Do not violently remove config_dir kwarg of config manager.

though, jupyter#893 argues that we might need it and that it will be complex to
reintroduce it.

This use a convoluted way to :

 - warn that this kwarg might not be given to config managers in future version
 - but do not warn on default installs with default config.
 - warn that the keyword is ignored when people use subclasses of out
   config manager, and pass the keyword to super().

Thus this actually advertise that the keyword **might** be removed,
by still allowing us to keep it if in the end it appears that we need
it.

Should help with jupyter#893 without un-fixing jupyter#882.

notebook/notebookapp.py

@@ -23,6 +23,7 @@
 import sys
 import threading
 import webbrowser
+import warnings
 
 
 from jinja2 import Environment, FileSystemLoader
@@ -825,10 +826,28 @@ def init_configurables(self):
             kernel_manager=self.kernel_manager,
             contents_manager=self.contents_manager,
         )
-        self.config_manager = self.config_manager_class(
-            parent=self,
-            log=self.log
-        )
+        if self.config_manager_class is ConfigManager:
+            # We know our ConfigManager ignore `config_dir`, 
+            # and will warn/raise a PendingDeprecation warning
+            # if given, so do not pass it (not to annoy user and show the
+            # warning on default install. .
+            self.config_manager = self.config_manager_class(
+                parent=self,
+                log=self.log,
+            )
+        else :
+            # In case it is a custom ConfigManager,  
+            # for potentially not breaking future backward 
+            # compatibility, will still pass it. 
+            if issubclass(self.config_manager_class, ConfigManager):
+                warnings.warn('Object `%s` will be passed a `config_dir` kwarg, which might be removed'
+                              'in future Notebook versions. Please make sure to handle this case.' % (self.config_manager_class),)
+            self.config_manager = self.config_manager_class(
+                parent=self,
+                log=self.log,
+                config_dir=os.path.join(self.config_dir, 'nbconfig'),
+            )
+
 
     def init_logging(self):
         # This prevents double log messages because tornado use a root logger that

notebook/services/config/manager.py

@@ -9,8 +9,17 @@
 from jupyter_core.paths import jupyter_config_dir
 from traitlets import Unicode
 
+import warnings
+
 class ConfigManager(BaseJSONConfigManager):
     """Config Manager used for storing notebook frontend config"""
+
+    def __init__(self, **kwargs):
+
+        if kwargs.get('config_dir', None) is not None:
+            warnings.warn('ConfigManager `config_dir` kwarg will likely have no effect and might be removed in future Notebook versions.')
+        super(ConfigManager, self).__init__(**kwargs)
+
 
     config_dir = Unicode(config=True)
     def _config_dir_default(self):