(#5849) Convert rst to markdown (#6040)

Converting some of the rst documentation to markdown.  Attempted to
preserve whitespace and line breaks to minimize cosmetic change.

docs/ancient_architecture_notes.md

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+> **Warning**
+>  These architecture notes are spectacularly old, and date back
+> to when Synapse was just federation code in isolation. This should be
+> merged into the main spec.
+
+# Server to Server
+
+## Server to Server Stack
+
+To use the server to server stack, home servers should only need to
+interact with the Messaging layer.
+
+The server to server side of things is designed into 4 distinct layers:
+
+1.  Messaging Layer
+2.  Pdu Layer
+3.  Transaction Layer
+4.  Transport Layer
+
+Where the bottom (the transport layer) is what talks to the internet via
+HTTP, and the top (the messaging layer) talks to the rest of the Home
+Server with a domain specific API.
+
+1. **Messaging Layer**
+
+    This is what the rest of the Home Server hits to send messages, join rooms,
+    etc. It also allows you to register callbacks for when it get's notified by
+    lower levels that e.g. a new message has been received.
+
+    It is responsible for serializing requests to send to the data
+    layer, and to parse requests received from the data layer.
+
+2. **PDU Layer**
+
+    This layer handles:
+
+		- duplicate `pdu_id`'s - i.e., it makes sure we ignore them.
+		- responding to requests for a given `pdu_id`
+		- responding to requests for all metadata for a given context (i.e. room)
+		- handling incoming backfill requests
+
+		So it has to parse incoming messages to discover which are metadata and
+    which aren't, and has to correctly clobber existing metadata where
+    appropriate.
+
+    For incoming PDUs, it has to check the PDUs it references to see
+    if we have missed any. If we have go and ask someone (another
+    home server) for it.
+
+3. **Transaction Layer**
+
+		This layer makes incoming requests idempotent. i.e., it stores
+		which transaction id's we have seen and what our response were.
+		If we have already seen a message with the given transaction id,
+		we do not notify higher levels but simply respond with the
+		previous response.
+
+		`transaction_id` is from "`GET /send/<tx_id>/`"
+
+		It's also responsible for batching PDUs into single transaction for
+		sending to remote destinations, so that we only ever have one
+		transaction in flight to a given destination at any one time.
+
+		This is also responsible for answering requests for things after a
+		given set of transactions, i.e., ask for everything after 'ver' X.
+
+4. **Transport Layer**
+
+		This is responsible for starting a HTTP server and hitting the
+		correct callbacks on the Transaction layer, as well as sending
+		both data and requests for data.
+
+## Persistence
+
+We persist things in a single sqlite3 database. All database queries get
+run on a separate, dedicated thread. This that we only ever have one
+query running at a time, making it a lot easier to do things in a safe
+manner.
+
+The queries are located in the `synapse.persistence.transactions` module,
+and the table information in the `synapse.persistence.tables` module.