docs: re-org nav so theory doesn't overwhelm practitioners

The Substrate group is Dav1d's formal Merkle-AGI research that drove the
design — valuable, but it sat third in the nav and read like required
reading. IA-only fix (no content touched):
- re-caption 'Substrate' -> 'Substrate theory (advanced)' + a preamble
  marking it optional (nothing in Getting started / API depends on it);
- reorder it BELOW the practical sections (now: Summary -> Getting started
  -> API -> Substrate theory -> Project);
- pull 'bench' out of Substrate into Getting started (it's the practical
  benchmark surface, not theory).
Practitioner path comes first; theory stays intact + credited, just last.

docs/_source/index.rst

@@ -20,16 +20,6 @@ Contents:
    quickstart
    concepts
    cookbook
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Substrate
-
-   merkle-agi-dag-v7
-   merkle-agi-v7w-spatial-temporal
-   merkle-agi-v8-consensus
-   v8-fork-score
-   pi-star
    bench
 
 .. toctree::
@@ -45,6 +35,25 @@ Contents:
    api/mesh
    api/cli
 
+Substrate theory (advanced)
+---------------------------
+
+The pages below formalize the **Merkle-AGI substrate** that drove
+arborist's design and business logic (the research line behind the
+tickets and code). They are **optional for users** — nothing in *Getting
+started* or the *API* depends on them. Read them only if you want the
+formal model.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Substrate theory (advanced)
+
+   merkle-agi-dag-v7
+   merkle-agi-v7w-spatial-temporal
+   merkle-agi-v8-consensus
+   v8-fork-score
+   pi-star
+
 .. toctree::
    :maxdepth: 1
    :caption: Project