docs: generate hierarchical per-module API reference pages

The API docs previously consisted of a single page (`docs/api.md`)
containing only `::: mcp`, which rendered just the top-level
`mcp/__init__.py` exports. Most of the public API surface (`MCPServer`,
`Context`, `Settings`, `Tool`, `Resource`, `Prompt`, etc.) was missing
because those classes live in subpackages not re-exported at the top
level.

This replaces the single-page approach with auto-generated per-module
pages using the standard mkdocstrings recipe:

- `mkdocs-gen-files` runs `scripts/gen_ref_pages.py` at build time to
  create a virtual `.md` stub for every module under `src/mcp/`
- `mkdocs-literate-nav` reads the generated `api/SUMMARY.md` to build a
  hierarchical sidebar navigation tree
- Material theme's `navigation.indexes` handles section index pages (the
  `mkdocs-section-index` plugin is not needed and conflicts with it)

Also updates `mkdocstrings` `paths` from `[src/mcp]` to `[src]` so that
fully-qualified module identifiers like `mcp.server.mcpserver.server`
resolve correctly.

Author: jonathanhefner

docs/api.md

@@ -64,4 +64,4 @@ npx -y @modelcontextprotocol/inspector
 
 ## API Reference
 
-Full API documentation is available in the [API Reference](api.md).
+Full API documentation is available in the [API Reference](api/mcp/index.md).

docs/index.md

@@ -828,6 +828,6 @@ The lowlevel `Server` also now exposes a `session_manager` property to access th
 
 If you encounter issues during migration:
 
-1. Check the [API Reference](api.md) for updated method signatures
+1. Check the [API Reference](api/mcp/index.md) for updated method signatures
 2. Review the [examples](https://github.com/modelcontextprotocol/python-sdk/tree/main/examples) for updated usage patterns
 3. Open an issue on [GitHub](https://github.com/modelcontextprotocol/python-sdk/issues) if you find a bug or need further assistance

docs/migration.md

@@ -25,7 +25,7 @@ nav:
           - Introduction: experimental/tasks.md
           - Server Implementation: experimental/tasks-server.md
           - Client Usage: experimental/tasks-client.md
-  - API Reference: api.md
+  - API Reference: api/
 
 theme:
   name: "material"
@@ -114,19 +114,22 @@ plugins:
   - search
   - social
   - glightbox
+  - gen-files:
+      scripts:
+        - scripts/gen_ref_pages.py
+  - literate-nav:
+      nav_file: SUMMARY.md
   - mkdocstrings:
       handlers:
         python:
-          paths: [src/mcp]
+          paths: [src]
           options:
             relative_crossrefs: true
             members_order: source
             separate_signature: true
             show_signature_annotations: true
             signature_crossrefs: true
             group_by_category: false
-            # 3 because docs are in pages with an H2 just above them
-            heading_level: 3
           inventories:
             - url: https://docs.python.org/3/objects.inv
             - url: https://docs.pydantic.dev/latest/objects.inv

mkdocs.yml

@@ -74,7 +74,9 @@ dev = [
 ]
 docs = [
     "mkdocs>=1.6.1",
+    "mkdocs-gen-files>=0.5.0",
     "mkdocs-glightbox>=0.4.0",
+    "mkdocs-literate-nav>=0.6.1",
     "mkdocs-material>=9.5.45",
     "mkdocstrings-python>=2.0.1",
 ]

pyproject.toml

@@ -0,0 +1,35 @@
+"""Generate the code reference pages and navigation."""
+
+from pathlib import Path
+
+import mkdocs_gen_files
+
+nav = mkdocs_gen_files.Nav()
+
+root = Path(__file__).parent.parent
+src = root / "src"
+
+for path in sorted(src.rglob("*.py")):
+    module_path = path.relative_to(src).with_suffix("")
+    doc_path = path.relative_to(src).with_suffix(".md")
+    full_doc_path = Path("api", doc_path)
+
+    parts = tuple(module_path.parts)
+
+    if parts[-1] == "__init__":
+        parts = parts[:-1]
+        doc_path = doc_path.with_name("index.md")
+        full_doc_path = full_doc_path.with_name("index.md")
+    elif parts[-1].startswith("_"):
+        continue
+
+    nav[parts] = doc_path.as_posix()
+
+    with mkdocs_gen_files.open(full_doc_path, "w") as fd:
+        ident = ".".join(parts)
+        fd.write(f"::: {ident}")
+
+    mkdocs_gen_files.set_edit_path(full_doc_path, path.relative_to(root))
+
+with mkdocs_gen_files.open("api/SUMMARY.md", "w") as nav_file:
+    nav_file.writelines(nav.build_literate_nav())