Fix clean hooks when override are presents

The issue appears to be that because the 'clean' operation might be run
while dependencies have not yet been compiled, we applied a partial app
detection mechanism with `rebar_app_disover:find_apps(..., ..., all,
...)`, which worked to parse "invalid" (unbuilt) apps, but also did not
apply overrides.

Instead, we trust the `install_deps` provider dependency by reusing the
apps as they were fully parsed _if_ they were valid, and falling back to
the `rebar_app_discover:find_apps/4` call only to cover the unreadable
ones.

This, it turns out, has the side effect of properly applying hooks when
apps are fully parsed, and fixes #2862

apps/rebar/src/rebar_prv_clean.erl

@@ -45,7 +45,14 @@ do(State) ->
     if All; Specific =/= [] ->
         DepsDir = rebar_dir:deps_dir(State1),
         DepsDirs = filelib:wildcard(filename:join(DepsDir, "*")),
-        AllApps = rebar_app_discover:find_apps(DepsDirs, all, State),
+        ProjectApps = rebar_state:project_apps(State),
+        Deps = rebar_state:all_deps(State),
+        KnownAppNames = [rebar_app_info:name(App) || App <- ProjectApps++Deps],
+        ParsedApps = rebar_app_discover:find_apps(DepsDirs, all, State),
+        AllApps = ProjectApps ++ Deps ++
+                  [App || App <- ParsedApps,
+                          not lists:member(rebar_app_info:name(App),
+                                           KnownAppNames)],
         Filter = case All of
             true -> fun(_) -> true end;
             false -> fun(AppInfo) -> filter_name(AppInfo, Specific) end