diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py
index 09916169..5dd139ec 100644
--- a/repo2docker/__main__.py
+++ b/repo2docker/__main__.py
@@ -66,6 +66,20 @@ def get_argparser():
         description="Fetch a repository and build a container image"
     )
 
+    argparser.add_argument(
+        "--help-all",
+        dest="help_all",
+        action="store_true",
+        help="Display all configurable options and exit.",
+    )
+
+    argparser.add_argument(
+        "--version",
+        dest="version",
+        action="store_true",
+        help="Print the repo2docker version and exit.",
+    )
+
     argparser.add_argument(
         "--config",
         default="repo2docker_config.py",
@@ -222,13 +236,6 @@ def get_argparser():
 
     argparser.add_argument("--subdir", type=str, help=Repo2Docker.subdir.help)
 
-    argparser.add_argument(
-        "--version",
-        dest="version",
-        action="store_true",
-        help="Print the repo2docker version and exit.",
-    )
-
     argparser.add_argument(
         "--cache-from", action="append", default=[], help=Repo2Docker.cache_from.help
     )
@@ -245,15 +252,24 @@ def make_r2d(argv=None):
     if argv is None:
         argv = sys.argv[1:]
 
+    argparser = get_argparser()
+
     # version must be checked before parse, as repo/cmd are required and
     # will spit out an error if allowed to be parsed first.
     if "--version" in argv:
         print(__version__)
         sys.exit(0)
 
-    args = get_argparser().parse_args(argv)
+    if "--help-all" in argv:
+        argparser.print_help()
+        print("\nAll configurable options:\n")
+        Repo2Docker().print_help(classes=True)
+        sys.exit(0)
+
+    args, traitlet_args = argparser.parse_known_args(argv)
 
     r2d = Repo2Docker()
+    r2d.parse_command_line(traitlet_args)
 
     if args.debug:
         r2d.log_level = logging.DEBUG
diff --git a/repo2docker/app.py b/repo2docker/app.py
index a03fe1df..8c896828 100755
--- a/repo2docker/app.py
+++ b/repo2docker/app.py
@@ -47,6 +47,10 @@ class Repo2Docker(Application):
     name = "jupyter-repo2docker"
     version = __version__
     description = __doc__
+    # disable aliases/flags because we don't use the traitlets for CLI parsing
+    # other than --Class.trait=value
+    aliases = {}
+    flags = {}
 
     @default("log_level")
     def _default_log_level(self):
@@ -490,7 +494,7 @@ class Repo2Docker(Application):
             extra=dict(phase="failed"),
         )
 
-    def initialize(self):
+    def initialize(self, *args, **kwargs):
         """Init repo2docker configuration before start"""
         # FIXME: Remove this function, move it to setters / traitlet reactors
         if self.json_logs: