diff --git a/docs/tools/tools-cli.rst b/docs/tools/tools-cli.rst
--- a/docs/tools/tools-cli.rst
+++ b/docs/tools/tools-cli.rst
@@ -12,6 +12,26 @@ The commands available with |RCT| can be
 - Local configuration commands used to help set up your |RCT| configuration.
 
 
+.. _tools-rhodecode-list-instance:
+
+rhodecode-list-instances
+------------------------
+
+Use this command to list the instance details configured in the
+:file:`/etc/rhodecode/conf/.rhoderc` file.
+
+.. code-block:: bash
+
+   $ ./rcstack cli cmd rhodecode-list-instances --config=/etc/rhodecode/conf/.rhoderc
+   [instance:production] - Config only
+   API-HOST: https://some.url.com
+   API-KEY:  some.auth.token
+
+   [instance:development] - Config only
+   API-HOST: http://some.ip.address
+   API-KEY:  some.auth.token
+
+
 rhodecode-tools
 ---------------
 
@@ -163,6 +183,7 @@ Example usage:
     removing gist /home/brian/repos/.rc_gist_store/5
     removing gist /home/brian/repos/.rc_gist_store/8FtCKdcbRKmEvRzTVsEt
 
+
 rhodecode-cleanup-repos
 -----------------------
 
@@ -201,30 +222,37 @@ Example usage:
 
 .. code-block:: bash
 
-    # Cleaning up repos using tools installed with RCE 350 and above
-    $ ~/.rccontrol/enterprise-4/profile/bin/rhodecode-cleanup-repos \
-        --instance-name=enterprise-4 --older-than=1d
-    Scanning for repositories in /home/brian/repos...
-    preparing to remove [2] found repositories older than 1 day, 0:00:00 (1d)
+
+    # create a .rhoderc file in your host config directory (in :file:`config/_shared/.rhoderc`):
+
+    [instance:rcstack-instance]
+    api_host = http://rhodecode:10020
+    api_key = <API_KEY>
+    repo_dir = /var/opt/rhodecode_repo_store
+
+    # Run rcstack cli
+    ./rcstack cli cmd rhodecode-cleanup-repos --instance-name=rcstack-instance --config=/etc/rhodecode/conf/.rhoderc
+
+    checking if config files needs bootstrapping
+    Scanning for repositories in /var/opt/rhodecode_repo_store...
 
     the following repositories will be deleted completely:
-    * REMOVED: 2015-08-05 00:23:18 | /home/brian/repos/rm__20150805_002318_831
-    * REMOVED: 2015-08-04 01:22:10 | /home/brian/repos/rm__20150804_012210_336
+    * REMOVED: 2015-08-05 00:23:18 | /var/opt/rhodecode_repo_store/rm__20150805_002318_831
+    * REMOVED: 2015-08-04 01:22:10 | /var/opt/rhodecode_repo_store/rm__20150804_012210_336
     are you sure you want to remove them? [y/N]:
 
     # Clean up repos older than 1 year
-    # If using virtualenv and pre RCE 350 tools installation
-    (venv)$ rhodecode-cleanup-repos --instance-name=enterprise-1 \
-        --older-than=365d
+    ./rcstack cli cmd rhodecode-cleanup-repos --instance-name=rcstack-instance --config=/etc/rhodecode/conf/.rhoderc --older-than=365d
 
-    Scanning for repositories in /home/brian/repos...
+    checking if config files needs bootstrapping
+    Scanning for repositories in /var/opt/rhodecode_repo_store...
     preparing to remove [343] found repositories older than 365 days
 
     # clean up repos older than 3 days
-    # If using virtualenv and pre RCE 350 tools installation
-    (venv)$ rhodecode-cleanup-repos --instance-name=enterprise-1 \
-        --older-than=3d
-    Scanning for repositories in /home/brian/repos...
+    ./rcstack cli cmd rhodecode-cleanup-repos --instance-name=rcstack-instance --config=/etc/rhodecode/conf/.rhoderc --older-than=3d
+
+    checking if config files needs bootstrapping
+    Scanning for repositories in /var/opt/rhodecode_repo_store...
     preparing to remove [3] found repositories older than 3 days
 
 .. _tools-config:
@@ -420,9 +448,8 @@ Example usage:
     }
 
     # Cat a file and pipe to gist
-    # in RCE 3.5.0 tools and above
-    $ cat ~/.rhoderc | ~/.rccontrol/{instance-id}/profile/bin/rhodecode-gist \
-       --instance-name=enterprise-4 -d '.rhoderc copy' create
+
+    $ cat ~/.rhoderc | ./rcstack cli cmd rhodecode-gist --instance-name=rcstack-instance --config=/etc/rhodecode/conf/.rhoderc -d '.rhoderc copy' create
     {
       "error": null,
       "id": 9253,
@@ -512,41 +539,18 @@ Example usage:
 
 .. code-block:: bash
 
-    # Run the indexer
-    $ ~/.rccontrol/enterprise-4/profile/bin/rhodecode-index \
-        --instance-name=enterprise-4
+    # Create the indexing mapping file
+    $ ./rcstack cli cmd rhodecode-index --instance-name=rcstack-instance --config=/etc/rhodecode/conf/.rhoderc --create-mapping search_mapping.ini
 
-    # Run indexer based on search_mapping.ini file
-    # This is using pre-350 virtualenv
-    (venv)$ rhodecode-index --instance-name=enterprise-1
+    # Run the indexer
+    $ ./rcstack cli cmd rhodecode-index --instance-name=rcstack-instance --config=/etc/rhodecode/conf/.rhoderc
+
+    # Run indexer based on search_mapping.ini file using rhodecode-tools virtualenv
+    (venv)$ rhodecode-index --instance-name=rcstack-instance
 
     # Index from the command line without creating
     # the .rhoderc file
-    $ rhodecode-index --apikey=key --apihost=http://rhodecode.server \
-        --instance-name=enterprise-2 --save-config
-
-    # Create the indexing mapping file
-    $ ~/.rccontrol/enterprise-4/profile/bin/rhodecode-index \
-        --create-mapping search_mapping.ini --instance-name=enterprise-4
-
-.. _tools-rhodecode-list-instance:
-
-rhodecode-list-instances
-------------------------
-
-Use this command to list the instance details configured in the
-:file:`~/.rhoderc` file.
-
-.. code-block:: bash
-
-   $ .rccontrol/enterprise-1/profile/bin/rhodecode-list-instances
-   [instance:production] - Config only
-   API-HOST: https://some.url.com
-   API-KEY:  some.auth.token
-
-   [instance:development] - Config only
-   API-HOST: http://some.ip.address
-   API-KEY:  some.auth.token
+    $ rhodecode-index --apikey=key --apihost=http://rhodecode.server --instance-name=rcstack-instance --save-config
 
 
 .. _tools-setup-config: