fix(docs): update oxidoc.toml sidebar paths and cross-links

Follow-up to 78268bd — the previous commit only captured the file
renames, not the content updates. This commit lands the sidebar path
updates in oxidoc.toml, the internal cross-link fix in crdt.rdx, and
the README directory tree.

Without this, oxidoc build fails with "Page not found: data-modeling/vector"
since the sidebar still pointed at the old paths.

Author: farhan-syah

README.md

@@ -10,7 +10,10 @@ Built with [Oxidoc](https://oxidoc.dev). Published at [nodedb.dev](https://noded
 docs/
 ├── introduction/       Getting started, installation, Docker
 ├── architecture/       Three-plane model, storage, cluster topology
-├── data-modeling/      Engines (Vector, Graph, Document, Columnar, KV, FTS, CRDT), indexes
+├── data-modeling/      Collections and schemas/types
+├── storage-engines/    Vector, Graph, Document, Columnar, KV, FTS, CRDT
+├── columnar-profiles/  Timeseries, Spatial
+├── indexes/            HNSW, CSR, R-tree, B-tree, inverted, hash
 ├── sql/                SQL reference, engine-specific queries, EXPLAIN
 ├── real-time/          LIVE SELECT, change streams, webhooks, cron
 ├── connectivity/       pgwire, HTTP, native protocol, RESP, ILP, client libraries

docs/storage-engines/crdt.rdx

@@ -47,4 +47,4 @@ Deltas that persistently fail constraint validation are routed to a dead-letter
 ## Related
 
 - [CRDT Sync](/docs/crdt-sync/overview) — Full sync protocol and offline patterns
-- [Document Engine](/docs/data-modeling/document) — Schemaless documents with CRDT sync
+- [Document Engine](/docs/storage-engines/document) — Schemaless documents with CRDT sync

oxidoc.toml

@@ -55,25 +55,25 @@ navigation = [
       "data-modeling/schemas-types",
     ] },
     { group = "Storage Engines", pages = [
-      "data-modeling/vector",
-      "data-modeling/graph",
-      "data-modeling/document",
-      "data-modeling/columnar",
-      "data-modeling/kv",
-      "data-modeling/fts",
-      "data-modeling/crdt",
+      "storage-engines/vector",
+      "storage-engines/graph",
+      "storage-engines/document",
+      "storage-engines/columnar",
+      "storage-engines/kv",
+      "storage-engines/fts",
+      "storage-engines/crdt",
     ] },
     { group = "Columnar Profiles", pages = [
-      "data-modeling/timeseries",
-      "data-modeling/spatial",
+      "columnar-profiles/timeseries",
+      "columnar-profiles/spatial",
     ] },
     { group = "Indexes", pages = [
-      "data-modeling/hnsw-index",
-      "data-modeling/csr-index",
-      "data-modeling/rtree-index",
-      "data-modeling/btree-index",
-      "data-modeling/inverted-index",
-      "data-modeling/hash-index",
+      "indexes/hnsw-index",
+      "indexes/csr-index",
+      "indexes/rtree-index",
+      "indexes/btree-index",
+      "indexes/inverted-index",
+      "indexes/hash-index",
     ] },
 
     # ── SQL Reference ──────────────────────────────────────────────