Hardcode defaults, per @jmchilton's comments

config/plugins/interactive_environments/ipython/config/ipython.ini.sample

@@ -14,13 +14,13 @@
 # additional parameters. This command string is re-used for a `docker inspect`
 # command and will likely cause errors if it is extensively modified, past the
 # usual group/sudo changes.
-command = docker run {docker_args}
+#command = docker run {docker_args}
 
 # The docker image name that should be started.
 image = bgruening/docker-ipython-notebook:dev
 
 # Additional arguments that are passed to the `docker run` command.
-command_inject = --sig-proxy=true -e DEBUG=false
+#command_inject = --sig-proxy=true -e DEBUG=false
 
 # URL to access the Galaxy API with from the spawn Docker containter, if empty
 # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the
@@ -34,4 +34,4 @@ command_inject = --sig-proxy=true -e DEBUG=false
 # Try to set the tempdirectory to world execute - this can fix the issue 
 # where	  'sudo docker' is not able to mount the folder otherwise.
 # "finalize namespace chdir to /import permission denied"
-wx_tempdir = False
+#wx_tempdir = False

config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample

@@ -1,5 +1,5 @@
 [main]
-# This cannot be changed
+# This CANNOT be changed. Eventually will be deprecated
 password_auth = True
 # Following options are ignored if using the Galaxy dynamic proxy but
 # are useful if mapping a range of ports for environment consumption.
@@ -15,13 +15,13 @@ password_auth = True
 # additional parameters. This command string is re-used for a `docker inspect`
 # command and will likely cause errors if it is extensively modified, past the
 # usual group/sudo changes.
-command = docker run {docker_args}
+#command = docker run {docker_args}
 
 # The docker image name that should be started.
 image = erasche/docker-rstudio-notebook:dev
 
 # Additional arguments that are passed to the `docker run` command.
-command_inject = --sig-proxy=true -e DEBUG=false
+#command_inject = --sig-proxy=true -e DEBUG=false
 
 # URL to access the Galaxy API with from the spawn Docker containter, if empty
 # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the
@@ -35,4 +35,4 @@ command_inject = --sig-proxy=true -e DEBUG=false
 # Try to set the tempdirectory to world execute - this can fix the issue 
 # where	  'sudo docker' is not able to mount the folder otherwise.
 # "finalize namespace chdir to /import permission denied"
-wx_tempdir = False
+#wx_tempdir = False

lib/galaxy/web/base/interactive_environments.py

@@ -65,10 +65,12 @@ def load_deploy_config(self, default_dict={}):
         # will need to be recorded here. The ConfigParser doesn't provide a
         # .get() that will ignore missing sections, so we must make use of
         # their defaults dictionary instead.
-        default_dict['command_inject'] = '--sig-proxy=true'
-        default_dict['docker_hostname'] = 'localhost'
-        default_dict['wx_tempdir'] = 'False'
-        default_dict['command_wrapper'] = ''
+        default_dict = {
+            'command': 'docker run {docker_args}',
+            'command_inject': '--sig-proxy=true -e DEBUG=false',
+            'docker_hostname': 'localhost',
+            'wx_tempdir': 'False',
+        }
         viz_config = ConfigParser.SafeConfigParser(default_dict)
         conf_path = os.path.join( self.attr.our_config_dir, self.attr.viz_id + ".ini" )
         if not os.path.exists( conf_path ):