diff --git a/README.md b/README.md
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+++ b/README.md
@@ -54,7 +54,6 @@ The following flags are a list of all the currently supported options that can b
  - **DOMAIN** : Set domain name for Lets Encrypt scripts
  - **RUN_SCRIPTS** : Set to 1 to execute scripts
 
-
 ### Dynamically Pulling code from git
 One of the nice features of this container is its ability to pull code from a git repository with a couple of environmental variables passed at run time. Please take a look at our recommended [repo layout guidelines](docs/repo_layout.md).
 
diff --git a/docs/repo_layout.md b/docs/repo_layout.md
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+## Repository Layout Guidelines
+
+We recommend laying out your source git repository in the following way, to enable you to use all the features of the container.
+
+It's important to note code will always be checked out to ```/var/www/html/``` this is for historic reasons and we may improve this in the future with a user configurable variable. If you just wish to check code out into a container and not do anything special simply put all your files in the root directory of your repository like so:
+
+```
+- repo root (/var/www/html)
+ - index.html
+ - more code here
+```
+
+However if you wish to use scripting support you'll want to split code and scripts up to ensure your scripts are not in the public part of your site.
+
+```
+ - repo root (/var/www/html)
+  - src
+    - your code here
+  - scripts
+    - 00-firstscript.sh
+    - 01-second.sh
+    - ......
+```
+
+### src
+If you use an alternative directory for your application root like the previous example of __src/__, you can use the __WEBROOT__ variable to instruct nginx that that is where the code should be served from.
+
+``` docker run -e 'WEBROOT=/var/www/html/src/' -e OTHER_VARS ........```
+
+One example would be, if you are running craft CMS you'll end up with a repo structure like this:
+
+```
+- repo root (/var/www/html)
+ - craft
+   - core craft
+ - public
+   - index.php
+   -    other public files
+```
+
+In this case __WEBROOT__ would be set as __/var/www/html/public__
+
+### scripts
+Scripts are executed in order so its worth numbering them ```00,01,..,99``` to control their run order. Bash scripts are supported but, of course, you could install other run times in the first script then write your scripts in your preferred language.