May 26, 2026, 10:49 AM

brain/GEMINI.md

@@ -16,7 +16,8 @@ The LLM writes and maintains all files under `wiki/`. The human curates raw sour
     - `wiki/journal/` — Research or session journal entries.
     - `wiki/presentations/` — Marp slide decks generated from wiki content.
     - `wiki/feynman_problems.md` — Central tracking of long-term problems.
-    - `wiki/index.md` — Master catalog. Every wiki page must appear here.
+    - `wiki/index.md` — Master catalog and portal to thematic indices.
+    - `wiki/indices/` — Thematic and type-based index files.
     - `wiki/log.md` — Append-only activity log.
 
 ## File Naming & Format
@@ -69,11 +70,12 @@ When the user says "ingest [source]" or adds a file to `raw/`:
 4. **Feynman Check**: Compare against `wiki/feynman_problems.md` and update it if connections are found.
 5. Create/Update concept and entity pages using the required sections.
 6. Add cross-links in both directions between all touched pages.
-7. Update `wiki/index.md` and `wiki/log.md`.
-8. Flag any contradictions with existing content.
+7. Update `wiki/log.md` and relevant indices in `wiki/indices/` (thematic and type-based).
+8. Update `wiki/index.md` if new categories are needed.
+9. Flag any contradictions with existing content.
 
 ### 2. Query
-1. Read `wiki/index.md` to find relevant pages.
+1. Read `wiki/index.md` and relevant thematic indices in `wiki/indices/` to find relevant pages.
 2. Synthesize an answer citing specific pages with wiki links.
 3. If new insight is found, create a synthesis page in `wiki/syntheses/`.