Describe installed file structure in docs

docs/README.md

@@ -5,6 +5,6 @@ https://openappstack.readthedocs.io/. It is also possible to build the
 documentation, using Sphinx:
 
 ```
-pip install sphinx
+pip install sphinx recommonmark sphinx_rtd_theme
 make html
 ```

docs/index.rst

@@ -28,3 +28,4 @@ For more information, go to `the OpenAppStack website`_.
 
    installation_instructions
    design
+   reference

docs/reference.md

+# Reference documentation
+
+## File structure
+
+During the installation process, the following files and directories are
+created:
+
+- `/etc/OpenAppStack`: directory containing all configuration files that you
+  may want to review and edit during normal usage. See the `README.md` file
+  inside this directory for more details.
+
+- `/var/lib/OpenAppStack/local-storage`: all application data (e.g., Nextcloud
+  files) are stored here.
+
+- `/var/lib/OpenAppStack/rke`: this contains some important files:
+  - `cluster.yml` is a configuration file describing the Kubernetes cluster;
+    this is used by `rke` to install all Kubernetes components;
+  - `kube_config_cluster.yml` contains credentials giving administrator access
+    to the Kubernetes cluster using `kubectl`.
+
+  These two files are also copied to your local machine, inside the
+  `cluster_data` directory, during installation.
+
+- `/var/lib/OpenAppStack/ssh`: some ssh configuration is stored here, including
+  an ssh key that is used by `rke` during cluster installation and upgrades.
+  This ssh connection is from the VPS to itself, and the ssh key does not leave
+  the VPS.
+
+- `/var/lib/OpenAppStack/source`: here local copies are stored of various git
+  repositories that are required during installation.