Added documentation for orphan cleanup

docs/user_guide/content_types.rst

@@ -13,3 +13,4 @@ New in Tripal v3 is the ability to create your own content types and manage thei
    ./content_types/configuring_page_display
    ./content_types/field_loading
    ./content_types/field_permissions
+   ./content_types/cleaning_orphans

docs/user_guide/content_types/cleaning_orphans.rst

@@ -0,0 +1,16 @@
+Handling Orphaned Entities
+==========================
+It is common for site developers to work directly with Chado, especially as they become more familiar with it. And sometimes, there may purpsefully or accidentally remove data that is published in Tripal. This results in an entity being "orphaned".  The entity will still have a page on the website but the data about that entity is no longer available.  If this occurs you can easily remove published entities that are "orphaned" by navigating to **Administer > Tripal Content Types** and clicking the **Unpublish Orphaned Content** link.  The following page appears.
+
+.. image:: cleaning_orphans.1.png
+
+Next, select the content type that has missing data in the **Content Type** select box.  For example, suppose an organism was removed:
+
+.. image:: cleaning_orphans.2.png
+
+A list of at most 10 entities that are orphaned are shown. If the content type has no orphaned entities then nothing is shown.  You can submit a job to clean the orphaned entities by clicking the 
+**Unpublish Orphaned Entities** button.
+
+.. image:: cleaning_orphans.3.png
+
+If you have automatic job execution enabled then the cleanup will occur automatically. Otherwise you should manually execute the job on the command-line using Drush as instructed.