diff --git a/earwigbot/bot.py b/earwigbot/bot.py
index 65c5442..15c5fef 100644
--- a/earwigbot/bot.py
+++ b/earwigbot/bot.py
@@ -23,10 +23,13 @@
 import threading
 from time import sleep, time
 
+from earwigbot.commands import CommandManager
 from earwigbot.config import BotConfig
 from earwigbot.irc import Frontend, Watcher
 from earwigbot.tasks import task_manager
 
+__all__ = ["Bot"]
+
 class Bot(object):
     """
     The Bot class is the core of EarwigBot, essentially responsible for
@@ -46,16 +49,14 @@ class Bot(object):
     def __init__(self, root_dir):
         self.config = BotConfig(root_dir)
         self.logger = logging.getLogger("earwigbot")
+        self.commands = CommandManager(self)
+        self.tasks = None
         self.frontend = None
         self.watcher = None
 
         self._keep_scheduling = True
         self._lock = threading.Lock()
 
-    def _start_thread(self, name, target):
-        thread = threading.Thread(name=name, target=target)
-        thread.start()
-
     def _wiki_scheduler(self):
         while self._keep_scheduling:
             time_start = time()
@@ -68,17 +69,18 @@ class Bot(object):
     def _start_components(self):
         if self.config.components.get("irc_frontend"):
             self.logger.info("Starting IRC frontend")
-            self.frontend = Frontend(self.config)
-            self._start_thread(name, self.frontend.loop)
+            self.frontend = Frontend(self)
+            self.commands.load()
+            threading.Thread(name=name, target=self.frontend.loop).start()
 
         if self.config.components.get("irc_watcher"):
             self.logger.info("Starting IRC watcher")
-            self.watcher = Watcher(self.config, self.frontend)
-            self._start_thread(name, self.watcher.loop)
+            self.watcher = Watcher(self)
+            threading.Thread(name=name, target=self.watcher.loop).start()
 
         if self.config.components.get("wiki_scheduler"):
             self.logger.info("Starting wiki scheduler")
-            self._start_thread(name, self._wiki_scheduler)
+            threading.Thread(name=name, target=self._wiki_scheduler).start()
 
     def _loop(self):
         while 1:
@@ -104,6 +106,7 @@ class Bot(object):
         with self._lock:
             self.config.load()
             #if self.config.components.get("irc_frontend"):
+            #   self.commands.load()
 
     def stop(self):
         if self.frontend:
@@ -111,3 +114,4 @@ class Bot(object):
         if self.watcher:
             self.watcher.stop()
         self._keep_scheduling = False
+        sleep(3)  # Give a few seconds to finish closing IRC connections
diff --git a/earwigbot/commands/__init__.py b/earwigbot/commands/__init__.py
index d5543bb..824fe2b 100644
--- a/earwigbot/commands/__init__.py
+++ b/earwigbot/commands/__init__.py
@@ -25,17 +25,16 @@ EarwigBot's IRC Command Manager
 
 This package provides the IRC "commands" used by the bot's front-end component.
 This module contains the BaseCommand class (import with
-`from earwigbot.commands import BaseCommand`) and an internal _CommandManager
-class. This can be accessed through the `command_manager` singleton.
+`from earwigbot.commands import BaseCommand`) and an internal CommandManager
+class. This can be accessed through `bot.commands`.
 """
 
+import imp
 import logging
-import os
-import sys
+from os import listdir, path
+from re import sub
 
-from earwigbot.config import config
-
-__all__ = ["BaseCommand", "command_manager"]
+__all__ = ["BaseCommand", "CommandManager"]
 
 class BaseCommand(object):
     """A base class for commands on IRC.
@@ -88,32 +87,33 @@ class BaseCommand(object):
         pass
 
 
-class _CommandManager(object):
-    def __init__(self):
+class CommandManager(object):
+    def __init__(self, bot):
+        self.bot = bot
         self.logger = logging.getLogger("earwigbot.tasks")
-        self._base_dir = os.path.dirname(os.path.abspath(__file__))
-        self._connection = None
+        self._dirs = [path.dirname(__file__), bot.config.root_dir]
         self._commands = {}
 
-    def _load_command(self, filename):
-        """Load a specific command from a module, identified by filename.
+    def _load_command(self, name, path):
+        """Load a specific command from a module, identified by name and path.
 
-        Given a Connection object and a filename, we'll first try to import
-        it, and if that works, make an instance of the 'Command' class inside
-        (assuming it is an instance of BaseCommand), add it to self._commands,
-        and log the addition. Any problems along the way will either be
-        ignored or logged.
+        We'll first try to import it using imp magic, and if that works, make
+        an instance of the 'Command' class inside (assuming it is an instance
+        of BaseCommand), add it to self._commands, and log the addition. Any
+        problems along the way will either be ignored or logged.
         """
-        # Strip .py from the filename's end and join with our package name:
-        name = ".".join(("commands", filename[:-3]))
+        f, path, desc = imp.find_module(name, [path])
         try:
-             __import__(name)
-        except:
-            self.logger.exception("Couldn't load file {0}".format(filename))
+             module = imp.load_module(name, f, path, desc)
+        except Exception:
+            e = "Couldn't load module {0} from {1}"
+            self.logger.exception(e.format(name, path))
             return
+        finally:
+            f.close()
 
         try:
-            command = sys.modules[name].Command(self._connection)
+            command = module.Command(self.bot.frontend)
         except AttributeError:
             return  # No command in this module
         if not isinstance(command, BaseCommand):
@@ -122,20 +122,16 @@ class _CommandManager(object):
         self._commands[command.name] = command
         self.logger.debug("Added command {0}".format(command.name))
 
-    def load(self, connection):
-        """Load all valid commands into self._commands.
-
-        `connection` is a Connection object that is given to each command's
-        constructor.
-        """
-        self._connection = connection
-
-        files = os.listdir(self._base_dir)
-        files.sort()
-        for filename in files:
-            if filename.startswith("_") or not filename.endswith(".py"):
-                continue
-            self._load_command(filename)
+    def load(self):
+        """Load (or reload) all valid commands into self._commands."""
+        dirs = [path.join(path.dirname(__file__), "commands"),
+                path.join(bot.config.root_dir, "commands")]
+        for dir in dirs:
+            files = listdir(dir)
+            files = [sub("\.pyc?$", "", f) for f in files if f[0] != "_"]
+            files = list(set(files))  # Remove duplicates
+            for filename in sorted(files):
+                self._load_command(filename, dir)
 
         msg = "Found {0} commands: {1}"
         commands = ", ".join(self._commands.keys())
@@ -158,6 +154,3 @@ class _CommandManager(object):
                         e = "Error executing command '{0}'"
                         self.logger.exception(e.format(data.command))
                     break
-
-
-command_manager = _CommandManager()
diff --git a/earwigbot/irc/frontend.py b/earwigbot/irc/frontend.py
index 13c6bc3..83a0780 100644
--- a/earwigbot/irc/frontend.py
+++ b/earwigbot/irc/frontend.py
@@ -23,7 +23,6 @@
 import logging
 import re
 
-from earwigbot.commands import command_manager
 from earwigbot.irc import IRCConnection, Data, BrokenSocketException
 
 __all__ = ["Frontend"]
@@ -40,14 +39,15 @@ class Frontend(IRCConnection):
     """
     sender_regex = re.compile(":(.*?)!(.*?)@(.*?)\Z")
 
-    def __init__(self, config):
-        self.config = config
+    def __init__(self, bot):
+        self.bot = bot
+        self.config = bot.config
         self.logger = logging.getLogger("earwigbot.frontend")
+
         cf = config.irc["frontend"]
         base = super(Frontend, self)
         base.__init__(cf["host"], cf["port"], cf["nick"], cf["ident"],
                       cf["realname"], self.logger)
-        command_manager.load(self)
         self._connect()
 
     def _process_message(self, line):
diff --git a/earwigbot/irc/watcher.py b/earwigbot/irc/watcher.py
index f387b13..b29f4f8 100644
--- a/earwigbot/irc/watcher.py
+++ b/earwigbot/irc/watcher.py
@@ -38,14 +38,16 @@ class Watcher(IRCConnection):
     to channels on the IRC frontend.
     """
 
-    def __init__(self, config, frontend=None):
-        self.config = config
+    def __init__(self, bot):
+        self.bot = bot
+        self.config = bot.config
+        self.frontend = bot.frontend
         self.logger = logging.getLogger("earwigbot.watcher")
+
         cf = config.irc["watcher"]
         base = super(Watcher, self)
         base.__init__(cf["host"], cf["port"], cf["nick"], cf["ident"],
                       cf["realname"], self.logger)
-        self.frontend = frontend
         self._prepare_process_hook()
         self._connect()
 
diff --git a/earwigbot/util.py b/earwigbot/util.py
index 6f87740..915747a 100755
--- a/earwigbot/util.py
+++ b/earwigbot/util.py
@@ -36,12 +36,22 @@ class BotUtility(object):
         return __version__
 
     def run(self):
-        print "EarwigBot v{0}\n".format(self.version())
-
-    def main(self):
         root_dir = path.abspath(path.curdir())
         bot = Bot(root_dir)
-        bot.run()
+        try:
+            bot.run()
+        finally:
+            bot.stop()
+
+    def main(self):
+        print "EarwigBot v{0}\n".format(self.version())
+        parser = argparse.ArgumentParser(description=BotUtility.__doc__)
+
+        parser.add_argument("-V", "--version", action="version",
+                            version=self.version())
+
+        args = parser.parse_args()
+#        args.func(args)
 
 
 main = BotUtility().main
diff --git a/setup.py b/setup.py
index 41dc7d9..348b593 100644
--- a/setup.py
+++ b/setup.py
@@ -30,8 +30,10 @@ from setuptools import setup
 setup(
     name = "earwigbot",
     entry_points = {"console_scripts": ["earwigbot = earwigbot.util:main"]},
-    install_requires = ["PyYAML>=3.10", "oursql>=0.9.3", "oauth2>=1.5.211",
-                        "numpy>=1.6.1", "matplotlib>=1.1.0"],
+    install_requires = ["PyYAML>=3.10",
+                        "oursql>=0.9.3",
+                        "oauth2>=1.5.211",
+                        "matplotlib>=1.1.0"],
     version = "0.1.dev",
     author = "Ben Kurtovic",
     author_email = "ben.kurtovic@verizon.net",