docs: convert bold cross-references into links, link SEP and RFC mentions

The book's bold chapter names were placeholder cross-references from the
initial rewrite. Convert the genuine chapter pointers into bold-wrapped
page-relative links (**[Title](path.md)**); bold that names a concept,
UI tab, or the page's own topic stays plain.

Also link external references: SEP-N mentions point at the spec-repo
proposal (issue or PR, whichever the number canonically is), RFCs point
at their datatracker pages, and the few unlinked third-party deps on the
installation page get their PyPI links. Existing SEP links that relied
on GitHub's issue-to-PR redirect now use the canonical URL.

Author: maxisbey

docs/advanced/authorization.md

@@ -32,11 +32,11 @@ The SDK has no opinion about what a valid token looks like. You tell it, by impl
 
 !!! tip
     `examples/servers/simple-auth/` in the SDK repository has an `IntrospectionTokenVerifier` that calls
-    a real authorization server's RFC 7662 endpoint. It's the shape most production verifiers take.
+    a real authorization server's [RFC 7662](https://datatracker.ietf.org/doc/html/rfc7662) endpoint. It's the shape most production verifiers take.
 
 ## What you get over HTTP
 
-Authorization lives in HTTP headers, so it exists only on the HTTP transports. Run it on the one you deploy: `mcp.run(transport="streamable-http")` puts it on `http://127.0.0.1:8000/mcp`, and **Running your server** has the rest. The app now has two routes:
+Authorization lives in HTTP headers, so it exists only on the HTTP transports. Run it on the one you deploy: `mcp.run(transport="streamable-http")` puts it on `http://127.0.0.1:8000/mcp`, and **[Running your server](../run/index.md)** has the rest. The app now has two routes:
 
 ```text
 /mcp
@@ -47,7 +47,7 @@ You registered one tool. The second route is the SDK's.
 
 ### Discovery
 
-`GET` that well-known path and you get **RFC 9728 Protected Resource Metadata**, built straight from your `AuthSettings`:
+`GET` that well-known path and you get **[RFC 9728](https://datatracker.ietf.org/doc/html/rfc9728) Protected Resource Metadata**, built straight from your `AuthSettings`:
 
 ```json
 {
@@ -109,15 +109,15 @@ To watch all three parties move, run `examples/servers/simple-auth/` from the SD
     server inside your MCP server. It predates the AS/RS separation that the MCP authorization spec
     is built around. New servers should not reach for it.
 
-An authorization server can also accept an enterprise identity provider's signed assertion in place of a user clicking through a consent screen, and the SDK supports both sides of that exchange. The grant, and the client that presents it, is **Identity assertion**.
+An authorization server can also accept an enterprise identity provider's signed assertion in place of a user clicking through a consent screen, and the SDK supports both sides of that exchange. The grant, and the client that presents it, is **[Identity assertion](identity-assertion.md)**.
 
 ## Recap
 
 * Over Streamable HTTP your server is an OAuth 2.1 **resource server**: it verifies tokens, it never issues them.
 * `TokenVerifier` is the whole integration surface: one async method, token in, `AccessToken | None` out.
 * `token_verifier=` and `auth=AuthSettings(issuer_url=..., resource_server_url=..., required_scopes=[...])` always travel together.
-* The SDK publishes RFC 9728 Protected Resource Metadata at `/.well-known/oauth-protected-resource/...` and answers unauthenticated requests with a 401 whose `WWW-Authenticate` header points at it. That is the entire discovery story.
+* The SDK publishes [RFC 9728](https://datatracker.ietf.org/doc/html/rfc9728) Protected Resource Metadata at `/.well-known/oauth-protected-resource/...` and answers unauthenticated requests with a 401 whose `WWW-Authenticate` header points at it. That is the entire discovery story.
 * `get_access_token()` in any handler is who's calling.
 * Authorization is an HTTP concern. `stdio` and the in-memory client never see it.
 
-The other side of the handshake, a client that discovers your authorization server and fetches the token for you, is **OAuth clients**.
+The other side of the handshake, a client that discovers your authorization server and fetches the token for you, is **[OAuth clients](oauth-clients.md)**.

docs/advanced/deprecated.md

@@ -8,16 +8,16 @@ The table below names each deprecated feature, why it is going away, and the rep
 
 | Deprecated | Why | What you do instead |
 |---|---|---|
-| **Roots**: `ctx.session.list_roots()`, `client.send_roots_list_changed()`, the `list_roots_callback=` you pass to `Client(...)` | [SEP-2577](https://github.com/modelcontextprotocol/modelcontextprotocol/pull/2577) retires the capability. | Take the paths as ordinary tool arguments or resource URIs, or embed a `ListRootsRequest` in an `InputRequiredResult` (see **Multi-round-trip requests**). |
-| **Server-initiated sampling**: `ctx.session.create_message()`, the `sampling_callback=` you pass to `Client(...)` | SEP-2577 retires the capability. | Return `InputRequiredResult` and let the client retry the call (see **Multi-round-trip requests**). |
-| **Protocol logging**: `ctx.log()`, `ctx.debug()`, `ctx.info()`, `ctx.warning()`, `ctx.error()`, `ctx.session.send_log_message()`, `client.set_logging_level()` | SEP-2577 retires the capability. Nothing in-protocol replaces it. | Ordinary `import logging` to stderr (see **Logging**). |
+| **Roots**: `ctx.session.list_roots()`, `client.send_roots_list_changed()`, the `list_roots_callback=` you pass to `Client(...)` | [SEP-2577](https://github.com/modelcontextprotocol/modelcontextprotocol/pull/2577) retires the capability. | Take the paths as ordinary tool arguments or resource URIs, or embed a `ListRootsRequest` in an `InputRequiredResult` (see **[Multi-round-trip requests](multi-round-trip.md)**). |
+| **Server-initiated sampling**: `ctx.session.create_message()`, the `sampling_callback=` you pass to `Client(...)` | SEP-2577 retires the capability. | Return `InputRequiredResult` and let the client retry the call (see **[Multi-round-trip requests](multi-round-trip.md)**). |
+| **Protocol logging**: `ctx.log()`, `ctx.debug()`, `ctx.info()`, `ctx.warning()`, `ctx.error()`, `ctx.session.send_log_message()`, `client.set_logging_level()` | SEP-2577 retires the capability. Nothing in-protocol replaces it. | Ordinary `import logging` to stderr (see **[Logging](../tutorial/logging.md)**). |
 | **`ping`**: `client.send_ping()` | **Removed** from the protocol, not merely deprecated. There is no `ping` method in 2026-07-28. | Nothing. It only works against a `mode="legacy"` connection. |
-| **Client->server progress**: `client.send_progress_notification()` | 2026-07-28 makes progress server->client only. | Nothing to send. Your *server* reports progress with `ctx.report_progress()` (see **Progress**). |
+| **Client->server progress**: `client.send_progress_notification()` | 2026-07-28 makes progress server->client only. | Nothing to send. Your *server* reports progress with `ctx.report_progress()` (see **[Progress](../tutorial/progress.md)**). |
 
 Three things fall out of that table:
 
 * Roots, sampling, and logging go together. One proposal, **SEP-2577**, deprecates all three capabilities at once.
-* Sampling and roots share a deeper problem: they are places a **server** sends a **request** to the **client**. That whole direction is what 2026-07-28 replaces with **Multi-round-trip requests**. It is the standalone RPC methods (`sampling/createMessage`, `roots/list`, and push-style `elicitation/create`) that are gone; the `CreateMessageRequest` / `ListRootsRequest` / `ElicitRequest` payload types survive, embedded in `InputRequiredResult.input_requests`, and on the client they hit the same callbacks.
+* Sampling and roots share a deeper problem: they are places a **server** sends a **request** to the **client**. That whole direction is what 2026-07-28 replaces with **[Multi-round-trip requests](multi-round-trip.md)**. It is the standalone RPC methods (`sampling/createMessage`, `roots/list`, and push-style `elicitation/create`) that are gone; the `CreateMessageRequest` / `ListRootsRequest` / `ElicitRequest` payload types survive, embedded in `InputRequiredResult.input_requests`, and on the client they hit the same callbacks.
 * `ping` is the odd one out. The protocol does not deprecate it, it removes it. The SDK method still warns (its message says *removed*, not *deprecated*) and calling it on a modern connection answers with *"Method not found"*.
 
 ## Deprecated is advisory
@@ -81,8 +81,8 @@ That is the whole API. There is no per-method switch, and you don't want one: th
 
 ## Recap
 
-* The 2026-07-28 spec deprecates **roots**, server-initiated **sampling**, and protocol **logging** (all SEP-2577), restricts **progress** to server-to-client, and removes **`ping`**.
-* The replacement column points you onward: **Multi-round-trip requests** for sampling and roots, **Logging** for logging, **Progress** for progress. `ping` needs nothing at all.
+* The 2026-07-28 spec deprecates **roots**, server-initiated **sampling**, and protocol **logging** (all [SEP-2577](https://github.com/modelcontextprotocol/modelcontextprotocol/pull/2577)), restricts **progress** to server-to-client, and removes **`ping`**.
+* The replacement column points you onward: **[Multi-round-trip requests](multi-round-trip.md)** for sampling and roots, **[Logging](../tutorial/logging.md)** for logging, **[Progress](../tutorial/progress.md)** for progress. `ping` needs nothing at all.
 * Deprecated is advisory: no wire changes, everything keeps working against pre-2026 sessions, and you get a visible `MCPDeprecationWarning` (a `UserWarning`, so it is on by default).
 * Sampling and roots additionally need a back-channel that a 2026-07-28 session does not have. On a modern connection they warn and then they raise.
 * `warnings.filterwarnings("ignore", category=MCPDeprecationWarning)` silences the whole category; `"error::mcp.MCPDeprecationWarning"` in pytest turns it into a test failure.