Documentation: Update WA3 Documentation

Update the documentation and build system for producing documentation for
WA3 with support for automatic building on readthedocs.

Note: This is currently a WIP.

doc/source/user_reference/configuration.rst

@@ -0,0 +1,54 @@
+.. _configuration-specification:
+
+
+Configuration
+=============
+
+Run Configuration
+------------------
+In addition to specifying run execution parameters through an agenda, the
+behaviour of WA can be modified through configuration file(s). The default
+configuration file is ``~/.workload_automation/config.yaml``  (the location can
+be changed by setting ``WA_USER_DIRECTORY`` environment variable, see
+:ref:`envvars` section below). This file will be created when you first run WA
+if it does not already exist. This file must always exist and will always be
+loaded. You can add to or override the contents of that file on invocation of
+Workload Automation by specifying an additional configuration file using
+``--config`` option. Variables with specific names  will be picked up by the
+framework and used to modify the behaviour of Workload automation.
+
+.. _available_settings:
+
+.. include:: run_config/Run_Configuration.rst
+
+Meta Configuration
+------------------
+
+There are also a couple of settings are used to provide additional metadata
+for a run. These may get picked up by instruments or output processors to
+attach context to results.
+
+.. include:: run_config/Meta_Configuration.rst
+
+
+.. _envvars:
+
+Environment Variables
+---------------------
+
+In addition to standard configuration described above, WA behaviour can be
+altered through environment variables. These can determine where WA looks for
+various assets when it starts.
+
+.. confval:: WA_USER_DIRECTORY
+
+   This is the location WA will look for config.yaml, plugins,  dependencies,
+   and it will also be used for local caches, etc. If this variable is not set,
+   the default location is ``~/.workload_automation`` (this is created when WA
+   is installed).
+
+   .. note:: This location **must** be writable by the user who runs WA.
+
+
+.. include:: user_reference/runtime_parameters.rst
+