ recompile_when_opts_change(Config) ->
     rebar_test_utils:run_and_check(Config, [], ["compile"], {ok, [{app, Name}]}),
 
     EbinDir = filename:join([AppDir, "_build", "default", "lib", Name, "ebin"]),
-    {ok, Files} = file:list_dir(EbinDir),
+    {ok, Files} = rebar_utils:list_dir(EbinDir),
     ModTime = [filelib:last_modified(filename:join([EbinDir, F]))
                || F <- Files, filename:extension(F) == ".beam"],
 
@@ -204,7 +689,7 @@ recompile_when_opts_change(Config) ->
 
     rebar_test_utils:run_and_check(Config, [], ["compile"], {ok, [{app, Name}]}),
 
-    {ok, NewFiles} = file:list_dir(EbinDir),
+    {ok, NewFiles} = rebar_utils:list_dir(EbinDir),
     NewModTime = [filelib:last_modified(filename:join([EbinDir, F]))
                   || F <- NewFiles, filename:extension(F) == ".beam"],
 
@@ -220,7 +705,7 @@ dont_recompile_when_opts_dont_change(Config) ->
     rebar_test_utils:run_and_check(Config, [], ["compile"], {ok, [{app, Name}]}),
 
     EbinDir = filename:join([AppDir, "_build", "default", "lib", Name, "ebin"]),
-    {ok, Files} = file:list_dir(EbinDir),
+    {ok, Files} = rebar_utils:list_dir(EbinDir),
     ModTime = [filelib:last_modified(filename:join([EbinDir, F]))
                || F <- Files, filename:extension(F) == ".beam"],
 
@@ -228,7 +713,7 @@ dont_recompile_when_opts_dont_change(Config) ->
 
     rebar_test_utils:run_and_check(Config, [], ["compile"], {ok, [{app, Name}]}),
 
-    {ok, NewFiles} = file:list_dir(EbinDir),
+    {ok, NewFiles} = rebar_utils:list_dir(EbinDir),
     NewModTime = [filelib:last_modified(filename:join([EbinDir, F]))
                   || F <- NewFiles, filename:extension(F) == ".beam"],
 
@@ -331,7 +816,8 @@ deps_in_path(Config) ->
     %% find pkg name in there
     ?assertNotEqual([], [Path || Path <- code:get_path(),
                                  {match, _} <- [re:run(Path, PkgName)]]),
-    code:set_path(StartPaths),
+
+    true = code:set_path(lists:filter(fun(P) -> ec_file:exists(P) end, StartPaths)),
     %% Make sure apps we look for are not visible again
     %% Hope not to find src name
     ?assertEqual([], [Path || Path <- code:get_path(),
@@ -638,10 +1124,10 @@ clean_all(Config) ->
     ),
 
     %% Clean all
-    rebar_test_utils:run_and_check(
-        Config, RConf, ["clean", "--all"],
-        {ok, [{app, Name, invalid}, {app, DepName, invalid}, {app, PkgName, invalid}]}
-    ).
+    rebar_test_utils:run_and_check(Config, [], ["clean", "--all"],
+                                   {ok, [{app, Name, invalid},
+                                         {app, DepName, invalid},
+                                         {app, PkgName, invalid}]}).
 
 override_deps(Config) ->
     mock_git_resource:mock([{deps, [{some_dep, "0.0.1"},{other_dep, "0.0.1"}]}]),
@@ -680,3 +1166,4 @@ profile_override_deps(Config) ->
         Config, RebarConfig, ["as", "a", "compile"],
         {ok, [{dep, "some_dep"},{dep_not_exist, "other_dep"}]}
     ).
+
diff --git a/test/rebar_cover_SUITE.erl b/test/rebar_cover_SUITE.erl
index 1fae92c..ba078c2 100644
--- a/test/rebar_cover_SUITE.erl
+++ b/test/rebar_cover_SUITE.erl
@@ -7,6 +7,9 @@
          all/0,
          flag_coverdata_written/1,
          config_coverdata_written/1,
+         basic_extra_src_dirs/1,
+         release_extra_src_dirs/1,
+         root_extra_src_dirs/1,
          index_written/1,
          flag_verbose/1,
          config_verbose/1]).
@@ -29,6 +32,8 @@ init_per_testcase(_, Config) ->
 
 all() ->
     [flag_coverdata_written, config_coverdata_written,
+     basic_extra_src_dirs, release_extra_src_dirs,
+     root_extra_src_dirs,
      index_written,
      flag_verbose, config_verbose].
 
@@ -62,6 +67,88 @@ config_coverdata_written(Config) ->
 
     true = filelib:is_file(filename:join([AppDir, "_build", "test", "cover", "eunit.coverdata"])).
 
+basic_extra_src_dirs(Config) ->
+    AppDir = ?config(apps, Config),
+
+    Name = rebar_test_utils:create_random_name("cover_extra_"),
+    Vsn = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_eunit_app(AppDir, Name, Vsn, [kernel, stdlib]),
+
+    ExtraSrc = io_lib:format("-module(~ts_extra).\n-export([ok/0]).\nok() -> ok.\n", [Name]),
+
+    ok = filelib:ensure_dir(filename:join([AppDir, "extra", "dummy"])),
+    ok = file:write_file(filename:join([AppDir, "extra", io_lib:format("~ts_extra.erl", [Name])]),
+                         ExtraSrc),
+
+    RebarConfig = [{erl_opts, [{d, some_define}]}, {extra_src_dirs, ["extra"]}],
+    rebar_test_utils:run_and_check(Config,
+                                   RebarConfig,
+                                   ["eunit", "--cover"],
+                                   {ok, [{app, Name}]}),
+
+    Mod = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name]))),
+    {file, _} = cover:is_compiled(Mod).
+
+release_extra_src_dirs(Config) ->
+    AppDir = ?config(apps, Config),
+
+    Name1 = rebar_test_utils:create_random_name("relapp1_"),
+    Vsn1 = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_app(filename:join([AppDir, "apps", Name1]), Name1, Vsn1, [kernel, stdlib]),
+
+    Name2 = rebar_test_utils:create_random_name("relapp2_"),
+    Vsn2 = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_app(filename:join([AppDir, "apps", Name2]), Name2, Vsn2, [kernel, stdlib]),
+
+    ExtraOne = io_lib:format("-module(~ts_extra).\n-export([ok/0]).\nok() -> ok.\n", [Name1]),
+
+    ok = filelib:ensure_dir(filename:join([AppDir, "apps", Name1, "extra", "dummy"])),
+    ok = file:write_file(filename:join([AppDir, "apps", Name1, "extra",
+                                        io_lib:format("~ts_extra.erl", [Name1])]),
+                         ExtraOne),
+
+    ExtraTwo = io_lib:format("-module(~ts_extra).\n-export([ok/0]).\nok() -> ok.\n", [Name2]),
+
+    ok = filelib:ensure_dir(filename:join([AppDir, "apps", Name2, "extra", "dummy"])),
+    ok = file:write_file(filename:join([AppDir, "apps", Name2, "extra",
+                                        io_lib:format("~ts_extra.erl", [Name2])]),
+                         ExtraTwo),
+
+    RebarConfig = [{erl_opts, [{d, some_define}]}, {extra_src_dirs, ["extra"]}],
+    rebar_test_utils:run_and_check(Config,
+                                   RebarConfig,
+                                   ["eunit", "--cover"],
+                                   {ok, [{app, Name1}, {app, Name2}]}),
+
+    Mod1 = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name1]))),
+    {file, _} = cover:is_compiled(Mod1),
+    Mod2 = list_to_atom(lists:flatten(io_lib:format("~ts_extra", [Name2]))),
+    {file, _} = cover:is_compiled(Mod2).
+
+root_extra_src_dirs(Config) ->
+    AppDir = ?config(apps, Config),
+
+    Name1 = rebar_test_utils:create_random_name("relapp1_"),
+    Vsn1 = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_app(filename:join([AppDir, "apps", Name1]), Name1, Vsn1, [kernel, stdlib]),
+
+    Name2 = rebar_test_utils:create_random_name("relapp2_"),
+    Vsn2 = rebar_test_utils:create_random_vsn(),
+    rebar_test_utils:create_app(filename:join([AppDir, "apps", Name2]), Name2, Vsn2, [kernel, stdlib]),
+
+    Extra = <<"-module(extra).\n-export([ok/0]).\nok() -> ok.\n">>,
+
+    ok = filelib:ensure_dir(filename:join([AppDir, "extra", "dummy"])),
+    ok = file:write_file(filename:join([AppDir, "extra", "extra.erl"]), Extra),
+
+    RebarConfig = [{erl_opts, [{d, some_define}]}, {extra_src_dirs, ["extra"]}],
+    rebar_test_utils:run_and_check(Config,
+                                   RebarConfig,
+                                   ["eunit", "--cover"],
+                                   {ok, [{app, Name1}, {app, Name2}]}),
+
+    {file, _} = cover:is_compiled(extra).
+
 index_written(Config) ->
     AppDir = ?config(apps, Config),
 
diff --git a/test/rebar_ct_SUITE.erl b/test/rebar_ct_SUITE.erl
index 95a411f..cdd3774 100644
--- a/test/rebar_ct_SUITE.erl
+++ b/test/rebar_ct_SUITE.erl
@@ -204,6 +204,7 @@ multi_app_default_beams(Config) ->
     File3 = filename:join([AppDir,
                            "_build",
                            "test",
+                           "extras",
                            "test",
                            "extras_SUITE.beam"]),
 
diff --git a/test/rebar_eunit_SUITE.erl b/test/rebar_eunit_SUITE.erl
index 903bd96..609be51 100644
--- a/test/rebar_eunit_SUITE.erl
+++ b/test/rebar_eunit_SUITE.erl
@@ -125,7 +125,9 @@ basic_app_files(Config) ->
     AppDir = ?config(apps, Config),
 
     lists:foreach(fun(F) -> true = ec_file:exists(filename:join([AppDir, "_build", "test", "lib", "basic_app", "ebin", F])) end,
-                  ["basic_app.app", "basic_app.beam", "basic_app_tests.beam", "basic_app_tests_helper.beam"]).
+                  ["basic_app.app", "basic_app.beam"]),
+    lists:foreach(fun(F) -> true = ec_file:exists(filename:join([AppDir, "_build", "test", "lib", "basic_app", "test", F])) end,
+                  ["basic_app_tests.beam", "basic_app_tests_helper.beam"]).
 
 %% check that the correct tests are exported from modules for project
 %% note that this implies `TEST` is set correctly
@@ -171,10 +173,14 @@ multi_app_files(Config) ->
     AppDir = ?config(apps, Config),
 
     lists:foreach(fun(F) -> true = ec_file:exists(filename:join([AppDir, "_build", "test", "lib", "multi_app_bar", "ebin", F])) end,
-                  ["multi_app_bar.app", "multi_app_bar.beam", "multi_app_bar_tests.beam", "multi_app_bar_tests_helper.beam"]),
+                  ["multi_app_bar.app", "multi_app_bar.beam"]),
     lists:foreach(fun(F) -> true = ec_file:exists(filename:join([AppDir, "_build", "test", "lib", "multi_app_baz", "ebin", F])) end,
-                  ["multi_app_baz.app", "multi_app_baz.beam", "multi_app_baz_tests.beam", "multi_app_baz_tests_helper.beam"]),
-    lists:foreach(fun(F) -> true = ec_file:exists(filename:join([AppDir, "_build", "test", "test", F])) end,
+                  ["multi_app_baz.app", "multi_app_baz.beam"]),
+    lists:foreach(fun(F) -> true = ec_file:exists(filename:join([AppDir, "_build", "test", "lib", "multi_app_bar", "test", F])) end,
+                  ["multi_app_bar_tests.beam", "multi_app_bar_tests_helper.beam"]),
+    lists:foreach(fun(F) -> true = ec_file:exists(filename:join([AppDir, "_build", "test", "lib", "multi_app_baz", "test", F])) end,
+                  ["multi_app_baz_tests.beam", "multi_app_baz_tests_helper.beam"]),
+    lists:foreach(fun(F) -> true = ec_file:exists(filename:join([AppDir, "_build", "test", "extras", "test", F])) end,
                   ["multi_app_tests.beam", "multi_app_tests_helper.beam"]).
 
 %% check that the correct tests are exported from modules for project
@@ -202,7 +208,9 @@ multi_app_testset(Config) ->
     AppDir = ?config(apps, Config),
     Result = ?config(result, Config),
 
-    Set = {ok, [{application, multi_app_bar}, {application, multi_app_baz}, {dir, filename:join([AppDir, "_build", "test", "test"])}]},
+    Set = {ok, [{application, multi_app_bar},
+                {application, multi_app_baz},
+                {dir, filename:join([AppDir, "test"])}]},
     Set = rebar_prv_eunit:prepare_tests(Result).
 
 
diff --git a/test/rebar_file_utils_SUITE.erl b/test/rebar_file_utils_SUITE.erl
index 4324a5f..a061325 100644
--- a/test/rebar_file_utils_SUITE.erl
+++ b/test/rebar_file_utils_SUITE.erl
@@ -64,7 +64,7 @@ reset_nonexistent_dir(Config) ->
     ?assertNot(filelib:is_dir(TmpDir)),
     ok = rebar_file_utils:reset_dir(TmpDir),
     ?assert(filelib:is_dir(TmpDir)),
-    {ok, []} = file:list_dir(TmpDir).
+    {ok, []} = rebar_utils:list_dir(TmpDir).
 
 reset_empty_dir(Config) ->
     TmpDir = ?config(tmpdir, Config),
@@ -73,7 +73,7 @@ reset_empty_dir(Config) ->
     ?assert(filelib:is_dir(TmpDir)),
     ok = rebar_file_utils:reset_dir(TmpDir),
     ?assert(filelib:is_dir(TmpDir)),
-    {ok, []} = file:list_dir(TmpDir).
+    {ok, []} = rebar_utils:list_dir(TmpDir).
 
 reset_dir(Config) ->
     TmpDir = ?config(tmpdir, Config),
@@ -86,7 +86,7 @@ reset_dir(Config) ->
                   ["a", "b", "c"]),
     ok = rebar_file_utils:reset_dir(TmpDir),
     ?assert(filelib:is_dir(TmpDir)),
-    {ok, []} = file:list_dir(TmpDir).
+    {ok, []} = rebar_utils:list_dir(TmpDir).
 
 path_from_ancestor(_Config) ->
     ?assertEqual({ok, "foo/bar/baz"}, rebar_file_utils:path_from_ancestor("/foo/bar/baz", "/")),
diff --git a/test/rebar_src_dirs_SUITE.erl b/test/rebar_src_dirs_SUITE.erl
index e29dcf0..5a00515 100644
--- a/test/rebar_src_dirs_SUITE.erl
+++ b/test/rebar_src_dirs_SUITE.erl
@@ -132,9 +132,9 @@ build_basic_app(Config) ->
 
     rebar_test_utils:run_and_check(Config, RebarConfig, ["compile"], {ok, [{app, Name}]}),
 
-    %% check that `extra.erl` was compiled to the `ebin` dir
-    Ebin = filename:join([AppDir, "_build", "default", "lib", Name, "ebin"]),
-    true = filelib:is_file(filename:join([Ebin, "extra.beam"])),
+    %% check that `extra.erl` was compiled to the `extra` dir
+    ExtraOut = filename:join([AppDir, "_build", "default", "lib", Name, "extra"]),
+    true = filelib:is_file(filename:join([ExtraOut, "extra.beam"])),
 
     %% check that `extra.erl` is not in the `modules` key of the app
     {ok, App} = file:consult(filename:join([AppDir,
@@ -176,11 +176,11 @@ build_multi_apps(Config) ->
     ),
 
     %% check that `extraX.erl` was compiled to the `ebin` dir
-    Ebin1 = filename:join([AppDir, "_build", "default", "lib", Name1, "ebin"]),
-    true = filelib:is_file(filename:join([Ebin1, "extra1.beam"])),
+    ExtraOut1 = filename:join([AppDir, "_build", "default", "lib", Name1, "extra"]),
+    true = filelib:is_file(filename:join([ExtraOut1, "extra1.beam"])),
 
-    Ebin2 = filename:join([AppDir, "_build", "default", "lib", Name2, "ebin"]),
-    true = filelib:is_file(filename:join([Ebin2, "extra2.beam"])),
+    ExtraOut2 = filename:join([AppDir, "_build", "default", "lib", Name2, "extra"]),
+    true = filelib:is_file(filename:join([ExtraOut2, "extra2.beam"])),
 
     %% check that `extraX.erl` is not in the `modules` key of the app
     {ok, App1} = file:consult(filename:join([AppDir,
@@ -221,10 +221,9 @@ src_dir_takes_precedence_over_extra(Config) ->
 
     rebar_test_utils:run_and_check(Config, RebarConfig, ["compile"], {ok, [{app, Name}]}),
 
-    %% check that `extra.erl` was compiled to the `ebin` dir
-    %% check that `extraX.erl` was compiled to the `ebin` dir
-    Ebin = filename:join([AppDir, "_build", "default", "lib", Name, "ebin"]),
-    true = filelib:is_file(filename:join([Ebin, "extra.beam"])),
+    %% check that `extra.erl` was compiled to the `extra` dir
+    ExtraOut = filename:join([AppDir, "_build", "default", "lib", Name, "extra"]),
+    true = filelib:is_file(filename:join([ExtraOut, "extra.beam"])),
 
     %% check that `extra.erl` is in the `modules` key of the app
     {ok, App} = file:consult(filename:join([AppDir,
diff --git a/test/rebar_test_utils.erl b/test/rebar_test_utils.erl
index ca5e91a..3943db7 100644
--- a/test/rebar_test_utils.erl
+++ b/test/rebar_test_utils.erl
@@ -334,7 +334,7 @@ check_results(AppDir, Expected, ProfileRun) ->
                     {ok, RelxState3} = rlx_prv_rel_discover:do(RelxState2),
 
                     LibDir = filename:join([ReleaseDir, Name, "lib"]),
-                    {ok, RelLibs} = file:list_dir(LibDir),
+                    {ok, RelLibs} = rebar_utils:list_dir(LibDir),
                     IsSymLinkFun =
                         fun(X) ->
                                 ec_file:is_symlink(filename:join(LibDir, X))
@@ -357,6 +357,9 @@ check_results(AppDir, Expected, ProfileRun) ->
         ;  ({file, Filename}) ->
                 ct:pal("Filename: ~s", [Filename]),
                 ?assert(filelib:is_file(Filename))
+        ;  ({dir, Dirname}) ->
+                ct:pal("Directory: ~s", [Dirname]),
+                ?assert(filelib:is_dir(Dirname))
         end, Expected).
 
 write_src_file(Dir, Name) ->
@@ -422,7 +425,7 @@ get_app_metadata(Name, Vsn, Deps) ->
 
 package_app(AppDir, DestDir, PkgName) ->
     Name = PkgName++".tar",
-    {ok, Fs} = file:list_dir(AppDir),
+    {ok, Fs} = rebar_utils:list_dir(AppDir),
     ok = erl_tar:create(filename:join(DestDir, "contents.tar.gz"),
                         lists:zip(Fs, [filename:join(AppDir,F) || F <- Fs]),
                         [compressed]),