diff --git a/amanuensis/cli/server.py b/amanuensis/cli/server.py
index 3dae84e..57876fb 100644
--- a/amanuensis/cli/server.py
+++ b/amanuensis/cli/server.py
@@ -1,6 +1,12 @@
-from cli.helpers import add_argument, no_argument, config_get, config_set, CONFIG_GET_ROOT_VALUE
+import os
 
-@add_argument("--update", action="store_true", help="Refresh an existing config directory")
+from cli.helpers import (
+	add_argument, no_argument,
+	config_get, config_set, CONFIG_GET_ROOT_VALUE)
+
+@add_argument(
+	"--refresh", action="store_true",
+	help="Refresh an existing config directory")
 def command_init(args):
 	"""
 	Initialize a config directory at --config-dir
@@ -8,10 +14,21 @@ def command_init(args):
 	A clean config directory will contain a config.json, a
 	pidfile, a lexicon config directory, and a user config
 	directory.
-	"""
-	import config.init
 
-	config.init.create_config_dir(args.config_dir, args.update)
+	Refreshing an existing directory will add keys to the global config that
+	are present in the default configs. Users and lexicons that are missing
+	from the indexes will be deleted, and stale index entries will be removed.
+	"""
+	# Module imports
+	from config.init import create_config_dir
+
+	# Verify arguments
+	if args.refresh and not os.path.isdir(args.config_dir):
+		print("Error: couldn't find directory '{}'".format(args.config_dir))
+
+	# Internal call
+	create_config_dir(args.config_dir, args.refresh)
+
 
 @no_argument
 def command_generate_secret(args):
@@ -30,6 +47,7 @@ def command_generate_secret(args):
 		cfg['secret_key'] = secret_key.hex()
 	config.logger.info("Regenerated Flask secret key")
 
+
 @add_argument("-a", "--address", default="127.0.0.1")
 @add_argument("-p", "--port", default="5000")
 def command_run(args):
@@ -47,6 +65,7 @@ def command_run(args):
 		return -1
 	server.app.run(host=args.address, port=args.port)
 
+
 @add_argument("--get", metavar="PATHSPEC", dest="get",
 	nargs="?", const=CONFIG_GET_ROOT_VALUE, help="Get the value of a config key")
 @add_argument("--set", metavar=("PATHSPEC", "VALUE"), dest="set",
diff --git a/amanuensis/config/init.py b/amanuensis/config/init.py
index bb2f9ed..e605c65 100644
--- a/amanuensis/config/init.py
+++ b/amanuensis/config/init.py
@@ -3,6 +3,7 @@ import copy
 import json
 import logging.config
 import os
+import shutil
 
 # Module imports
 from errors import MissingConfigError, MalformedConfigError
@@ -10,9 +11,9 @@ import config
 from config.loader import json_ro
 import resources
 
-def create_config_dir(config_dir, update=False):
+def create_config_dir(config_dir, refresh=False):
 	"""
-	Create or update a config directory
+	Create or refresh a config directory
 	"""
 	from collections import OrderedDict
 	import fcntl
@@ -27,14 +28,14 @@ def create_config_dir(config_dir, update=False):
 	config.CONFIG_DIR = config_dir
 
 	# The directory should be empty if we're not updating an existing one.
-	if len(os.listdir(config_dir)) > 0 and not update:
+	if len(os.listdir(config_dir)) > 0 and not refresh:
 		print("Directory {} is not empty".format(config_dir))
 		return -1
 
 	# Update or create global config.
 	def_cfg = resources.get_stream("global.json")
 	global_config_path = path("config.json")
-	if update and os.path.isfile(global_config_path):
+	if refresh and os.path.isfile(global_config_path):
 		# We need to write an entirely different ordereddict to the config
 		# file, so we mimic the config.loader functionality manually.
 		with open(global_config_path, 'r+', encoding='utf8') as cfg_file:
@@ -77,6 +78,30 @@ def create_config_dir(config_dir, update=False):
 		with open(path('user', 'index.json'), 'w') as f:
 			json.dump({}, f)
 
+	if refresh:
+		for dir_name in ('lexicon', 'user'):
+			# Clean up unindexed folders
+			with config.json_ro(dir_name, 'index.json') as index:
+				known = list(index.values())
+			entries = os.listdir(path(dir_name))
+			for dir_entry in entries:
+				if dir_entry == "index.json":
+					continue
+				if dir_entry in known:
+					continue
+				print("Removing unindexed folder: '{}/{}'"
+					.format(dir_name, dir_entry))
+				shutil.rmtree(path(dir_name, dir_entry))
+
+			# Remove orphaned index listings
+			with config.json_rw(dir_name, 'index.json') as index:
+				for name, entry in index.items():
+					if not os.path.isdir(path(dir_name, entry)):
+						print("Removing stale {} index entry '{}: {}'"
+							.format(dir_name, name, entry))
+						del index[name]
+
+
 def verify_config_dir(config_dir):
 	"""
 	Verifies that the given directory has a valid global config in it and
@@ -99,6 +124,7 @@ def verify_config_dir(config_dir):
 	# Configs verified
 	return True
 
+
 def init_logging(args, logging_config):
 	"""
 	Initializes logging by using the logging section of the global config