[Docs] Reorganise and add sections from wiki

- Change the layout and contents of docs to be better organised and
  follow ideas from: https://www.divio.com/blog/documentation/
- Use markdown for non-technical documents to speed up writing.
- Added new sections and imported documents from Trac wiki.

Build fixes:

- Added a patch to fix recommonmark 0.4 and doc referencing:
    https://github.com/rtfd/recommonmark/issues/93
- Set docs build in tox to Py2.7 since there are problems with autodoc
  mocking multiple inheritance on Python 3 resulting in metaclass errors.
- Supressed warning about `modules.rst` not in the toctree by creating
  a static `modules.rst` with `:orphan:` file directive and add to git.
  Also skip creating this toc file with sphinx-apidoc in setup and tox.
- Simplified finding exported RPC and JSON API methods by adding an
  autodoc custom class directive. Removed unneeded __rpcapi.py.

docs/source/reference/api.rst

@@ -0,0 +1,12 @@
+Deluge RPC API
+==============
+
+* :doc:`rpc`
+
+.. autoclass:: deluge.core.core.Core
+    :members:
+    :exported:
+
+.. autoclass:: deluge.core.daemon.Daemon
+    :members:
+    :exported:

docs/source/reference/index.rst

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+Reference
+=========
+
+Technical reference material.
+
+.. toctree::
+
+    Web UI <web>
+    Deluge RPC <rpc>
+    RPC API <api>
+    Web API <webapi>

docs/source/reference/rpc.rst

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+Deluge RPC
+==========
+---------------
+Message Formats
+---------------
+DelugeRPC is a protocol used for daemon/client communication. There are four
+types of messages involved in the protocol: RPC Request, RPC Response,
+RPC Error and Event. All messages are zlib compressed rencoded strings and
+their data formats are detailed below.
+
+"""""""""""
+RPC Request
+"""""""""""
+This message is created and sent by the client to the server requesting that a
+remote method be called. Multiple requests can be bundled in a list.
+
+**[[request_id, method, [args], {kwargs}], ...]**
+
+**request_id** (int)
+    An integer determined by the client that is used in replies from the server.
+    This is used to ensure the client knows which request the data is in
+    response to. Another alternative would be to respond in the same order the
+    requests come in, but this could cause lag if an earlier request takes
+    longer to process.
+
+**method** (str)
+    The name of the remote method to call. This name can be in dotted format to
+    call other objects or plugins methods.
+
+**args** (list)
+    The arguments to call the method with.
+
+**kwargs** (dict)
+    The keyword arguments to call the method with.
+
+""""""""""""
+RPC Response
+""""""""""""
+This message is created and sent in response to a RPC Request from a client. It
+will hold the return value of the requested method call. In the case of an
+error, a RPC Error message will be sent instead.
+
+**[message_type, request_id, [return_value]]**
+
+**message_type** (int)
+    This will be a RPC_RESPONSE type id. This is used on the client side to
+    determine what kind of message is being received from the daemon.
+
+**request_id** (int)
+    The request_id is the same as the one sent by the client in the initial
+    request. It used on the client side to determine what message this is in
+    response to.
+
+**return_value** (list)
+    The return value of the method call.
+
+"""""""""
+RPC Error
+"""""""""
+This message is created in response to an error generated while processing a
+RPC Request and will serve as a replacement for a RPC Response message.
+
+**[message_type, request_id, exception_type, exception_msg, traceback]**
+
+**message_type** (int)
+    This will be a RPC_ERROR type id.
+
+**request_id** (int)
+    The request_id is the same as the one sent by the client in the initial
+    request.
+
+**exception_type** (str)
+    The type of exception raised.
+
+**exception_msg** (str)
+    The message as to why the exception was raised.
+
+**traceback** (str)
+    The traceback of the generated exception.
+
+"""""
+Event
+"""""
+This message is created by the daemon and sent to the clients without being in
+response to a RPC Request. Events are generally sent for changes in the
+daemon's state that the clients need to be made aware of.
+
+**[message_type, event_name, data]**
+
+**message_type** (int)
+    This will be a RPC_EVENT type id.
+
+**event_name** (str)
+    This is the name of the event being emitted by the daemon.
+
+**data** (list)
+    Additional data to be sent with the event. This is dependent upon the event
+    being emitted.

docs/source/reference/web.md

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+# Deluge Web UI
+
+The Deluge web interface is intended to be a full featured interface built using
+the ExtJS framework, running on top of a Twisted webserver.
+
+## SSL Configuration
+
+By default the web interface will use the same private key and certificate as
+the Deluge daemon. If you wish to use a different certificate/key (see
+[How to Create a SSL Certificate](http://www.yatblog.com/2007/02/27/how-to-create-a-ssl-certificate/))
+for information on creating one) you are able to specify which you want to use.
+
+There are 2 ways to enable SSL encryption in the webserver, 1 is to specify it
+in your configuration (accessible via the Preferences window). The other is to
+add '--ssl' when running the webserver, which will override the configuration
+value and enable SSL.

docs/source/reference/webapi.rst

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+Deluge Web JSON-RPC API
+=======================
+
+* Spec: `JSON-RPC v1 <https://www.jsonrpc.org/specification_v1>`_
+* URL: ``/json``
+* :doc:`api`
+
+
+.. autoclass:: deluge.ui.web.json_api.WebApi
+    :members:
+    :exported:
+    :noindex:
+
+.. autoclass:: deluge.ui.web.json_api.WebUtils
+    :members:
+    :exported:
+    :noindex: