Change location & type of fix

The initial plan was to modify our copy of the environment variables as
set via cli argparsing at the point-of-use. However, that function's
purpose is to launch a container.  Adding argument processing doesn't
feel right.

The new plan is to modify our copy of the environment when the arguments
are parsed. `argparse` provides a hook to do such work: custom actions.

repo2docker/__main__.py

@@ -158,6 +158,10 @@ def get_argparser():
         "--user-name", help="Username of the primary user in the image"
     )
 
+    # Process the environment options the same way that docker does, as
+    # they are passed directly to docker as the environment to use. This
+    # requires a custom action for argparse.
+    # see https://docs.docker.com/engine/reference/commandline/run/#set-environment-variables--e---env---env-file
     argparser.add_argument(
         "--env",
         "-e",

repo2docker/app.py

@@ -560,8 +560,6 @@ class Repo2Docker(Application):
                     "mode": "rw",
                 }
 
-        # self.environment needs to be modified to match the semantics
-        # of docker's --env option
         run_kwargs = dict(
             publish_all_ports=self.all_ports,
             ports=ports,