diff --git a/realms/__init__.py b/realms/__init__.py
index df06208..8c4c571 100644
--- a/realms/__init__.py
+++ b/realms/__init__.py
@@ -1,3 +1,4 @@
+import functools
 import sys
 
 # Set default encoding to UTF-8
@@ -75,7 +76,9 @@ class Application(Flask):
 
             # Click
             if hasattr(sources, 'commands'):
-                cli.add_command(sources.commands.cli, name=module_name)
+                if sources.commands.cli.name == 'cli':
+                    sources.commands.cli.name = module_name
+                cli.add_command(sources.commands.cli)
 
             # Hooks
             if hasattr(sources, 'hooks'):
@@ -287,9 +290,8 @@ class AppGroup(click.Group):
         kwargs.setdefault('cls', AppGroup)
         return click.Group.group(self, *args, **kwargs)
 
-flask_cli = AppGroup()
+cli = AppGroup()
 
+# Decorator to be used in modules instead of click.group
+cli_group = functools.partial(click.group, cls=AppGroup)
 
-@flask_cli.group()
-def cli():
-    pass
diff --git a/realms/commands.py b/realms/commands.py
index acb50fb..ac228c9 100644
--- a/realms/commands.py
+++ b/realms/commands.py
@@ -1,4 +1,4 @@
-from realms import config, create_app, db, __version__, flask_cli as cli, cache
+from realms import config, create_app, db, __version__, cli, cache
 from realms.lib.util import random_string, in_virtualenv, green, yellow, red
 from subprocess import call, Popen
 from multiprocessing import cpu_count
diff --git a/realms/modules/auth/local/commands.py b/realms/modules/auth/local/commands.py
index 20183be..ae4a7e9 100644
--- a/realms/modules/auth/local/commands.py
+++ b/realms/modules/auth/local/commands.py
@@ -2,10 +2,10 @@ import click
 from realms.lib.util import random_string
 from realms.modules.auth.local.models import User
 from realms.lib.util import green, red, yellow
-from realms import flask_cli
+from realms import cli_group
 
 
-@flask_cli.group(short_help="Auth Module")
+@cli_group(short_help="Auth Module")
 def cli():
     pass
 
diff --git a/realms/modules/search/commands.py b/realms/modules/search/commands.py
index c11edb8..eab1556 100644
--- a/realms/modules/search/commands.py
+++ b/realms/modules/search/commands.py
@@ -1,10 +1,10 @@
 import click
-from realms import create_app, search, flask_cli
+from flask import current_app
+from realms import search, cli_group
 from realms.modules.wiki.models import Wiki
-from realms.lib.util import filename_to_cname
 
 
-@flask_cli.group(short_help="Search Module")
+@cli_group(short_help="Search Module")
 def cli():
     pass
 
@@ -13,29 +13,25 @@ def cli():
 def rebuild_index():
     """ Rebuild search index
     """
-    app = create_app()
-
-    if app.config.get('SEARCH_TYPE') == 'simple':
+    if current_app.config.get('SEARCH_TYPE') == 'simple':
         click.echo("Search type is simple, try using elasticsearch.")
         return
 
-    with app.app_context():
-        # Wiki
-        search.delete_index('wiki')
-        wiki = Wiki(app.config['WIKI_PATH'])
-        for entry in wiki.get_index():
-            page = wiki.get_page(entry['name'])
-            if not page:
-                # Some non-markdown files may have issues
-                continue
-            name = filename_to_cname(page['path'])
-            # TODO add email?
-            # TODO I have concens about indexing the commit info from latest revision, see #148
-            info = next(page.history)
-            body = dict(name=name,
-                        content=page.data,
-                        message=info['message'],
-                        username=info['author'],
-                        updated_on=entry['mtime'],
-                        created_on=entry['ctime'])
-            search.index_wiki(name, body)
+    # Wiki
+    search.delete_index('wiki')
+    wiki = Wiki(current_app.config['WIKI_PATH'])
+    for entry in wiki.get_index():
+        page = wiki.get_page(entry['name'])
+        if not page:
+            # Some non-markdown files may have issues
+            continue
+        # TODO add email?
+        # TODO I have concens about indexing the commit info from latest revision, see #148
+        info = next(page.history)
+        body = dict(name=page.name,
+                    content=page.data,
+                    message=info['message'],
+                    username=info['author'],
+                    updated_on=entry['mtime'],
+                    created_on=entry['ctime'])
+        search.index_wiki(page.name, body)