diff --git a/IPython/config/default/ipython_config.py b/IPython/config/default/ipython_config.py
index 0f1ad8a..c60f159 100644
--- a/IPython/config/default/ipython_config.py
+++ b/IPython/config/default/ipython_config.py
@@ -1,81 +1,66 @@
 #-----------------------------------------------------------------------------
-# IPython Shell Configuration Defaults
+# Global options
 #-----------------------------------------------------------------------------
 
+Global.classic = False
+Global.nosep = False
+
 #-----------------------------------------------------------------------------
-# Startup
+# InteractiveShell options
 #-----------------------------------------------------------------------------
 
-AUTOCALL = True
-
-AUTOEDIT_SYNTAX = False
-
-AUTOINDENT = True
-
-AUTOMAGIC = True
-
-CACHE_SIZE = 1000
 
-CLASSIC = False
+InteractiveShell.autocall = 1
 
-COLORS = 'Linux'
+InteractiveShell.autoedit_syntax = False
 
-COLOR_INFO = True
+InteractiveShell.autoindent = True
 
-CONFIRM_EXIT = True
+InteractiveShell.automagic = False
 
-DEEP_RELOAD = False
+InteractiveShell.banner1 = 'This if for overriding the default IPython banner'
+ 
+InteractiveShell.banner2 = "This is for extra banner text"
 
-EDITOR = 0
+InteractiveShell.cache_size = 1000
 
-LOG = True
+InteractiveShell.colors = 'LightBG'
 
-LOGFILE = ''
+InteractiveShell.color_info = True
 
-BANNER = True
+InteractiveShell.confirm_exit = True
 
-MESSAGES = True
+InteractiveShell.deep_reload = False
 
-PDB = False
+InteractiveShell.display_banner = True
 
-PPRINT = True
+InteractiveShell.editor = 'nano'
 
-PROMPT_IN1 = 'In [\#]: '
+InteractiveShell.logstart = True
 
-PROMPT_IN2 = '   .\D.: '
+InteractiveShell.logfile = 'ipython_log.py'
 
-PROMPT_OUT = 'Out[\#]: '
+InteractiveShell.logplay = 'mylog.py'
 
-PROMPTS_PAD_LEFT = True
+InteractiveShell.object_info_string_level = 0
 
-QUICK = False
+InteractiveShell.pager = 'less'
 
-SCREEN_LENGTH = 0
+InteractiveShell.pdb = False
 
-SEPARATE_IN = '\n'
-SEPARATE_OUT = ''
-SEPARATE_OUT2 = ''
-NOSEP = False
+InteractiveShell.pprint = True
 
-WILDCARDS_CASE_SENSITIVE = True
+InteractiveShell.prompt_in1 = 'In [\#]: '
+InteractiveShell.prompt_in2 = '   .\D.: '
+InteractiveShell.prompt_out = 'Out[\#]: '
+InteractiveShell.prompts_pad_left = True
 
-OBJECT_INFO_STRING_LEVEL = 0
+InteractiveShell.quiet = False
 
-XMODE = 'Context'
+# Readline 
+InteractiveShell.readline_use = False
 
-MULTI_LINE_SPECIALS = True
-
-SYSTEM_HEADER = "IPython system call: "
-
-SYSTEM_VERBOSE = True
-
-#-----------------------------------------------------------------------------
-# Readline
-#-----------------------------------------------------------------------------
-
-READLINE = True
-
-READLINE_PARSE_AND_BIND = [
+InteractiveShell.readline_parse_and_bind = [
     'tab: complete',
     '"\C-l": possible-completions',
     'set show-all-if-ambiguous on',
@@ -92,29 +77,39 @@ READLINE_PARSE_AND_BIND = [
     '"\C-k": kill-line',
     '"\C-u": unix-line-discard',
 ]
+InteractiveShell.readline_remove_delims = '-/~'
+InteractiveShell.readline_merge_completions = True
+InteractiveShell.readline_omit_names = 0
+
+InteractiveShell.screen_length = 0
+
+InteractiveShell.separate_in = '\n'
+InteractiveShell.separate_out = ''
+InteractiveShell.separate_out2 = ''
+
+InteractiveShell.system_header = "IPython system call: "
 
-READLINE_REMOVE_DELIMS = '-/~'
+InteractiveShell.system_verbose = True
 
-READLINE_MERGE_COMPLETIONS = True
+InteractiveShell.term_title = False
 
-READLINE_OMIT_NAMES = 0
+InteractiveShell.wildcards_case_sensitive = True
+
+InteractiveShell.xmode = 'Context'
 
 #-----------------------------------------------------------------------------
-# Code to execute
+# PrefilterManager options
 #-----------------------------------------------------------------------------
 
-EXECUTE = [
-    'import numpy as np',
-    'import sympy',
-    'a = 10'
-]
-
-EXECFILE = []
+PrefilterManager.multi_line_specials = True
 
 #-----------------------------------------------------------------------------
-# Alias
+# AliasManager options
 #-----------------------------------------------------------------------------
 
-ALIAS = [
-    ('myls', 'ls -la')
+# Do this to enable all defaults
+# AliasManager.default_aliases = []
+
+AliasManger.user_aliases = [
+    ('foo', 'echo Hi')
 ]
\ No newline at end of file
diff --git a/IPython/config/loader.py b/IPython/config/loader.py
index c77b1b8..aae5b02 100644
--- a/IPython/config/loader.py
+++ b/IPython/config/loader.py
@@ -1,6 +1,10 @@
 #!/usr/bin/env python
 # encoding: utf-8
-"""A factory for creating configuration objects.
+"""A simple configuration system.
+
+Authors:
+
+* Brian Granger
 """
 
 #-----------------------------------------------------------------------------
@@ -14,22 +18,138 @@
 # Imports
 #-----------------------------------------------------------------------------
 
+import __builtin__
 import os
 import sys
 
 from IPython.external import argparse
-from IPython.utils.ipstruct import Struct
 from IPython.utils.genutils import filefind
 
 #-----------------------------------------------------------------------------
-# Code
+# Exceptions
 #-----------------------------------------------------------------------------
 
 
-class ConfigLoaderError(Exception):
+class ConfigError(Exception):
     pass
 
 
+class ConfigLoaderError(ConfigError):
+    pass
+
+
+#-----------------------------------------------------------------------------
+# Config class for holding config information
+#-----------------------------------------------------------------------------
+
+
+class Config(dict):
+    """An attribute based dict that can do smart merges."""
+
+    def __init__(self, *args, **kwds):
+        dict.__init__(self, *args, **kwds)
+        # This sets self.__dict__ = self, but it has to be done this way
+        # because we are also overriding __setattr__.
+        dict.__setattr__(self, '__dict__', self)
+
+    def _merge(self, other):
+        to_update = {}
+        for k, v in other.items():
+            if not self.has_key(k):
+                to_update[k] = v
+            else: # I have this key
+                if isinstance(v, Config):
+                    # Recursively merge common sub Configs
+                    self[k]._merge(v)
+                else:
+                    # Plain updates for non-Configs
+                    to_update[k] = v
+
+        self.update(to_update)
+
+    def _is_section_key(self, key):
+        if key[0].upper()==key[0] and not key.startswith('_'):
+            return True
+        else:
+            return False
+
+    def has_key(self, key):
+        if self._is_section_key(key):
+            return True
+        else:
+            return dict.has_key(self, key)
+
+    def _has_section(self, key):
+        if self._is_section_key(key):
+            if dict.has_key(self, key):
+                return True
+        return False
+
+    def copy(self):
+        return type(self)(dict.copy(self))
+
+    def __copy__(self):
+        return self.copy()
+
+    def __deepcopy__(self, memo):
+        import copy
+        return type(self)(copy.deepcopy(self.items()))
+
+    def __getitem__(self, key):
+        # Because we use this for an exec namespace, we need to delegate
+        # the lookup of names in __builtin__ to itself.  This means
+        # that you can't have section or attribute names that are 
+        # builtins.
+        try:
+            return getattr(__builtin__, key)
+        except AttributeError:
+            pass
+        if self._is_section_key(key):
+            try:
+                return dict.__getitem__(self, key)
+            except KeyError:
+                c = Config()
+                dict.__setitem__(self, key, c)
+                return c
+        else:
+            return dict.__getitem__(self, key)
+
+    def __setitem__(self, key, value):
+        # Don't allow names in __builtin__ to be modified.
+        if hasattr(__builtin__, key):
+            raise ConfigError('Config variable names cannot have the same name '
+                              'as a Python builtin: %s' % key)
+        if self._is_section_key(key):
+            if not isinstance(value, Config):
+                raise ValueError('values whose keys begin with an uppercase '
+                                 'char must be Config instances: %r, %r' % (key, value))
+        else:
+            dict.__setitem__(self, key, value)
+
+    def __getattr__(self, key):
+        try:
+            return self.__getitem__(key)
+        except KeyError, e:
+            raise AttributeError(e)
+
+    def __setattr__(self, key, value):
+        try:
+            self.__setitem__(key, value)
+        except KeyError, e:
+            raise AttributeError(e)
+
+    def __delattr__(self, key):
+        try:
+            dict.__delitem__(self, key)
+        except KeyError, e:
+            raise AttributeError(e)
+
+
+#-----------------------------------------------------------------------------
+# Config loading classes
+#-----------------------------------------------------------------------------
+
+
 class ConfigLoader(object):
     """A object for loading configurations from just about anywhere.
     
@@ -59,7 +179,7 @@ class ConfigLoader(object):
         self.clear()
 
     def clear(self):
-        self.config = Struct()
+        self.config = Config()
 
     def load_config(self):
         """Load a config from somewhere, return a Struct.
@@ -106,7 +226,7 @@ class PyFileConfigLoader(FileConfigLoader):
         """Load the config from a file and return it as a Struct."""
         self._find_file()
         self._read_file_as_dict()
-        self._convert_to_struct()
+        self._convert_to_config()
         return self.config
 
     def _find_file(self):
@@ -114,15 +234,12 @@ class PyFileConfigLoader(FileConfigLoader):
         self.full_filename = filefind(self.filename, self.path)
 
     def _read_file_as_dict(self):
-        self.data = {}
-        execfile(self.full_filename, self.data)
+        execfile(self.full_filename, self.config)
 
-    def _convert_to_struct(self):
+    def _convert_to_config(self):
         if self.data is None:
             ConfigLoaderError('self.data does not exist')
-        for k, v in self.data.iteritems():
-            if k == k.upper():
-                self.config[k] = v
+        del self.config['__builtins__']
 
 
 class CommandLineConfigLoader(ConfigLoader):
@@ -133,8 +250,8 @@ class CommandLineConfigLoader(ConfigLoader):
     """
 
 
-class NoDefault(object): pass
-NoDefault = NoDefault()
+class NoConfigDefault(object): pass
+NoConfigDefault = NoConfigDefault()
 
 class ArgParseConfigLoader(CommandLineConfigLoader):
     
@@ -155,7 +272,7 @@ class ArgParseConfigLoader(CommandLineConfigLoader):
         """Parse command line arguments and return as a Struct."""
         self._create_parser()
         self._parse_args(args)
-        self._convert_to_struct()
+        self._convert_to_config()
         return self.config
 
     def _create_parser(self):
@@ -169,7 +286,7 @@ class ArgParseConfigLoader(CommandLineConfigLoader):
     def _add_arguments(self):
         for argument in self.arguments:
             if not argument[1].has_key('default'):
-                argument[1]['default'] = NoDefault
+                argument[1]['default'] = NoConfigDefault
             self.parser.add_argument(*argument[0],**argument[1])
 
     def _parse_args(self, args=None):
@@ -179,25 +296,10 @@ class ArgParseConfigLoader(CommandLineConfigLoader):
         else:
             self.parsed_data = self.parser.parse_args(args)
 
-    def _convert_to_struct(self):
+    def _convert_to_config(self):
         """self.parsed_data->self.config"""
-        self.config = Struct()
         for k, v in vars(self.parsed_data).items():
-            if v is not NoDefault:
-                setattr(self.config, k, v)
-
-class IPythonArgParseConfigLoader(ArgParseConfigLoader):
+            if v is not NoConfigDefault:
+                exec_str = 'self.config.' + k + '= v'
+                exec exec_str in locals(), globals()
 
-    def _add_other_arguments(self):
-        self.parser.add_argument('-ipythondir',dest='IPYTHONDIR',type=str,
-            help='Set to override default location of IPYTHONDIR.',
-            default=NoDefault)
-        self.parser.add_argument('-p','-profile',dest='PROFILE',type=str,
-            help='The string name of the ipython profile to be used.',
-            default=NoDefault)
-        self.parser.add_argument('-debug',dest="DEBUG",action='store_true',
-            help='Debug the application startup process.',
-            default=NoDefault)
-        self.parser.add_argument('-config_file',dest='CONFIG_FILE',type=str,
-            help='Set the config file name to override default.',
-            default=NoDefault)
diff --git a/IPython/config/tests/test_loader.py b/IPython/config/tests/test_loader.py
index 5cb71b4..23e1890 100644
--- a/IPython/config/tests/test_loader.py
+++ b/IPython/config/tests/test_loader.py
@@ -24,7 +24,12 @@ import os
 from tempfile import mkstemp
 from unittest import TestCase
 
-from IPython.config.loader import PyFileConfigLoader, ArgParseConfigLoader
+from IPython.config.loader import (
+    Config,
+    PyFileConfigLoader, 
+    ArgParseConfigLoader,
+    ConfigError
+)
 
 #-----------------------------------------------------------------------------
 # Actual tests
@@ -32,10 +37,11 @@ from IPython.config.loader import PyFileConfigLoader, ArgParseConfigLoader
 
 
 pyfile = """
-A = 10
-B = range(10)
-C = True
-D = 'hi there'
+a = 10
+b = 20
+Foo.Bar.value = 10
+Foo.Bam.value = range(10)
+D.C.value = 'hi there'
 """
 
 class TestPyFileCL(TestCase):
@@ -48,10 +54,11 @@ class TestPyFileCL(TestCase):
         # Unlink the file
         cl = PyFileConfigLoader(fname)
         config = cl.load_config()
-        self.assertEquals(config.A, 10)
-        self.assertEquals(config.B, range(10))
-        self.assertEquals(config.C, True)
-        self.assertEquals(config.D, 'hi there')
+        self.assertEquals(config.a, 10)
+        self.assertEquals(config.b, 20)
+        self.assertEquals(config.Foo.Bar.value, 10)
+        self.assertEquals(config.Foo.Bam.value, range(10))
+        self.assertEquals(config.D.C.value, 'hi there')
 
 
 class TestArgParseCL(TestCase):
@@ -60,18 +67,18 @@ class TestArgParseCL(TestCase):
 
         class MyLoader(ArgParseConfigLoader):
             arguments = (
-                (('-f','--foo'), dict(dest='FOO', type=str)),
-                (('-b',), dict(dest='BAR', type=int)),
-                (('-n',), dict(dest='N', action='store_true')),
-                (('BAM',), dict(type=str))
+                (('-f','--foo'), dict(dest='Global.foo', type=str)),
+                (('-b',), dict(dest='MyClass.bar', type=int)),
+                (('-n',), dict(dest='n', action='store_true')),
+                (('Global.bam',), dict(type=str))
             )
 
         cl = MyLoader()
         config = cl.load_config('-f hi -b 10 -n wow'.split())
-        self.assertEquals(config.FOO, 'hi')
-        self.assertEquals(config.BAR, 10)
-        self.assertEquals(config.N, True)
-        self.assertEquals(config.BAM, 'wow')
+        self.assertEquals(config.Global.foo, 'hi')
+        self.assertEquals(config.MyClass.bar, 10)
+        self.assertEquals(config.n, True)
+        self.assertEquals(config.Global.bam, 'wow')
 
     def test_add_arguments(self):
 
@@ -79,7 +86,7 @@ class TestArgParseCL(TestCase):
             def _add_arguments(self):
                 subparsers = self.parser.add_subparsers(dest='subparser_name')
                 subparser1 = subparsers.add_parser('1')
-                subparser1.add_argument('-x')
+                subparser1.add_argument('-x',dest='Global.x')
                 subparser2 = subparsers.add_parser('2')
                 subparser2.add_argument('y')
 
@@ -89,5 +96,68 @@ class TestArgParseCL(TestCase):
         self.assertEquals(config.y, 'frobble')
         config = cl.load_config('1 -x frobble'.split())
         self.assertEquals(config.subparser_name, '1')
-        self.assertEquals(config.x, 'frobble')
-
+        self.assertEquals(config.Global.x, 'frobble')
+
+class TestConfig(TestCase):
+
+    def test_setget(self):
+        c = Config()
+        c.a = 10
+        self.assertEquals(c.a, 10)
+        self.assertEquals(c.has_key('b'), False)
+
+    def test_auto_section(self):
+        c = Config()
+        self.assertEquals(c.has_key('A'), True)
+        self.assertEquals(c._has_section('A'), False)
+        A = c.A
+        A.foo = 'hi there'
+        self.assertEquals(c._has_section('A'), True)
+        self.assertEquals(c.A.foo, 'hi there')
+        del c.A
+        self.assertEquals(len(c.A.keys()),0)
+
+    def test_merge_doesnt_exist(self):
+        c1 = Config()
+        c2 = Config()
+        c2.bar = 10
+        c2.Foo.bar = 10
+        c1._merge(c2)
+        self.assertEquals(c1.Foo.bar, 10)
+        self.assertEquals(c1.bar, 10)
+        c2.Bar.bar = 10
+        c1._merge(c2)
+        self.assertEquals(c1.Bar.bar, 10)
+
+    def test_merge_exists(self):
+        c1 = Config()
+        c2 = Config()
+        c1.Foo.bar = 10
+        c1.Foo.bam = 30
+        c2.Foo.bar = 20
+        c2.Foo.wow = 40
+        c1._merge(c2)
+        self.assertEquals(c1.Foo.bam, 30)
+        self.assertEquals(c1.Foo.bar, 20)
+        self.assertEquals(c1.Foo.wow, 40)
+        c2.Foo.Bam.bam = 10
+        c1._merge(c2)
+        self.assertEquals(c1.Foo.Bam.bam, 10)
+
+    def test_deepcopy(self):
+        c1 = Config()
+        c1.Foo.bar = 10
+        c1.Foo.bam = 30
+        c1.a = 'asdf'
+        c1.b = range(10)
+        import copy
+        c2 = copy.deepcopy(c1)
+        self.assertEquals(c1, c2)
+        self.assert_(c1 is not c2)
+        self.assert_(c1.Foo is not c2.Foo)
+
+    def test_builtin(self):
+        c1 = Config()
+        exec 'foo = True' in c1
+        self.assertEquals(c1.foo, True)
+        self.assertRaises(ConfigError, setattr, c1, 'ValueError', 10)
diff --git a/IPython/core/alias.py b/IPython/core/alias.py
index a2b8bbf..60cabc1 100644
--- a/IPython/core/alias.py
+++ b/IPython/core/alias.py
@@ -43,7 +43,7 @@ def default_aliases():
     # Make some aliases automatically
     # Prepare list of shell aliases to auto-define
     if os.name == 'posix':
-        auto_alias = ('mkdir mkdir', 'rmdir rmdir',
+        default_aliases = ('mkdir mkdir', 'rmdir rmdir',
                       'mv mv -i','rm rm -i','cp cp -i',
                       'cat cat','less less','clear clear',
                       # a better ls
@@ -75,15 +75,15 @@ def default_aliases():
                          # things which are executable
                          'lx ls -lF | grep ^-..x',
                          )
-        auto_alias = auto_alias + ls_extra
+        default_aliases = default_aliases + ls_extra
     elif os.name in ['nt','dos']:
-        auto_alias = ('ls dir /on',
+        default_aliases = ('ls dir /on',
                       'ddir dir /ad /on', 'ldir dir /ad /on',
                       'mkdir mkdir','rmdir rmdir','echo echo',
                       'ren ren','cls cls','copy copy')
     else:
-        auto_alias = ()
-    return [s.split(None,1) for s in auto_alias]
+        default_aliases = ()
+    return [s.split(None,1) for s in default_aliases]
 
 
 class AliasError(Exception):
@@ -101,8 +101,8 @@ class InvalidAliasError(AliasError):
 
 class AliasManager(Component):
 
-    auto_alias = List(default_aliases())
-    user_alias = List(default_value=[], config_key='USER_ALIAS')
+    default_aliases = List(default_aliases(), config=True)
+    user_aliases = List(default_value=[], config=True)
 
     def __init__(self, parent, config=None):
         super(AliasManager, self).__init__(parent, config=config)
@@ -137,13 +137,16 @@ class AliasManager(Component):
 
     def init_aliases(self):
         # Load default aliases
-        for name, cmd in self.auto_alias:
+        for name, cmd in self.default_aliases:
             self.soft_define_alias(name, cmd)
 
         # Load user aliases
-        for name, cmd in self.user_alias:
+        for name, cmd in self.user_aliases:
             self.soft_define_alias(name, cmd)
 
+    def clear_aliases(self):
+        self.alias_table.clear()
+
     def soft_define_alias(self, name, cmd):
         """Define an alias, but don't raise on an AliasError."""
         try:
@@ -160,6 +163,10 @@ class AliasManager(Component):
         nargs = self.validate_alias(name, cmd)
         self.alias_table[name] = (nargs, cmd)
 
+    def undefine_alias(self, name):
+        if self.alias_table.has_key(name):
+            del self.alias_table[name]
+
     def validate_alias(self, name, cmd):
         """Validate an alias and return the its number of arguments."""
         if name in self.no_alias:
diff --git a/IPython/core/application.py b/IPython/core/application.py
index 9378f9e..882064b 100644
--- a/IPython/core/application.py
+++ b/IPython/core/application.py
@@ -26,13 +26,14 @@ Notes
 import os
 import sys
 import traceback
-
 from copy import deepcopy
-from IPython.utils.ipstruct import Struct
+
 from IPython.utils.genutils import get_ipython_dir, filefind
 from IPython.config.loader import (
-    IPythonArgParseConfigLoader,
-    PyFileConfigLoader
+    PyFileConfigLoader,
+    ArgParseConfigLoader,
+    Config,
+    NoConfigDefault
 )
 
 #-----------------------------------------------------------------------------
@@ -40,6 +41,27 @@ from IPython.config.loader import (
 #-----------------------------------------------------------------------------
 
 
+class IPythonArgParseConfigLoader(ArgParseConfigLoader):
+    """Default command line options for IPython based applications."""
+
+    def _add_other_arguments(self):
+        self.parser.add_argument('-ipythondir',dest='Global.ipythondir',type=str,
+            help='Set to override default location of Global.ipythondir.',
+            default=NoConfigDefault,
+            metavar='Global.ipythondir')
+        self.parser.add_argument('-p','-profile',dest='Global.profile',type=str,
+            help='The string name of the ipython profile to be used.',
+            default=NoConfigDefault,
+            metavar='Global.profile')
+        self.parser.add_argument('-debug',dest="Global.debug",action='store_true',
+            help='Debug the application startup process.',
+            default=NoConfigDefault)
+        self.parser.add_argument('-config_file',dest='Global.config_file',type=str,
+            help='Set the config file name to override default.',
+            default=NoConfigDefault,
+            metavar='Global.config_file')
+
+
 class ApplicationError(Exception):
     pass
 
@@ -79,8 +101,8 @@ class Application(object):
 
     def create_default_config(self):
         """Create defaults that can't be set elsewhere."""
-        self.default_config = Struct()
-        self.default_config.IPYTHONDIR = get_ipython_dir()
+        self.default_config = Config()
+        self.default_config.Global.ipythondir = get_ipython_dir()
 
     def create_command_line_config(self):
         """Create and return a command line config loader."""
@@ -99,7 +121,7 @@ class Application(object):
         loader = self.create_command_line_config()
         self.command_line_config = loader.load_config()
         try:
-            self.debug = self.command_line_config.DEBUG
+            self.debug = self.command_line_config.Global.debug
         except AttributeError:
             pass # use class default
         self.log("Default config loaded:", self.default_config)
@@ -120,9 +142,9 @@ class Application(object):
         """
 
         try:
-            self.ipythondir = self.command_line_config.IPYTHONDIR
+            self.ipythondir = self.command_line_config.Global.ipythondir
         except AttributeError:
-            self.ipythondir = self.default_config.IPYTHONDIR
+            self.ipythondir = self.default_config.Global.ipythondir
         sys.path.append(os.path.abspath(self.ipythondir))
         if not os.path.isdir(self.ipythondir):
             os.makedirs(self.ipythondir, mode = 0777)
@@ -138,12 +160,12 @@ class Application(object):
         """
 
         try:
-            self.config_file_name = self.command_line_config.CONFIG_FILE
+            self.config_file_name = self.command_line_config.Global.config_file
         except AttributeError:
             pass
 
         try:
-            self.profile_name = self.command_line_config.PROFILE
+            self.profile_name = self.command_line_config.Global.profile
             name_parts = self.config_file_name.split('.')
             name_parts.insert(1, '_' + self.profile_name + '.')
             self.config_file_name = ''.join(name_parts)
@@ -165,15 +187,15 @@ class Application(object):
         ``CONFIG_FILE`` config variable is set to the resolved config file
         location.  If not successful, an empty config is used.
         """
-        loader = PyFileConfigLoader(self.config_file_name, 
-                                    self.config_file_paths)
+        loader = PyFileConfigLoader(self.config_file_name,
+                                    path=self.config_file_paths)
         try:
             self.file_config = loader.load_config()
-            self.file_config.CONFIG_FILE = loader.full_filename
+            self.file_config.Global.config_file = loader.full_filename
         except IOError:
             self.log("Config file not found, skipping: %s" % \
                      self.config_file_name)
-            self.file_config = Struct()
+            self.file_config = Config()
         else:
             self.log("Config file loaded: %s" % loader.full_filename,
                      self.file_config)
@@ -184,10 +206,10 @@ class Application(object):
 
     def merge_configs(self):
         """Merge the default, command line and file config objects."""
-        config = Struct()
-        config.update(self.default_config)
-        config.update(self.file_config)
-        config.update(self.command_line_config)
+        config = Config()
+        config._merge(self.default_config)
+        config._merge(self.file_config)
+        config._merge(self.command_line_config)
         self.master_config = config
         self.log("Master config created:", self.master_config)
 
@@ -223,12 +245,13 @@ class Application(object):
     def attempt(self, func, action='abort'):
         try:
             func()
+        except SystemExit:
+            self.exit()
         except:
             if action == 'abort':
                 self.print_traceback()
                 self.abort()
             elif action == 'exit':
-                self.print_traceback()
                 self.exit()
 
     def print_traceback(self):
diff --git a/IPython/core/builtin_trap.py b/IPython/core/builtin_trap.py
index 106f566..a05fc49 100644
--- a/IPython/core/builtin_trap.py
+++ b/IPython/core/builtin_trap.py
@@ -40,6 +40,9 @@ class BuiltinTrap(Component):
     def __init__(self, parent):
         super(BuiltinTrap, self).__init__(parent, None, None)
         self._orig_builtins = {}
+        # We define this to track if a single BuiltinTrap is nested.
+        # Only turn off the trap when the outermost call to __exit__ is made.
+        self._nested_level = 0
 
     @auto_attr
     def shell(self):
@@ -50,12 +53,16 @@ class BuiltinTrap(Component):
         return shell
 
     def __enter__(self):
-        self.set()
+        if self._nested_level == 0:
+            self.set()
+        self._nested_level += 1
         # I return self, so callers can use add_builtin in a with clause.
         return self
 
     def __exit__(self, type, value, traceback):
-        self.unset()
+        if self._nested_level == 1:
+            self.unset()
+        self._nested_level -= 1
         return True
 
     def add_builtin(self, key, value):
@@ -108,4 +115,4 @@ class BuiltinTrap(Component):
         try:
             del __builtin__.__dict__['__IPYTHON__active']
         except KeyError:
-            pass
\ No newline at end of file
+            pass
diff --git a/IPython/core/component.py b/IPython/core/component.py
index 176dcd4..04b70a0 100644
--- a/IPython/core/component.py
+++ b/IPython/core/component.py
@@ -25,7 +25,7 @@ import datetime
 from weakref import WeakValueDictionary
 
 from IPython.utils.importstring import import_item
-from IPython.utils.ipstruct import Struct
+from IPython.config.loader import Config
 from IPython.utils.traitlets import (
     HasTraitlets, TraitletError, MetaHasTraitlets, Instance, This
 )
@@ -187,7 +187,7 @@ class Component(HasTraitlets):
     __metaclass__ = MetaComponent
 
     # Traitlets are fun!
-    config = Instance(Struct,(),{})
+    config = Instance(Config,(),{})
     parent = This()
     root = This()
     created = None
@@ -203,7 +203,7 @@ class Component(HasTraitlets):
         name : str
             The unique name of the component.  If empty, then a unique
             one will be autogenerated.
-        config : Struct
+        config : Config
             If this is empty, self.config = parent.config, otherwise
             self.config = config and root.config is ignored.  This argument
             should only be used to *override* the automatic inheritance of 
@@ -232,7 +232,7 @@ class Component(HasTraitlets):
         else:
             self.name = name
         self.root = self # This is the default, it is set when parent is set
-        self.parent = parent     
+        self.parent = parent
         if config is not None:
             self.config = deepcopy(config)
         else:
@@ -274,15 +274,20 @@ class Component(HasTraitlets):
         In the future, we might want to do a pop here so stale config info
         is not passed onto children.
         """
-        # Get all traitlets with a config_key metadata entry
-        traitlets = self.traitlets('config_key')
-        for k, v in traitlets.items():
-            try:
-                config_value = new[v.get_metadata('config_key')]
-            except KeyError:
-                pass
-            else:
-                setattr(self, k, config_value)
+        # Get all traitlets with a config metadata entry that is True
+        traitlets = self.traitlets(config=True)
+
+        # Don't do a blind getattr as that would cause the config to 
+        # dynamically create the section with name self.__class__.__name__.
+        if new._has_section(self.__class__.__name__):
+            my_config = new[self.__class__.__name__]
+            for k, v in traitlets.items():
+                try:
+                    config_value = my_config[k]
+                except KeyError:
+                    pass
+                else:
+                    setattr(self, k, config_value)
 
     @property
     def children(self):
diff --git a/IPython/core/display_trap.py b/IPython/core/display_trap.py
index 89252a2..ff41a81 100644
--- a/IPython/core/display_trap.py
+++ b/IPython/core/display_trap.py
@@ -40,9 +40,11 @@ class DisplayTrap(Component):
 
     def __init__(self, parent, hook):
         super(DisplayTrap, self).__init__(parent, None, None)
-
         self.hook = hook
         self.old_hook = None
+        # We define this to track if a single BuiltinTrap is nested.
+        # Only turn off the trap when the outermost call to __exit__ is made.
+        self._nested_level = 0
 
     @auto_attr
     def shell(self):
@@ -53,11 +55,15 @@ class DisplayTrap(Component):
         return shell
 
     def __enter__(self):
-        self.set()
+        if self._nested_level == 0:
+            self.set()
+        self._nested_level += 1
         return self
 
     def __exit__(self, type, value, traceback):
-        self.unset()
+        if self._nested_level == 1:
+            self.unset()
+        self._nested_level -= 1
         return True
 
     def set(self):
diff --git a/IPython/core/embed.py b/IPython/core/embed.py
index bb34f8e..bed686e 100644
--- a/IPython/core/embed.py
+++ b/IPython/core/embed.py
@@ -30,10 +30,12 @@ from contextlib import nested
 
 from IPython.core import ultratb
 from IPython.core.iplib import InteractiveShell
+from IPython.core.ipapp import load_default_config
 
 from IPython.utils.traitlets import Bool, Str, CBool
 from IPython.utils.genutils import ask_yes_no
 
+
 #-----------------------------------------------------------------------------
 # Classes and functions
 #-----------------------------------------------------------------------------
@@ -260,6 +262,8 @@ def embed(header='', config=None, usage=None, banner1=None, banner2=None,
     Full customization can be done by passing a :class:`Struct` in as the 
     config argument.
     """
+    if config is None:
+        config = load_default_config()
     global _embedded_shell
     if _embedded_shell is None:
         _embedded_shell = InteractiveShellEmbed(config=config,
diff --git a/IPython/core/ipapp.py b/IPython/core/ipapp.py
index 6988fb1..2c4ace6 100644
--- a/IPython/core/ipapp.py
+++ b/IPython/core/ipapp.py
@@ -27,13 +27,17 @@ import os
 import sys
 import warnings
 
-from IPython.core.application import Application
+from IPython.core.application import Application, IPythonArgParseConfigLoader
 from IPython.core import release
 from IPython.core.iplib import InteractiveShell
-from IPython.config.loader import IPythonArgParseConfigLoader, NoDefault
+from IPython.config.loader import (
+    NoConfigDefault, 
+    Config,
+    PyFileConfigLoader
+)
 
 from IPython.utils.ipstruct import Struct
-
+from IPython.utils.genutils import get_ipython_dir
 
 #-----------------------------------------------------------------------------
 # Utilities and helpers
@@ -62,172 +66,187 @@ deprecated.  See the %gui magic for information on the new interface.
 
 cl_args = (
     (('-autocall',), dict(
-        type=int, dest='AUTOCALL', default=NoDefault,
-        help='Set the autocall value (0,1,2).')
+        type=int, dest='InteractiveShell.autocall', default=NoConfigDefault,
+        help='Set the autocall value (0,1,2).',
+        metavar='InteractiveShell.autocall')
     ),
     (('-autoindent',), dict(
-        action='store_true', dest='AUTOINDENT', default=NoDefault,
+        action='store_true', dest='InteractiveShell.autoindent', default=NoConfigDefault,
         help='Turn on autoindenting.')
     ),
     (('-noautoindent',), dict(
-        action='store_false', dest='AUTOINDENT', default=NoDefault,
+        action='store_false', dest='InteractiveShell.autoindent', default=NoConfigDefault,
         help='Turn off autoindenting.')
     ),
     (('-automagic',), dict(
-        action='store_true', dest='AUTOMAGIC', default=NoDefault,
+        action='store_true', dest='InteractiveShell.automagic', default=NoConfigDefault,
         help='Turn on the auto calling of magic commands.')
     ),
     (('-noautomagic',), dict(
-        action='store_false', dest='AUTOMAGIC', default=NoDefault,
+        action='store_false', dest='InteractiveShell.automagic', default=NoConfigDefault,
         help='Turn off the auto calling of magic commands.')
     ),
     (('-autoedit_syntax',), dict(
-        action='store_true', dest='AUTOEDIT_SYNTAX', default=NoDefault,
+        action='store_true', dest='InteractiveShell.autoedit_syntax', default=NoConfigDefault,
         help='Turn on auto editing of files with syntax errors.')
     ),
     (('-noautoedit_syntax',), dict(
-        action='store_false', dest='AUTOEDIT_SYNTAX', default=NoDefault,
+        action='store_false', dest='InteractiveShell.autoedit_syntax', default=NoConfigDefault,
         help='Turn off auto editing of files with syntax errors.')
     ),
     (('-banner',), dict(
-        action='store_true', dest='DISPLAY_BANNER', default=NoDefault,
+        action='store_true', dest='InteractiveShell.display_banner', default=NoConfigDefault,
         help='Display a banner upon starting IPython.')
     ),
     (('-nobanner',), dict(
-        action='store_false', dest='DISPLAY_BANNER', default=NoDefault,
+        action='store_false', dest='InteractiveShell.display_banner', default=NoConfigDefault,
         help="Don't display a banner upon starting IPython.")
     ),
     (('-c',), dict(
-        type=str, dest='C', default=NoDefault,
-        help="Execute  the  given  command  string.")
+        type=str, dest='InteractiveShell.c', default=NoConfigDefault,
+        help="Execute the given command string.",
+        metavar='InteractiveShell.c')
     ),
     (('-cache_size',), dict(
-        type=int, dest='CACHE_SIZE', default=NoDefault,
-        help="Set the size of the output cache.")
+        type=int, dest='InteractiveShell.cache_size', default=NoConfigDefault,
+        help="Set the size of the output cache.",
+        metavar='InteractiveShell.cache_size')
     ),
     (('-classic',), dict(
-        action='store_true', dest='CLASSIC', default=NoDefault,
+        action='store_true', dest='Global.classic', default=NoConfigDefault,
         help="Gives IPython a similar feel to the classic Python prompt.")
     ),
     (('-colors',), dict(
-        type=str, dest='COLORS', default=NoDefault,
-        help="Set the color scheme (NoColor, Linux, and LightBG).")
+        type=str, dest='InteractiveShell.colors', default=NoConfigDefault,
+        help="Set the color scheme (NoColor, Linux, and LightBG).",
+        metavar='InteractiveShell.colors')
     ),
     (('-color_info',), dict(
-        action='store_true', dest='COLOR_INFO', default=NoDefault,
+        action='store_true', dest='InteractiveShell.color_info', default=NoConfigDefault,
         help="Enable using colors for info related things.")
     ),
     (('-nocolor_info',), dict(
-        action='store_false', dest='COLOR_INFO', default=NoDefault,
+        action='store_false', dest='InteractiveShell.color_info', default=NoConfigDefault,
         help="Disable using colors for info related things.")
     ),
     (('-confirm_exit',), dict(
-        action='store_true', dest='CONFIRM_EXIT', default=NoDefault,
+        action='store_true', dest='InteractiveShell.confirm_exit', default=NoConfigDefault,
         help="Prompt the user when existing.")
     ),
     (('-noconfirm_exit',), dict(
-        action='store_false', dest='CONFIRM_EXIT', default=NoDefault,
+        action='store_false', dest='InteractiveShell.confirm_exit', default=NoConfigDefault,
         help="Don't prompt the user when existing.")
     ),
     (('-deep_reload',), dict(
-        action='store_true', dest='DEEP_RELOAD', default=NoDefault,
+        action='store_true', dest='InteractiveShell.deep_reload', default=NoConfigDefault,
         help="Enable deep (recursive) reloading by default.")
     ),
     (('-nodeep_reload',), dict(
-        action='store_false', dest='DEEP_RELOAD', default=NoDefault,
+        action='store_false', dest='InteractiveShell.deep_reload', default=NoConfigDefault,
         help="Disable deep (recursive) reloading by default.")
     ),
     (('-editor',), dict(
-        type=str, dest='EDITOR', default=NoDefault,
-        help="Set the editor used by IPython (default to $EDITOR/vi/notepad).")
+        type=str, dest='InteractiveShell.editor', default=NoConfigDefault,
+        help="Set the editor used by IPython (default to $EDITOR/vi/notepad).",
+        metavar='InteractiveShell.editor')
     ),
     (('-log','-l'), dict(
-        action='store_true', dest='LOGSTART', default=NoDefault,
+        action='store_true', dest='InteractiveShell.logstart', default=NoConfigDefault,
         help="Start logging to the default file (./ipython_log.py).")
     ),
     (('-logfile','-lf'), dict(
-        type=str, dest='LOGFILE', default=NoDefault,
-        help="Specify the name of your logfile.")
+        type=str, dest='InteractiveShell.logfile', default=NoConfigDefault,
+        help="Specify the name of your logfile.",
+        metavar='InteractiveShell.logfile')
     ),
     (('-logplay','-lp'), dict(
-        type=str, dest='LOGPLAY', default=NoDefault,
-        help="Re-play a log file and then append to it.")
+        type=str, dest='InteractiveShell.logplay', default=NoConfigDefault,
+        help="Re-play a log file and then append to it.",
+        metavar='InteractiveShell.logplay')
     ),
     (('-pdb',), dict(
-        action='store_true', dest='PDB', default=NoDefault,
+        action='store_true', dest='InteractiveShell.pdb', default=NoConfigDefault,
         help="Enable auto calling the pdb debugger after every exception.")
     ),
     (('-nopdb',), dict(
-        action='store_false', dest='PDB', default=NoDefault,
+        action='store_false', dest='InteractiveShell.pdb', default=NoConfigDefault,
         help="Disable auto calling the pdb debugger after every exception.")
     ),
     (('-pprint',), dict(
-        action='store_true', dest='PPRINT', default=NoDefault,
+        action='store_true', dest='InteractiveShell.pprint', default=NoConfigDefault,
         help="Enable auto pretty printing of results.")
     ),
     (('-nopprint',), dict(
-        action='store_false', dest='PPRINT', default=NoDefault,
+        action='store_false', dest='InteractiveShell.pprint', default=NoConfigDefault,
         help="Disable auto auto pretty printing of results.")
     ),
     (('-prompt_in1','-pi1'), dict(
-        type=str, dest='PROMPT_IN1', default=NoDefault,
-        help="Set the main input prompt ('In [\#]: ')")
+        type=str, dest='InteractiveShell.prompt_in1', default=NoConfigDefault,
+        help="Set the main input prompt ('In [\#]: ')",
+        metavar='InteractiveShell.prompt_in1')
     ),
     (('-prompt_in2','-pi2'), dict(
-        type=str, dest='PROMPT_IN2', default=NoDefault,
-        help="Set the secondary input prompt (' .\D.: ')")
+        type=str, dest='InteractiveShell.prompt_in2', default=NoConfigDefault,
+        help="Set the secondary input prompt (' .\D.: ')",
+        metavar='InteractiveShell.prompt_in2')
     ),
     (('-prompt_out','-po'), dict(
-        type=str, dest='PROMPT_OUT', default=NoDefault,
-        help="Set the output prompt ('Out[\#]:')")
+        type=str, dest='InteractiveShell.prompt_out', default=NoConfigDefault,
+        help="Set the output prompt ('Out[\#]:')",
+        metavar='InteractiveShell.prompt_out')
     ),
     (('-quick',), dict(
-        action='store_true', dest='QUICK', default=NoDefault,
+        action='store_true', dest='Global.quick', default=NoConfigDefault,
         help="Enable quick startup with no config files.")
     ),
     (('-readline',), dict(
-        action='store_true', dest='READLINE_USE', default=NoDefault,
+        action='store_true', dest='InteractiveShell.readline_use', default=NoConfigDefault,
         help="Enable readline for command line usage.")
     ),
     (('-noreadline',), dict(
-        action='store_false', dest='READLINE_USE', default=NoDefault,
+        action='store_false', dest='InteractiveShell.readline_use', default=NoConfigDefault,
         help="Disable readline for command line usage.")
     ),
     (('-screen_length','-sl'), dict(
-        type=int, dest='SCREEN_LENGTH', default=NoDefault,
-        help='Number of lines on screen, used to control printing of long strings.')
+        type=int, dest='InteractiveShell.screen_length', default=NoConfigDefault,
+        help='Number of lines on screen, used to control printing of long strings.',
+        metavar='InteractiveShell.screen_length')
     ),
     (('-separate_in','-si'), dict(
-        type=str, dest='SEPARATE_IN', default=NoDefault,
-        help="Separator before input prompts.  Default '\n'.")
+        type=str, dest='InteractiveShell.separate_in', default=NoConfigDefault,
+        help="Separator before input prompts.  Default '\n'.",
+        metavar='InteractiveShell.separate_in')
     ),
     (('-separate_out','-so'), dict(
-        type=str, dest='SEPARATE_OUT', default=NoDefault,
-        help="Separator before output prompts.  Default 0 (nothing).")
+        type=str, dest='InteractiveShell.separate_out', default=NoConfigDefault,
+        help="Separator before output prompts.  Default 0 (nothing).",
+        metavar='InteractiveShell.separate_out')
     ),
     (('-separate_out2','-so2'), dict(
-        type=str, dest='SEPARATE_OUT2', default=NoDefault,
-        help="Separator after output prompts.  Default 0 (nonight).")
+        type=str, dest='InteractiveShell.separate_out2', default=NoConfigDefault,
+        help="Separator after output prompts.  Default 0 (nonight).",
+        metavar='InteractiveShell.separate_out2')
     ),
     (('-nosep',), dict(
-        action='store_true', dest='NOSEP', default=NoDefault,
+        action='store_true', dest='Global.nosep', default=NoConfigDefault,
         help="Eliminate all spacing between prompts.")
     ),
     (('-term_title',), dict(
-        action='store_true', dest='TERM_TITLE', default=NoDefault,
+        action='store_true', dest='InteractiveShell.term_title', default=NoConfigDefault,
         help="Enable auto setting the terminal title.")
     ),
     (('-noterm_title',), dict(
-        action='store_false', dest='TERM_TITLE', default=NoDefault,
+        action='store_false', dest='InteractiveShell.term_title', default=NoConfigDefault,
         help="Disable auto setting the terminal title.")
     ),
     (('-xmode',), dict(
-        type=str, dest='XMODE', default=NoDefault,
-        help="Exception mode ('Plain','Context','Verbose')")
+        type=str, dest='InteractiveShell.xmode', default=NoConfigDefault,
+        help="Exception mode ('Plain','Context','Verbose')",
+        metavar='InteractiveShell.xmode')
     ),
     # These are only here to get the proper deprecation warnings
     (('-pylab','-wthread','-qthread','-q4thread','-gthread'), dict(
-        action='store_true', dest='THREADED_SHELL', default=NoDefault,
+        action='store_true', dest='Global.threaded_shell', default=NoConfigDefault,
         help="These command line flags are deprecated, see the 'gui' magic.")
     ),
 )
@@ -238,9 +257,11 @@ class IPythonAppCLConfigLoader(IPythonArgParseConfigLoader):
     arguments = cl_args
 
 
+_default_config_file_name = 'ipython_config.py'
+
 class IPythonApp(Application):
     name = 'ipython'
-    config_file_name = 'ipython_config.py'
+    config_file_name = _default_config_file_name
 
     def create_command_line_config(self):
         """Create and return a command line config loader."""
@@ -252,19 +273,15 @@ class IPythonApp(Application):
         """Do actions after loading cl config."""
         clc = self.command_line_config
 
-        # This needs to be set here, the rest are set in pre_construct.
-        if hasattr(clc, 'CLASSIC'):
-            if clc.CLASSIC: clc.QUICK = 1
-
         # Display the deprecation warnings about threaded shells
-        if hasattr(clc, 'THREADED_SHELL'):
+        if hasattr(clc.Global, 'threaded_shell'):
             threaded_shell_warning()
-            del clc['THREADED_SHELL']
+            del clc.Global['threaded_shell']
 
     def load_file_config(self):
-        if hasattr(self.command_line_config, 'QUICK'):
-            if self.command_line_config.QUICK:
-                self.file_config = Struct()
+        if hasattr(self.command_line_config.Global, 'quick'):
+            if self.command_line_config.Global.quick:
+                self.file_config = Config()
                 return
         super(IPythonApp, self).load_file_config()
 
@@ -274,25 +291,28 @@ class IPythonApp(Application):
     def pre_construct(self):
         config = self.master_config
 
-        if hasattr(config, 'CLASSIC'):
-            if config.CLASSIC:
-                config.QUICK = 1
-                config.CACHE_SIZE = 0
-                config.PPRINT = 0
-                config.PROMPT_IN1 = '>>> '
-                config.PROMPT_IN2 = '... '
-                config.PROMPT_OUT = ''
-                config.SEPARATE_IN = config.SEPARATE_OUT = config.SEPARATE_OUT2 = ''
-                config.COLORS = 'NoColor'
-                config.XMODE = 'Plain'
+        if hasattr(config.Global, 'classic'):
+            if config.Global.classic:
+                config.InteractiveShell.cache_size = 0
+                config.InteractiveShell.pprint = 0
+                config.InteractiveShell.prompt_in1 = '>>> '
+                config.InteractiveShell.prompt_in2 = '... '
+                config.InteractiveShell.prompt_out = ''
+                config.InteractiveShell.separate_in = \
+                    config.InteractiveShell.separate_out = \
+                    config.InteractiveShell.separate_out2 = ''
+                config.InteractiveShell.colors = 'NoColor'
+                config.InteractiveShell.xmode = 'Plain'
 
         # All this should be moved to traitlet handlers in InteractiveShell
         # But, currently InteractiveShell doesn't have support for changing
         # these values at runtime.  Once we support that, this should
         # be moved there!!!
-        if hasattr(config, 'NOSEP'):
-            if config.NOSEP:
-                config.SEPARATE_IN = config.SEPARATE_OUT = config.SEPARATE_OUT2 = '0'
+        if hasattr(config.Global, 'nosep'):
+            if config.Global.nosep:
+                config.InteractiveShell.separate_in = \
+                config.InteractiveShell.separate_out = \
+                config.InteractiveShell.separate_out2 = '0'
 
     def construct(self):
         # I am a little hesitant to put these into InteractiveShell itself.
@@ -307,12 +327,23 @@ class IPythonApp(Application):
             parent=None,
             config=self.master_config
         )
-        print self.shell
     
     def start_app(self):
         self.shell.mainloop()
 
 
+def load_default_config(ipythondir=None):
+    """Load the default config file from the default ipythondir.
+
+    This is useful for embedded shells.
+    """
+    if ipythondir is None:
+        ipythondir = get_ipython_dir()
+    cl = PyFileConfigLoader(_default_config_file_name, ipythondir)
+    config = cl.load_config()
+    return config
+
+
 if __name__ == '__main__':
     app = IPythonApp()
     app.start()
\ No newline at end of file
diff --git a/IPython/core/iplib.py b/IPython/core/iplib.py
index d39c09d..200acfb 100644
--- a/IPython/core/iplib.py
+++ b/IPython/core/iplib.py
@@ -62,6 +62,7 @@ from IPython.lib.backgroundjobs import BackgroundJobManager
 from IPython.utils.ipstruct import Struct
 from IPython.utils import PyColorize
 from IPython.utils.genutils import *
+from IPython.utils.genutils import get_ipython_dir
 from IPython.utils.strdispatch import StrDispatch
 from IPython.utils.platutils import toggle_set_term_title, set_term_title
 
@@ -188,50 +189,47 @@ class SeparateStr(Str):
 class InteractiveShell(Component, Magic):
     """An enhanced, interactive shell for Python."""
 
-    autocall = Enum((0,1,2), config_key='AUTOCALL')
-    autoedit_syntax = CBool(False, config_key='AUTOEDIT_SYNTAX')
-    autoindent = CBool(True, config_key='AUTOINDENT')
-    automagic = CBool(True, config_key='AUTOMAGIC')
-    display_banner = CBool(True, config_key='DISPLAY_BANNER')
+    autocall = Enum((0,1,2), config=True)
+    autoedit_syntax = CBool(False, config=True)
+    autoindent = CBool(True, config=True)
+    automagic = CBool(True, config=True)
+    display_banner = CBool(True, config=True)
     banner = Str('')
-    banner1 = Str(default_banner, config_key='BANNER1')
-    banner2 = Str('', config_key='BANNER2')
-    c = Str('', config_key='C')
-    cache_size = Int(1000, config_key='CACHE_SIZE')
-    classic = CBool(False, config_key='CLASSIC')
-    color_info = CBool(True, config_key='COLOR_INFO')
+    banner1 = Str(default_banner, config=True)
+    banner2 = Str('', config=True)
+    c = Str('', config=True)
+    cache_size = Int(1000, config=True)
+    color_info = CBool(True, config=True)
     colors = CaselessStrEnum(('NoColor','LightBG','Linux'), 
-                             default_value='LightBG', config_key='COLORS')
-    confirm_exit = CBool(True, config_key='CONFIRM_EXIT')
-    debug = CBool(False, config_key='DEBUG')
-    deep_reload = CBool(False, config_key='DEEP_RELOAD')
+                             default_value='LightBG', config=True)
+    confirm_exit = CBool(True, config=True)
+    debug = CBool(False, config=True)
+    deep_reload = CBool(False, config=True)
     embedded = CBool(False)
     embedded_active = CBool(False)
-    editor = Str(get_default_editor(), config_key='EDITOR')
+    editor = Str(get_default_editor(), config=True)
     filename = Str("<ipython console>")
-    interactive = CBool(False, config_key='INTERACTIVE')
-    ipythondir= Unicode('', config_key='IPYTHONDIR') # Set to os.getcwd() in __init__
-    logstart = CBool(False, config_key='LOGSTART')
-    logfile = Str('', config_key='LOGFILE')
-    logplay = Str('', config_key='LOGPLAY')
+    interactive = CBool(False, config=True)
+    ipythondir= Unicode('', config=True) # Set to get_ipython_dir() in __init__
+    logstart = CBool(False, config=True)
+    logfile = Str('', config=True)
+    logplay = Str('', config=True)
     object_info_string_level = Enum((0,1,2), default_value=0,
-                                    config_keys='OBJECT_INFO_STRING_LEVEL')
-    pager = Str('less', config_key='PAGER')
-    pdb = CBool(False, config_key='PDB')
-    pprint = CBool(True, config_key='PPRINT')
-    profile = Str('', config_key='PROFILE')
-    prompt_in1 = Str('In [\\#]: ', config_key='PROMPT_IN1')
-    prompt_in2 = Str('   .\\D.: ', config_key='PROMPT_IN2')
-    prompt_out = Str('Out[\\#]: ', config_key='PROMPT_OUT1')
-    prompts_pad_left = CBool(True, config_key='PROMPTS_PAD_LEFT')
-    quiet = CBool(False, config_key='QUIET')
-
-    readline_use = CBool(True, config_key='READLINE_USE')
-    readline_merge_completions = CBool(True, 
-                                       config_key='READLINE_MERGE_COMPLETIONS')
-    readline_omit__names = Enum((0,1,2), default_value=0, 
-                                config_key='READLINE_OMIT_NAMES')
-    readline_remove_delims = Str('-/~', config_key='READLINE_REMOVE_DELIMS')
+                                    config=True)
+    pager = Str('less', config=True)
+    pdb = CBool(False, config=True)
+    pprint = CBool(True, config=True)
+    profile = Str('', config=True)
+    prompt_in1 = Str('In [\\#]: ', config=True)
+    prompt_in2 = Str('   .\\D.: ', config=True)
+    prompt_out = Str('Out[\\#]: ', config=True)
+    prompts_pad_left = CBool(True, config=True)
+    quiet = CBool(False, config=True)
+
+    readline_use = CBool(True, config=True)
+    readline_merge_completions = CBool(True, config=True)
+    readline_omit__names = Enum((0,1,2), default_value=0, config=True)
+    readline_remove_delims = Str('-/~', config=True)
     readline_parse_and_bind = List([
             'tab: complete',
             '"\C-l": possible-completions',
@@ -248,24 +246,22 @@ class InteractiveShell(Component, Magic):
             '"\e[B": history-search-forward',
             '"\C-k": kill-line',
             '"\C-u": unix-line-discard',
-        ], allow_none=False, config_key='READLINE_PARSE_AND_BIND'
-    )
+        ], allow_none=False, config=True)
 
-    screen_length = Int(0, config_key='SCREEN_LENGTH')
+    screen_length = Int(0, config=True)
     
     # Use custom TraitletTypes that convert '0'->'' and '\\n'->'\n'
-    separate_in = SeparateStr('\n', config_key='SEPARATE_IN')
-    separate_out = SeparateStr('', config_key='SEPARATE_OUT')
-    separate_out2 = SeparateStr('', config_key='SEPARATE_OUT2')
-
-    system_header = Str('IPython system call: ', config_key='SYSTEM_HEADER')
-    system_verbose = CBool(False, config_key='SYSTEM_VERBOSE')
-    term_title = CBool(False, config_key='TERM_TITLE')
-    wildcards_case_sensitive = CBool(True, config_key='WILDCARDS_CASE_SENSITIVE')
+    separate_in = SeparateStr('\n', config=True)
+    separate_out = SeparateStr('', config=True)
+    separate_out2 = SeparateStr('', config=True)
+
+    system_header = Str('IPython system call: ', config=True)
+    system_verbose = CBool(False, config=True)
+    term_title = CBool(False, config=True)
+    wildcards_case_sensitive = CBool(True, config=True)
     xmode = CaselessStrEnum(('Context','Plain', 'Verbose'), 
-                            default_value='Context', config_key='XMODE')
+                            default_value='Context', config=True)
 
-    alias = List(allow_none=False, config_key='ALIAS')
     autoexec = List(allow_none=False)
 
     # class attribute to indicate whether the class supports threads or not.
@@ -279,7 +275,7 @@ class InteractiveShell(Component, Magic):
 
         # This is where traitlets with a config_key argument are updated
         # from the values on config.
-        super(InteractiveShell, self).__init__(parent, config=config, name='__IP')
+        super(InteractiveShell, self).__init__(parent, config=config)
 
         # These are relatively independent and stateless
         self.init_ipythondir(ipythondir)
@@ -288,7 +284,7 @@ class InteractiveShell(Component, Magic):
         self.init_usage(usage)
         self.init_banner(banner1, banner2)
 
-        # Create namespaces (user_ns, user_global_ns, alias_table, etc.)
+        # Create namespaces (user_ns, user_global_ns, etc.)
         self.init_create_namespaces(user_ns, user_global_ns)
         # This has to be done after init_create_namespaces because it uses
         # something in self.user_ns, but before init_sys_modules, which
@@ -327,6 +323,9 @@ class InteractiveShell(Component, Magic):
         self.init_pdb()
         self.hooks.late_startup_hook()
 
+    def get_ipython(self):
+        return self
+
     #-------------------------------------------------------------------------
     # Traitlet changed handlers
     #-------------------------------------------------------------------------
@@ -337,6 +336,10 @@ class InteractiveShell(Component, Magic):
     def _banner2_changed(self):
         self.compute_banner()
 
+    def _ipythondir_changed(self, name, new):
+        if not os.path.isdir(new):
+            os.makedirs(new, mode = 0777)
+
     @property
     def usable_screen_length(self):
         if self.screen_length == 0:
@@ -370,22 +373,16 @@ class InteractiveShell(Component, Magic):
     def init_ipythondir(self, ipythondir):
         if ipythondir is not None:
             self.ipythondir = ipythondir
-            self.config.IPYTHONDIR = self.ipythondir
+            self.config.Global.ipythondir = self.ipythondir
             return
 
-        if hasattr(self.config, 'IPYTHONDIR'):
-            self.ipythondir = self.config.IPYTHONDIR
-        if not hasattr(self.config, 'IPYTHONDIR'):
-            # cdw is always defined
-            self.ipythondir = os.getcwd()
-
-        # The caller must make sure that ipythondir exists.  We should
-        # probably handle this using a Dir traitlet.
-        if not os.path.isdir(self.ipythondir):
-            raise IOError('IPython dir does not exist: %s' % self.ipythondir)
+        if hasattr(self.config.Global, 'ipythondir'):
+            self.ipythondir = self.config.Global.ipythondir
+        else:
+            self.ipythondir = get_ipython_dir()
 
         # All children can just read this
-        self.config.IPYTHONDIR = self.ipythondir
+        self.config.Global.ipythondir = self.ipythondir
 
     def init_instance_attrs(self):
         self.jobs = BackgroundJobManager()
@@ -825,11 +822,6 @@ class InteractiveShell(Component, Magic):
         # them from cluttering user-visible stuff.  Will be updated later
         self.internal_ns = {}
 
-        # Namespace of system aliases.  Each entry in the alias
-        # table must be a 2-tuple of the form (N,name), where N is the number
-        # of positional arguments of the alias.
-        self.alias_table = {}
-
         # Now that FakeModule produces a real module, we've run into a nasty
         # problem: after script execution (via %run), the module where the user
         # code ran is deleted.  Now that this object is a true module (needed
@@ -863,7 +855,6 @@ class InteractiveShell(Component, Magic):
         # introspection facilities can search easily.
         self.ns_table = {'user':user_ns,
                          'user_global':user_global_ns,
-                         'alias':self.alias_table,
                          'internal':self.internal_ns,
                          'builtin':__builtin__.__dict__
                          }
@@ -872,8 +863,7 @@ class InteractiveShell(Component, Magic):
         # we can safely clear (so it can NOT include builtin).  This one can be
         # a simple list.
         self.ns_refs_table = [ user_ns, user_global_ns, self.user_config_ns,
-                               self.alias_table, self.internal_ns,
-                               self._main_ns_cache ]
+                               self.internal_ns, self._main_ns_cache ]
 
     def init_sys_modules(self):
         # We need to insert into sys.modules something that looks like a
@@ -961,11 +951,8 @@ class InteractiveShell(Component, Magic):
         method.  If they were not empty before, data will simply be added to
         therm.
         """
-        # The user namespace MUST have a pointer to the shell itself.
-        self.user_ns[self.name] = self
-
         # Store myself as the public api!!!
-        self.user_ns['_ip'] = self
+        self.user_ns['get_ipython'] = self.get_ipython
 
         # make global variables for user access to the histories
         self.user_ns['_ih'] = self.input_hist
@@ -994,13 +981,19 @@ class InteractiveShell(Component, Magic):
         for ns in self.ns_refs_table:
             ns.clear()
 
+        self.alias_manager.clear_aliases()
+
         # Clear input and output histories
         self.input_hist[:] = []
         self.input_hist_raw[:] = []
         self.output_hist.clear()
+
         # Restore the user namespaces to minimal usability
         self.init_user_ns()
 
+        # Restore the default and user aliases
+        self.alias_manager.init_aliases()
+
     def push(self, variables, interactive=True):
         """Inject a group of variables into the IPython user namespace.
 
@@ -1076,7 +1069,7 @@ class InteractiveShell(Component, Magic):
             histfname = 'history-%s' % self.profile
         except AttributeError:
             histfname = 'history'
-        self.histfile = os.path.join(self.config.IPYTHONDIR, histfname)
+        self.histfile = os.path.join(self.ipythondir, histfname)
 
         # Fill the history zero entry, user counter starts at 1
         self.input_hist.append('\n')
@@ -1084,12 +1077,12 @@ class InteractiveShell(Component, Magic):
 
     def init_shadow_hist(self):
         try:
-            self.db = pickleshare.PickleShareDB(self.config.IPYTHONDIR + "/db")
+            self.db = pickleshare.PickleShareDB(self.ipythondir + "/db")
         except exceptions.UnicodeDecodeError:
             print "Your ipythondir can't be decoded to unicode!"
             print "Please set HOME environment variable to something that"
             print r"only has ASCII characters, e.g. c:\home"
-            print "Now it is", self.config.IPYTHONDIR
+            print "Now it is", self.ipythondir
             sys.exit()
         self.shadowhist = ipcorehist.ShadowHist(self.db)
 
@@ -1472,10 +1465,10 @@ class InteractiveShell(Component, Magic):
             import atexit
             from IPython.core.completer import IPCompleter
             self.Completer = IPCompleter(self,
-                                            self.user_ns,
-                                            self.user_global_ns,
-                                            self.readline_omit__names,
-                                            self.alias_table)
+                                         self.user_ns,
+                                         self.user_global_ns,
+                                         self.readline_omit__names,
+                                         self.alias_manager.alias_table)
             sdisp = self.strdispatchers.get('complete_command', StrDispatch())
             self.strdispatchers['complete_command'] = sdisp
             self.Completer.custom_completers = sdisp
@@ -1607,8 +1600,11 @@ class InteractiveShell(Component, Magic):
             error("Magic function `%s` not found." % magic_name)
         else:
             magic_args = self.var_expand(magic_args,1)
-            with nested(self.builtin_trap, self.display_trap):
-                return fn(magic_args)
+            with nested(self.builtin_trap,):
+                result = fn(magic_args)
+            # Unfortunately, the return statement is what will trigger
+            # the displayhook, but it is no longer set!
+            return result
 
     def define_magic(self, magicname, func):
         """Expose own function as magic function for ipython 
@@ -1666,6 +1662,7 @@ class InteractiveShell(Component, Magic):
 
     def init_alias(self):
         self.alias_manager = AliasManager(self, config=self.config)
+        self.ns_table['alias'] = self.alias_manager.alias_table,
 
     #-------------------------------------------------------------------------
     # Things related to the running of code
@@ -1673,7 +1670,7 @@ class InteractiveShell(Component, Magic):
 
     def ex(self, cmd):
         """Execute a normal python statement in user namespace."""
-        with nested(self.builtin_trap, self.display_trap):
+        with nested(self.builtin_trap,):
             exec cmd in self.user_global_ns, self.user_ns
 
     def ev(self, expr):
@@ -1681,7 +1678,7 @@ class InteractiveShell(Component, Magic):
 
         Returns the result of evaluation
         """
-        with nested(self.builtin_trap, self.display_trap):
+        with nested(self.builtin_trap,):
             return eval(expr, self.user_global_ns, self.user_ns)
 
     def mainloop(self, banner=None):
diff --git a/IPython/core/magic.py b/IPython/core/magic.py
index b7d1398..9d33b97 100644
--- a/IPython/core/magic.py
+++ b/IPython/core/magic.py
@@ -47,6 +47,7 @@ from IPython.utils import wildcard
 from IPython.core import debugger, oinspect
 from IPython.core.error import TryNext
 from IPython.core.fakemodule import FakeModule
+from IPython.core.prefilter import ESC_MAGIC
 from IPython.external.Itpl import Itpl, itpl, printpl,itplns
 from IPython.utils.PyColorize import Parser
 from IPython.utils.ipstruct import Struct
@@ -205,9 +206,9 @@ python-profiler package from non-free.""")
             namespaces = [ ('Interactive', self.shell.user_ns),
                            ('IPython internal', self.shell.internal_ns),
                            ('Python builtin', __builtin__.__dict__),
-                           ('Alias', self.shell.alias_table),
+                           ('Alias', self.shell.alias_manager.alias_table),
                            ]
-            alias_ns = self.shell.alias_table
+            alias_ns = self.shell.alias_manager.alias_table
 
         # initialize results to 'null'
         found = 0; obj = None;  ospace = None;  ds = None;
@@ -244,7 +245,7 @@ python-profiler package from non-free.""")
 
         # Try to see if it's magic
         if not found:
-            if oname.startswith(self.shell.ESC_MAGIC):
+            if oname.startswith(ESC_MAGIC):
                 oname = oname[1:]
             obj = getattr(self,'magic_'+oname,None)
             if obj is not None:
@@ -272,10 +273,10 @@ python-profiler package from non-free.""")
         # Characters that need to be escaped for latex:
         escape_re = re.compile(r'(%|_|\$|#|&)',re.MULTILINE)
         # Magic command names as headers:
-        cmd_name_re = re.compile(r'^(%s.*?):' % self.shell.ESC_MAGIC,
+        cmd_name_re = re.compile(r'^(%s.*?):' % ESC_MAGIC,
                                  re.MULTILINE)
         # Magic commands 
-        cmd_re = re.compile(r'(?P<cmd>%s.+?\b)(?!\}\}:)' % self.shell.ESC_MAGIC,
+        cmd_re = re.compile(r'(?P<cmd>%s.+?\b)(?!\}\}:)' % ESC_MAGIC,
                             re.MULTILINE)
         # Paragraph continue
         par_re = re.compile(r'\\$',re.MULTILINE)
@@ -376,7 +377,7 @@ python-profiler package from non-free.""")
     # Functions for IPython shell work (vars,funcs, config, etc)
     def magic_lsmagic(self, parameter_s = ''):
         """List currently available magic functions."""
-        mesc = self.shell.ESC_MAGIC
+        mesc = ESC_MAGIC
         print 'Available magic functions:\n'+mesc+\
               ('  '+mesc).join(self.lsmagic())
         print '\n' + Magic.auto_status[self.shell.automagic]
@@ -424,11 +425,11 @@ python-profiler package from non-free.""")
                 
                 
             if mode == 'rest':
-                rest_docs.append('**%s%s**::\n\n\t%s\n\n' %(self.shell.ESC_MAGIC,
+                rest_docs.append('**%s%s**::\n\n\t%s\n\n' %(ESC_MAGIC,
                                                     fname,fndoc))
                 
             else:
-                magic_docs.append('%s%s:\n\t%s\n' %(self.shell.ESC_MAGIC,
+                magic_docs.append('%s%s:\n\t%s\n' %(ESC_MAGIC,
                                                     fname,fndoc))
                 
         magic_docs = ''.join(magic_docs)
@@ -479,7 +480,7 @@ of any of them, type %magic_name?, e.g. '%cd?'.
 
 Currently the magic system has the following functions:\n"""
 
-        mesc = self.shell.ESC_MAGIC
+        mesc = ESC_MAGIC
         outmsg = ("%s\n%s\n\nSummary of magic functions (from %slsmagic):"
                   "\n\n%s%s\n\n%s" % (outmsg,
                                      magic_docs,mesc,mesc,
@@ -2620,52 +2621,27 @@ Defaulting color scheme to 'NoColor'"""
         par = parameter_s.strip()
         if not par:
             stored = self.db.get('stored_aliases', {} )
-            atab = self.shell.alias_table
-            aliases = atab.keys()
-            aliases.sort()
-            res = []
-            showlast = []
-            for alias in aliases:
-                special = False
-                try:
-                    tgt = atab[alias][1]
-                except (TypeError, AttributeError):
-                    # unsubscriptable? probably a callable
-                    tgt = atab[alias]
-                    special = True
-                # 'interesting' aliases
-                if (alias in stored or
-                    special or 
-                    alias.lower() != os.path.splitext(tgt)[0].lower() or
-                    ' ' in tgt):
-                    showlast.append((alias, tgt))
-                else:
-                    res.append((alias, tgt ))                
-            
-            # show most interesting aliases last
-            res.extend(showlast)
-            print "Total number of aliases:",len(aliases)
-            return res
+            aliases = sorted(self.shell.alias_manager.aliases)
+            # for k, v in stored:
+            #     atab.append(k, v[0])
+
+            print "Total number of aliases:", len(aliases)
+            return aliases
+        
+        # Now try to define a new one
         try:
-            alias,cmd = par.split(None,1)
+            alias,cmd = par.split(None, 1)
         except:
             print oinspect.getdoc(self.magic_alias)
         else:
-            nargs = cmd.count('%s')
-            if nargs>0 and cmd.find('%l')>=0:
-                error('The %s and %l specifiers are mutually exclusive '
-                      'in alias definitions.')
-            else:  # all looks OK
-                self.shell.alias_table[alias] = (nargs,cmd)
-                self.shell.alias_table_validate(verbose=0)
+            self.shell.alias_manager.soft_define_alias(alias, cmd)
     # end magic_alias
 
     def magic_unalias(self, parameter_s = ''):
         """Remove an alias"""
 
         aname = parameter_s.strip()
-        if aname in self.shell.alias_table:
-            del self.shell.alias_table[aname]
+        self.shell.alias_manager.undefine_alias(aname)
         stored = self.db.get('stored_aliases', {} )
         if aname in stored:
             print "Removing %stored alias",aname
@@ -2686,6 +2662,7 @@ Defaulting color scheme to 'NoColor'"""
         This function also resets the root module cache of module completer,
         used on slow filesystems.
         """
+        from IPython.core.alias import InvalidAliasError
 
         # for the benefit of module completer in ipy_completers.py
         del self.db['rootmodules']
@@ -2693,14 +2670,13 @@ Defaulting color scheme to 'NoColor'"""
         path = [os.path.abspath(os.path.expanduser(p)) for p in 
             os.environ.get('PATH','').split(os.pathsep)]
         path = filter(os.path.isdir,path)
-        
-        alias_table = self.shell.alias_table
+
         syscmdlist = []
+        # Now define isexec in a cross platform manner.
         if os.name == 'posix':
             isexec = lambda fname:os.path.isfile(fname) and \
                      os.access(fname,os.X_OK)
         else:
-
             try:
                 winext = os.environ['pathext'].replace(';','|').replace('.','')
             except KeyError:
@@ -2710,6 +2686,8 @@ Defaulting color scheme to 'NoColor'"""
             execre = re.compile(r'(.*)\.(%s)$' % winext,re.IGNORECASE)
             isexec = lambda fname:os.path.isfile(fname) and execre.match(fname)
         savedir = os.getcwd()
+
+        # Now walk the paths looking for executables to alias.
         try:
             # write the whole loop for posix/Windows so we don't have an if in
             # the innermost part
@@ -2717,14 +2695,16 @@ Defaulting color scheme to 'NoColor'"""
                 for pdir in path:
                     os.chdir(pdir)
                     for ff in os.listdir(pdir):
-                        if isexec(ff) and ff not in self.shell.no_alias:
-                            # each entry in the alias table must be (N,name),
-                            # where N is the number of positional arguments of the
-                            # alias.                            
-                            # Dots will be removed from alias names, since ipython
-                            # assumes names with dots to be python code
-                            alias_table[ff.replace('.','')] = (0,ff)
-                            syscmdlist.append(ff)
+                        if isexec(ff):
+                            try:
+                                # Removes dots from the name since ipython
+                                # will assume names with dots to be python.
+                                self.shell.alias_manager.define_alias(
+                                    ff.replace('.',''), ff)
+                            except InvalidAliasError:
+                                pass
+                            else:
+                                syscmdlist.append(ff)
             else:
                 for pdir in path:
                     os.chdir(pdir)
@@ -2733,16 +2713,14 @@ Defaulting color scheme to 'NoColor'"""
                         if isexec(ff) and base.lower() not in self.shell.no_alias:
                             if ext.lower() == '.exe':
                                 ff = base
-                            alias_table[base.lower().replace('.','')] = (0,ff)
-                            syscmdlist.append(ff)
-            # Make sure the alias table doesn't contain keywords or builtins
-            self.shell.alias_table_validate()
-            # Call again init_auto_alias() so we get 'rm -i' and other
-            # modified aliases since %rehashx will probably clobber them
-            
-            # no, we don't want them. if %rehashx clobbers them, good,
-            # we'll probably get better versions
-            # self.shell.init_auto_alias()
+                                try:
+                                    # Removes dots from the name since ipython
+                                    # will assume names with dots to be python.
+                                    self.shell.alias_manager.define_alias(
+                                        base.lower().replace('.',''), ff)
+                                except InvalidAliasError:
+                                    pass
+                                syscmdlist.append(ff)
             db = self.db
             db['syscmdlist'] = syscmdlist
         finally:
@@ -3167,7 +3145,7 @@ Defaulting color scheme to 'NoColor'"""
         """
 
         start = parameter_s.strip()
-        esc_magic = self.shell.ESC_MAGIC
+        esc_magic = ESC_MAGIC
         # Identify magic commands even if automagic is on (which means
         # the in-memory version is different from that typed by the user).
         if self.shell.automagic:
diff --git a/IPython/core/prefilter.py b/IPython/core/prefilter.py
index 77f2401..fd994a1 100644
--- a/IPython/core/prefilter.py
+++ b/IPython/core/prefilter.py
@@ -174,7 +174,7 @@ class PrefilterManager(Component):
     to transform the input line.
     """
 
-    multi_line_specials = CBool(True, config_key='MULTI_LINE_SPECIALS')
+    multi_line_specials = CBool(True, config=True)
 
     def __init__(self, parent, config=None):
         super(PrefilterManager, self).__init__(parent, config=config)
@@ -274,16 +274,16 @@ class PrefilterManager(Component):
         # the input history needs to track even empty lines
         stripped = line.strip()
 
-        handle_normal = self.get_handler_by_name('normal')        
+        normal_handler = self.get_handler_by_name('normal')        
         if not stripped:
             if not continue_prompt:
                 self.shell.outputcache.prompt_count -= 1
 
-            return handle_normal(line_info)
+            return normal_handler.handle(line_info)
 
         # special handlers are only allowed for single line statements
         if continue_prompt and not self.multi_line_specials:
-            return handle_normal(line_info)
+            return normal_handler.handle(line_info)
 
         return self.prefilter_line_info(line_info)
 
@@ -310,7 +310,7 @@ class PrefilterManager(Component):
 class PrefilterChecker(Component):
     """Inspect an input line and return a handler for that line."""
 
-    priority = Int(100)
+    priority = Int(100, config=True)
     shell = Any
     prefilter_manager = Any
 
@@ -336,7 +336,7 @@ class PrefilterChecker(Component):
 
 class EmacsChecker(PrefilterChecker):
 
-    priority = Int(100)
+    priority = Int(100, config=True)
 
     def check(self, line_info):
         "Emacs ipython-mode tags certain input lines."
@@ -348,7 +348,7 @@ class EmacsChecker(PrefilterChecker):
 
 class ShellEscapeChecker(PrefilterChecker):
 
-    priority = Int(200)
+    priority = Int(200, config=True)
 
     def check(self, line_info):
         if line_info.line.lstrip().startswith(ESC_SHELL):
@@ -357,7 +357,7 @@ class ShellEscapeChecker(PrefilterChecker):
 
 class IPyAutocallChecker(PrefilterChecker):
 
-    priority = Int(300)
+    priority = Int(300, config=True)
 
     def check(self, line_info):
         "Instances of IPyAutocall in user_ns get autocalled immediately"
@@ -371,7 +371,7 @@ class IPyAutocallChecker(PrefilterChecker):
 
 class MultiLineMagicChecker(PrefilterChecker):
 
-    priority = Int(400)
+    priority = Int(400, config=True)
 
     def check(self, line_info):
         "Allow ! and !! in multi-line statements if multi_line_specials is on"
@@ -388,7 +388,7 @@ class MultiLineMagicChecker(PrefilterChecker):
 
 class EscCharsChecker(PrefilterChecker):
 
-    priority = Int(500)
+    priority = Int(500, config=True)
 
     def check(self, line_info):
         """Check for escape character and return either a handler to handle it,
@@ -406,7 +406,7 @@ class EscCharsChecker(PrefilterChecker):
 
 class AssignmentChecker(PrefilterChecker):
 
-    priority = Int(600)
+    priority = Int(600, config=True)
 
     def check(self, line_info):
         """Check to see if user is assigning to a var for the first time, in
@@ -423,7 +423,7 @@ class AssignmentChecker(PrefilterChecker):
 
 class AutoMagicChecker(PrefilterChecker):
 
-    priority = Int(700)
+    priority = Int(700, config=True)
 
     def check(self, line_info):
         """If the ifun is magic, and automagic is on, run it.  Note: normal,
@@ -447,7 +447,7 @@ class AutoMagicChecker(PrefilterChecker):
 
 class AliasChecker(PrefilterChecker):
 
-    priority = Int(800)
+    priority = Int(800, config=True)
 
     @auto_attr
     def alias_manager(self):
@@ -467,7 +467,7 @@ class AliasChecker(PrefilterChecker):
 
 class PythonOpsChecker(PrefilterChecker):
 
-    priority = Int(900)
+    priority = Int(900, config=True)
 
     def check(self, line_info):
         """If the 'rest' of the line begins with a function call or pretty much
@@ -482,7 +482,7 @@ class PythonOpsChecker(PrefilterChecker):
 
 class AutocallChecker(PrefilterChecker):
 
-    priority = Int(1000)
+    priority = Int(1000, config=True)
 
     def check(self, line_info):
         "Check if the initial word/function is callable and autocall is on."
@@ -567,7 +567,7 @@ class AliasHandler(PrefilterHandler):
         transformed = self.alias_manager.expand_aliases(line_info.ifun,line_info.the_rest)
         # pre is needed, because it carries the leading whitespace.  Otherwise
         # aliases won't work in indented sections.
-        line_out = '%s_ip.system(%s)' % (line_info.pre_whitespace,
+        line_out = '%sget_ipython().system(%s)' % (line_info.pre_whitespace,
                                          make_quoted_expr(transformed))
         
         self.shell.log(line_info.line, line_out, line_info.continue_prompt)
@@ -597,7 +597,7 @@ class ShellEscapeHandler(PrefilterHandler):
             return magic_handler.handle(line_info)
         else:
             cmd = line.lstrip().lstrip(ESC_SHELL)
-            line_out = '%s_ip.system(%s)' % (line_info.pre_whitespace,
+            line_out = '%sget_ipython().system(%s)' % (line_info.pre_whitespace,
                                              make_quoted_expr(cmd))
         # update cache/log and return
         self.shell.log(line, line_out, line_info.continue_prompt)
@@ -607,13 +607,13 @@ class ShellEscapeHandler(PrefilterHandler):
 class MagicHandler(PrefilterHandler):
 
     handler_name = Str('magic')
-    esc_strings = List(['%'])
+    esc_strings = List([ESC_MAGIC])
 
     def handle(self, line_info):
         """Execute magic functions."""
         ifun    = line_info.ifun
         the_rest = line_info.the_rest
-        cmd = '%s_ip.magic(%s)' % (line_info.pre_whitespace,
+        cmd = '%sget_ipython().magic(%s)' % (line_info.pre_whitespace,
                                    make_quoted_expr(ifun + " " + the_rest))
         self.shell.log(line_info.line, cmd, line_info.continue_prompt)
         return cmd
@@ -656,7 +656,7 @@ class AutoHandler(PrefilterHandler):
             # We only apply it to argument-less calls if the autocall
             # parameter is set to 2.  We only need to check that autocall is <
             # 2, since this function isn't called unless it's at least 1.
-            if not the_rest and (self.autocall < 2) and not force_auto:
+            if not the_rest and (self.shell.autocall < 2) and not force_auto:
                 newcmd = '%s %s' % (ifun,the_rest)
                 auto_rewrite = False
             else:
diff --git a/IPython/core/prompts.py b/IPython/core/prompts.py
index 5bb31bc..228edb7 100644
--- a/IPython/core/prompts.py
+++ b/IPython/core/prompts.py
@@ -546,8 +546,11 @@ class CachedOutput:
             # don't use print, puts an extra space
             cout_write(self.output_sep)
             outprompt = self.shell.hooks.generate_output_prompt()
+            # print "Got prompt: ", outprompt
             if self.do_full_cache:
                 cout_write(outprompt)
+            else:
+                print "self.do_full_cache = False"
 
             # and now call a possibly user-defined print mechanism
             manipulated_val = self.display(arg)
diff --git a/IPython/core/tests/obj_del.py b/IPython/core/tests/obj_del.py
index 56c8700..d925dc6 100644
--- a/IPython/core/tests/obj_del.py
+++ b/IPython/core/tests/obj_del.py
@@ -31,4 +31,5 @@ class A(object):
 a = A()
 
 # Now, we force an exit, the caller will check that the del printout was given
+_ip = get_ipython()
 _ip.ask_exit()
diff --git a/IPython/core/tests/test_component.py b/IPython/core/tests/test_component.py
index 5db9ed9..e6713a9 100644
--- a/IPython/core/tests/test_component.py
+++ b/IPython/core/tests/test_component.py
@@ -26,7 +26,7 @@ from IPython.core.component import Component, ComponentError
 from IPython.utils.traitlets import (
     TraitletError, Int, Float, Str
 )
-from IPython.utils.ipstruct import Struct
+from IPython.config.loader import Config
 
 
 #-----------------------------------------------------------------------------
@@ -138,9 +138,9 @@ class TestComponentConfig(TestCase):
         self.assertEquals(c2.config, c3.config)
 
     def test_custom(self):
-        config = Struct()
-        config.FOO = 'foo'
-        config.BAR = 'bar'
+        config = Config()
+        config.foo = 'foo'
+        config.bar = 'bar'
         c1 = Component(None, config=config)
         c2 = Component(c1)
         c3 = Component(c2)
@@ -156,19 +156,19 @@ class TestComponentConfig(TestCase):
         
     def test_inheritance(self):
         class MyComponent(Component):
-            a = Int(1, config_key='A')
-            b = Float(1.0, config_key='B')
+            a = Int(1, config=True)
+            b = Float(1.0, config=True)
             c = Str('no config')
-        config = Struct()
-        config.A = 2
-        config.B = 2.0
+        config = Config()
+        config.MyComponent.a = 2
+        config.MyComponent.b = 2.0
         c1 = MyComponent(None, config=config)
         c2 = MyComponent(c1)
-        self.assertEquals(c1.a, config.A)
-        self.assertEquals(c1.b, config.B)
-        self.assertEquals(c2.a, config.A)
-        self.assertEquals(c2.b, config.B)
-        c4 = MyComponent(c2, config=Struct())
+        self.assertEquals(c1.a, config.MyComponent.a)
+        self.assertEquals(c1.b, config.MyComponent.b)
+        self.assertEquals(c2.a, config.MyComponent.a)
+        self.assertEquals(c2.b, config.MyComponent.b)
+        c4 = MyComponent(c2, config=Config())
         self.assertEquals(c4.a, 1)
         self.assertEquals(c4.b, 1.0)
 
diff --git a/IPython/core/tests/test_magic.py b/IPython/core/tests/test_magic.py
index f1f97a8..f2eb516 100644
--- a/IPython/core/tests/test_magic.py
+++ b/IPython/core/tests/test_magic.py
@@ -20,14 +20,15 @@ from IPython.testing import tools as tt
 
 def test_rehashx():
     # clear up everything
-    _ip.alias_table.clear()
+    _ip = get_ipython()
+    _ip.alias_manager.alias_table.clear()
     del _ip.db['syscmdlist']
     
     _ip.magic('rehashx')
     # Practically ALL ipython development systems will have more than 10 aliases
 
-    yield (nt.assert_true, len(_ip.alias_table) > 10)
-    for key, val in _ip.alias_table.items():
+    yield (nt.assert_true, len(_ip.alias_manager.alias_table) > 10)
+    for key, val in _ip.alias_manager.alias_table.items():
         # we must strip dots from alias names
         nt.assert_true('.' not in key)
 
@@ -65,6 +66,7 @@ def doctest_hist_r():
 # This test is known to fail on win32.
 # See ticket https://bugs.launchpad.net/bugs/366334
 def test_obj_del():
+    _ip = get_ipython()
     """Test that object's __del__ methods are called on exit."""
     test_dir = os.path.dirname(__file__)
     del_file = os.path.join(test_dir,'obj_del.py')
@@ -221,13 +223,14 @@ class TestMagicRun(object):
         self.fname = fname
 
     def run_tmpfile(self):
+        _ip = get_ipython()
         # This fails on Windows if self.tmpfile.name has spaces or "~" in it.
         # See below and ticket https://bugs.launchpad.net/bugs/366353
         _ip.magic('run "%s"' % self.fname)
 
     def test_builtins_id(self):
         """Check that %run doesn't damage __builtins__ """
-
+        _ip = get_ipython()
         # Test that the id of __builtins__ is not modified by %run
         bid1 = id(_ip.user_ns['__builtins__'])
         self.run_tmpfile()
@@ -241,12 +244,14 @@ class TestMagicRun(object):
         be a dict (it should be a module) by a previous use of %run.  So we
         also check explicitly that it really is a module:
         """
+        _ip = get_ipython()
         self.run_tmpfile()
         tt.assert_equals(type(_ip.user_ns['__builtins__']),type(sys))
 
     def test_prompts(self):
         """Test that prompts correctly generate after %run"""
         self.run_tmpfile()
+        _ip = get_ipython()
         p2 = str(_ip.outputcache.prompt2).strip()
         nt.assert_equals(p2[:3], '...')
 
@@ -261,7 +266,7 @@ class TestMagicRun(object):
 
 # Multiple tests for clipboard pasting
 def test_paste():
-
+    _ip = get_ipython()
     def paste(txt, flags='-q'):
         """Paste input text, by default in quiet mode"""
         hooks.clipboard_get = lambda : txt
diff --git a/IPython/extensions/ext_rescapture.py b/IPython/extensions/ext_rescapture.py
index fdb7a4d..d4b8508 100644
--- a/IPython/extensions/ext_rescapture.py
+++ b/IPython/extensions/ext_rescapture.py
@@ -21,14 +21,14 @@ def hnd_magic(line,mo):
     var = mo.group('varname')
     cmd = mo.group('cmd')
     expr = make_quoted_expr(cmd)
-    return itpl('$var = _ip.magic($expr)')
+    return itpl('$var = get_ipython().magic($expr)')
 
 def hnd_syscmd(line,mo):
     """ Handle a = !ls """
     var = mo.group('varname')
     cmd = mo.group('cmd')
     expr = make_quoted_expr(itpl("sc -l =$cmd"))
-    return itpl('$var = _ip.magic($expr)')
+    return itpl('$var = get_ipython().magic($expr)')
 
 def install_re_handler(pat, hnd):
     ip.meta.re_prefilters.append((re.compile(pat), hnd))
diff --git a/IPython/extensions/ipipe.py b/IPython/extensions/ipipe.py
index 13b18ba..74215bc 100644
--- a/IPython/extensions/ipipe.py
+++ b/IPython/extensions/ipipe.py
@@ -1644,7 +1644,7 @@ class ialias(Table):
     def __iter__(self):
         api = ipapi.get()
 
-        for (name, (args, command)) in api.alias_table.iteritems():
+        for (name, (args, command)) in api.alias_manager.alias_table.iteritems():
             yield Alias(name, args, command)
 
 
diff --git a/IPython/extensions/ipy_profile_sh.py b/IPython/extensions/ipy_profile_sh.py
index d678e57..571f5c4 100644
--- a/IPython/extensions/ipy_profile_sh.py
+++ b/IPython/extensions/ipy_profile_sh.py
@@ -109,7 +109,7 @@ def main():
             cmd = noext
         
         key = mapper(cmd)
-        if key not in ip.alias_table:
+        if key not in ip.alias_manager.alias_table:
             # Dots will be removed from alias names, since ipython
             # assumes names with dots to be python code
             
@@ -159,7 +159,7 @@ def slash_prefilter_f(self,line):
     """
     from IPython.utils import genutils
     if re.match('(?:[.~]|/[a-zA-Z_0-9]+)/', line):
-        return "_ip.system(" + genutils.make_quoted_expr(line)+")"
+        return "get_ipython().system(" + genutils.make_quoted_expr(line)+")"
     raise TryNext
 
 # XXX You do not need to understand the next function!
diff --git a/IPython/extensions/ipy_rehashdir.py b/IPython/extensions/ipy_rehashdir.py
index 274c932..7250470 100644
--- a/IPython/extensions/ipy_rehashdir.py
+++ b/IPython/extensions/ipy_rehashdir.py
@@ -88,7 +88,7 @@ def rehashdir_f(self,arg):
     if not arg:
         arg = '.'
     path = map(os.path.abspath,arg.split(';'))
-    alias_table = self.shell.alias_table
+    alias_table = self.shell.alias_manager.alias_table
         
     if os.name == 'posix':
         isexec = lambda fname:os.path.isfile(fname) and \
diff --git a/IPython/extensions/jobctrl.py b/IPython/extensions/jobctrl.py
index 8d1aa3a..9a38ce5 100644
--- a/IPython/extensions/jobctrl.py
+++ b/IPython/extensions/jobctrl.py
@@ -126,8 +126,8 @@ def jobctrl_prefilter_f(self,line):
         
         line = ip.expand_aliases(fn,rest)
         if not _jobq:
-            return '_ip.startjob(%s)' % genutils.make_quoted_expr(line)
-        return '_ip.jobq(%s)' % genutils.make_quoted_expr(line)
+            return 'get_ipython().startjob(%s)' % genutils.make_quoted_expr(line)
+        return 'get_ipython().jobq(%s)' % genutils.make_quoted_expr(line)
 
     raise TryNext
 
diff --git a/IPython/extensions/pspersistence.py b/IPython/extensions/pspersistence.py
index c937b49..dbba916 100644
--- a/IPython/extensions/pspersistence.py
+++ b/IPython/extensions/pspersistence.py
@@ -157,6 +157,7 @@ def magic_store(self, parameter_s=''):
             obj = ip.user_ns[args[0]]
         except KeyError:
             # it might be an alias
+            # This needs to be refactored to use the new AliasManager stuff.
             if args[0] in self.alias_table:
                 staliases = db.get('stored_aliases',{})
                 staliases[ args[0] ] = self.alias_table[ args[0] ]
diff --git a/IPython/kernel/magic.py b/IPython/kernel/magic.py
index 4eab117..0d40f6a 100644
--- a/IPython/kernel/magic.py
+++ b/IPython/kernel/magic.py
@@ -99,7 +99,7 @@ def pxrunsource(self, source, filename="<input>", symbol="single"):
     # Case 3
     # Because autopx is enabled, we now call executeAll or disable autopx if
     # %autopx or autopx has been called
-    if '_ip.magic("%autopx' in source or '_ip.magic("autopx' in source:
+    if 'get_ipython().magic("%autopx' in source or 'get_ipython().magic("autopx' in source:
         _disable_autopx(self)
         return False
     else:
diff --git a/IPython/utils/tests/test_traitlets.py b/IPython/utils/tests/test_traitlets.py
index 09661eb..e7c0e75 100644
--- a/IPython/utils/tests/test_traitlets.py
+++ b/IPython/utils/tests/test_traitlets.py
@@ -353,14 +353,17 @@ class TestHasTraitlets(TestCase):
         class A(HasTraitlets):
             i = Int(config_key='VALUE1', other_thing='VALUE2')
             f = Float(config_key='VALUE3', other_thing='VALUE2')
+            j = Int(0)
         a = A()
-        self.assertEquals(a.traitlets(), dict(i=A.i, f=A.f))
-        traitlets = a.traitlets(config_key=lambda v: True)
-        self.assertEquals(traitlets, dict(i=A.i, f=A.f))
+        self.assertEquals(a.traitlets(), dict(i=A.i, f=A.f, j=A.j))
         traitlets = a.traitlets(config_key='VALUE1', other_thing='VALUE2')
         self.assertEquals(traitlets, dict(i=A.i))
-        traitlets = a.traitlets('config_key')
-        self.assertEquals(traitlets, dict(i=A.i, f=A.f))
+
+        # This passes, but it shouldn't because I am replicating a bug in 
+        # traits.
+        traitlets = a.traitlets(config_key=lambda v: True)
+        self.assertEquals(traitlets, dict(i=A.i, f=A.f, j=A.j))
+
 
 #-----------------------------------------------------------------------------
 # Tests for specific traitlet types
diff --git a/IPython/utils/traitlets.py b/IPython/utils/traitlets.py
index 9438d9a..b02e165 100644
--- a/IPython/utils/traitlets.py
+++ b/IPython/utils/traitlets.py
@@ -458,19 +458,22 @@ class HasTraitlets(object):
         """Get a list of all the names of this classes traitlets."""
         return self.traitlets(**metadata).keys()
 
-    def traitlets(self, *args, **metadata):
+    def traitlets(self, **metadata):
         """Get a list of all the traitlets of this class.
 
         The TraitletTypes returned don't know anything about the values
         that the various HasTraitlet's instances are holding.
+
+        This follows the same algorithm as traits does and does not allow
+        for any simple way of specifying merely that a metadata name
+        exists, but has any value.  This is because get_metadata returns
+        None if a metadata key doesn't exist.
         """
         traitlets = dict([memb for memb in inspect.getmembers(self.__class__) if \
                      isinstance(memb[1], TraitletType)])
-        if len(metadata) == 0 and len(args) == 0:
-            return traitlets
 
-        for meta_name in args:
-            metadata[meta_name] = lambda _: True
+        if len(metadata) == 0:
+            return traitlets
 
         for meta_name, meta_eval in metadata.items():
             if type(meta_eval) is not FunctionType: