feat: geometric graph topology + module pages + phantom link cleanup

Graph topology (Metatron's Cube pattern — 1 center + 12 outer nodes):
- index: now links to ALL 12 other nodes (complete hub)
- Inner ring cycle: hot→log→overview→dashboard→concepts/_index→entities/_index
  - Added: hot↔WikiMap, log↔sources/_index, dashboard↔concepts/_index
  - Added: entities/_index↔hot, entities/_index↔LLM Wiki Pattern
  - Added: sources/_index↔log, sources/_index↔entities/_index
- Outer ring: concepts connected in triangle + Karpathy/sources cross-linked
  - Added: dashboard↔Compounding, entities/_index↔LLM Wiki Pattern

graph.json physics for geometric arrangement:
- repelStrength: 80 (strong push-apart for uniform spacing)
- linkStrength: 3.0 (locks ring geometry)
- linkDistance: 80 (tighter rings)
- centerStrength: 0.25 (moderate center pull)
- nodeSizeMultiplier: 2.0 (hub nodes visually dominant)
- Added colors: questions=yellow, comparisons=red, nav=teal

Phantom links removed from Hot Cache.md:
- Removed [[Page A]], [[Page B]], [[New Page 1]], [[Existing Page]]

New module pages:
- wiki/questions/How does the LLM Wiki pattern work.md
- wiki/comparisons/Wiki vs RAG.md
- Adds questions/ and comparisons/ domains to the graph (yellow + red nodes)

.obsidian/graph.json

@@ -7,52 +7,24 @@
   "showOrphans": false,
   "collapse-color-groups": false,
   "colorGroups": [
-    {
+    { "query": "path:wiki/entities",    "color": { "a": 1, "rgb": 12945088 } },
-      "query": "path:wiki/entities",
+    { "query": "path:wiki/concepts",    "color": { "a": 1, "rgb": 5227007  } },
-      "color": {
+    { "query": "path:wiki/sources",     "color": { "a": 1, "rgb": 6986069  } },
-        "a": 1,
+    { "query": "path:wiki/questions",   "color": { "a": 1, "rgb": 14474410 } },
-        "rgb": 12945088
+    { "query": "path:wiki/comparisons", "color": { "a": 1, "rgb": 13724009 } },
-      }
+    { "query": "path:wiki/meta",        "color": { "a": 1, "rgb": 5676246  } },
-    },
+    { "query": "path:wiki",             "color": { "a": 1, "rgb": 4473924  } }
-    {
-      "query": "path:wiki/concepts",
-      "color": {
-        "a": 1,
-        "rgb": 5227007
-      }
-    },
-    {
-      "query": "path:wiki/sources",
-      "color": {
-        "a": 1,
-        "rgb": 6986069
-      }
-    },
-    {
-      "query": "path:wiki/meta",
-      "color": {
-        "a": 1,
-        "rgb": 5676246
-      }
-    },
-    {
-      "query": "path:wiki",
-      "color": {
-        "a": 1,
-        "rgb": 5676246
-      }
-    }
   ],
   "collapse-display": true,
   "showArrow": true,
   "textFadeMultiplier": -1,
-  "nodeSizeMultiplier": 1.8,
+  "nodeSizeMultiplier": 2.0,
-  "lineSizeMultiplier": 1.2,
+  "lineSizeMultiplier": 0.8,
   "collapse-forces": false,
-  "centerStrength": 0.5,
+  "centerStrength": 0.25,
-  "repelStrength": 20,
+  "repelStrength": 80,
-  "linkStrength": 1,
+  "linkStrength": 3.0,
-  "linkDistance": 385,
+  "linkDistance": 80,
-  "scale": 0.48198745386564384,
+  "scale": 1.2,
   "close": false
 }

.obsidian/workspace.json

@@ -16,19 +16,8 @@
               "icon": "lucide-git-fork",
               "title": "Graph view"
             }
-          },
-          {
-            "id": "c0d470cf50ffdf79",
-            "type": "leaf",
-            "state": {
-              "type": "graph",
-              "state": {},
-              "icon": "lucide-git-fork",
-              "title": "Graph view"
           }
-          }
+        ]
-        ],
-        "currentTab": 1
       }
     ],
     "direction": "vertical"
@@ -187,21 +176,24 @@
       "bases:Create new base": false
     }
   },
-  "active": "c0d470cf50ffdf79",
+  "active": "0ae3ce8edab2ab7f",
   "lastOpenFiles": [
-    "README.md.tmp.224546.1775555737152",
+    "wiki/comparisons/Wiki vs RAG.md",
+    "wiki/comparisons/Wiki vs RAG.md.tmp.224546.1775556215080",
+    "wiki/questions/How does the LLM Wiki pattern work.md",
+    "wiki/questions/How does the LLM Wiki pattern work.md.tmp.224546.1775556203684",
+    "wiki/comparisons",
+    "wiki/questions",
+    "wiki/concepts/_index.md.tmp.224546.1775556164132",
+    "wiki/index.md.tmp.224546.1775556150463",
+    "wiki/log.md.tmp.224546.1775556137750",
+    "wiki/hot.md.tmp.224546.1775556127364",
+    "wiki/sources/_index.md.tmp.224546.1775556114770",
+    "wiki/entities/_index.md.tmp.224546.1775556102633",
     "wiki/meta/workflow-loop.gif",
     "wiki/meta/wiki-graph-grow.gif",
-    "wiki/Wiki Map.canvas.tmp.224546.1775555483542",
-    "wiki/entities/Andrej Karpathy.md.tmp.224546.1775555435117",
-    "wiki/concepts/Hot Cache.md.tmp.224546.1775555433665",
-    "README.md.tmp.224546.1775555144441",
     "cover.gif",
-    "bin/setup-vault.sh.tmp.224546.1775554739080",
     "projects/visual-vault/design-ideas.canvas",
-    "projects/visual-vault/design-ideas.canvas.tmp.224546.1775554654804",
-    "projects/visual-vault",
-    "projects",
     "_attachments/images/skool-hub/wp-mcp-cover.png",
     "_attachments/images/skool-hub/v3-cover-10.png",
     "_attachments/images/skool-hub/v3-cover-05.png",
@@ -209,8 +201,6 @@
     "_attachments/images/skool-hub/sq-portrait-clean.png",
     "_attachments/images/skool-hub/sq-10.png",
     "_attachments/images/skool-hub/sq-01.png",
-    "_attachments/images/skool-hub",
-    "_attachments/images",
     "wiki/entities/_index.md",
     "wiki/meta/dashboard.md",
     "wiki/sources/_index.md",
@@ -235,7 +225,6 @@
     "skills/wiki/references/mcp-setup.md",
     "skills/wiki/references/git-setup.md",
     "skills/wiki/references/frontmatter.md",
-    "skills/wiki/references/css-snippets.md",
+    "skills/wiki/references/css-snippets.md"
-    "skills/autoresearch/references/program.md"
   ]
 }

wiki/comparisons/Wiki vs RAG.md

@@ -0,0 +1,56 @@
+---
+type: comparison
+title: "Wiki vs RAG"
+subjects:
+  - "[[LLM Wiki Pattern]]"
+  - "RAG (Retrieval-Augmented Generation)"
+dimensions:
+  - "How knowledge is stored"
+  - "Query cost"
+  - "Infrastructure"
+  - "Maintenance"
+  - "Scale limit"
+verdict: "Wiki wins at <1000 pages. RAG wins at enterprise scale."
+created: 2026-04-07
+updated: 2026-04-07
+tags:
+  - comparison
+  - llm-wiki
+  - knowledge-management
+status: mature
+related:
+  - "[[LLM Wiki Pattern]]"
+  - "[[Compounding Knowledge]]"
+  - "[[index]]"
+  - "[[How does the LLM Wiki pattern work]]"
+sources: []
+---
+
+# Wiki vs RAG
+
+## Overview
+
+Both approaches let you query a large document collection. They differ fundamentally in when synthesis happens.
+
+## Comparison
+
+| Dimension | LLM Wiki | Semantic RAG |
+|-----------|----------|-------------|
+| **How knowledge is stored** | Pre-compiled markdown pages with cross-references already built | Raw chunks in a vector database |
+| **Finding answers** | Read index → follow links → synthesize | Embed query → similarity search → assemble |
+| **Query cost** | Low — synthesis already done | Higher — re-derives on every query |
+| **Infrastructure** | Just markdown files | Embedding model + vector DB + chunking pipeline |
+| **Maintenance** | Run a lint pass | Re-embed when content changes |
+| **Scale limit** | ~hundreds of pages (index file navigation) | Millions of documents |
+| **Setup time** | 5 minutes | Hours to days |
+| **Contradiction detection** | Built in — LLM flags on ingest | Manual |
+
+## Verdict
+
+**Under 1000 pages → LLM Wiki.** The index file is sufficient for navigation, token cost is low, setup is minimal, and the pre-compiled synthesis means every query benefits from everything ever read.
+
+**Over 100K pages → RAG.** The index file becomes too large to read, and embedding-based retrieval becomes more efficient than full-index scanning.
+
+The sweet spot: run the wiki pattern for active research (where things are being added, synthesized, and connected), then export to a vector store if the collection grows beyond the index threshold.
+
+(Source: [[LLM Wiki Pattern]], [[Compounding Knowledge]])

wiki/concepts/Hot Cache.md

@@ -60,9 +60,9 @@ YYYY-MM-DD — [what happened]
 - [Second]
 
 ## Recent Changes
-- Created: [[New Page 1]]
+- Created: new wiki pages from this ingest
-- Updated: [[Existing Page]] (added section on X)
+- Updated: existing pages with new connections
-- Flagged: Contradiction between [[Page A]] and [[Page B]]
+- Flagged: contradictions between sources where found
 
 ## Active Threads
 - User is researching [topic]

wiki/concepts/_index.md

@@ -10,6 +10,11 @@ domain: knowledge-management
 status: evergreen
 related:
   - "[[index]]"
+  - "[[dashboard]]"
+  - "[[Wiki Map]]"
+  - "[[Hot Cache]]"
+  - "[[LLM Wiki Pattern]]"
+  - "[[Compounding Knowledge]]"
   - "[[LLM Wiki Pattern]]"
   - "[[Hot Cache]]"
   - "[[Compounding Knowledge]]"

wiki/entities/_index.md

@@ -10,6 +10,8 @@ status: evergreen
 related:
   - "[[index]]"
   - "[[Andrej Karpathy]]"
+  - "[[hot]]"
+  - "[[LLM Wiki Pattern]]"
 ---
 
 # Entities Index

wiki/hot.md

@@ -9,6 +9,8 @@ status: evergreen
 related:
   - "[[index]]"
   - "[[log]]"
+  - "[[Wiki Map]]"
+  - "[[entities/_index]]"
 ---
 
 # Recent Context

wiki/index.md

@@ -10,6 +10,15 @@ related:
   - "[[overview]]"
   - "[[log]]"
   - "[[hot]]"
+  - "[[dashboard]]"
+  - "[[Wiki Map]]"
+  - "[[concepts/_index]]"
+  - "[[entities/_index]]"
+  - "[[sources/_index]]"
+  - "[[LLM Wiki Pattern]]"
+  - "[[Hot Cache]]"
+  - "[[Compounding Knowledge]]"
+  - "[[Andrej Karpathy]]"
 ---
 
 # Wiki Index

wiki/log.md

@@ -9,6 +9,8 @@ status: evergreen
 related:
   - "[[index]]"
   - "[[hot]]"
+  - "[[overview]]"
+  - "[[sources/_index]]"
 ---
 
 # Operation Log

wiki/meta/dashboard.md

@@ -10,6 +10,8 @@ related:
   - "[[index]]"
   - "[[overview]]"
   - "[[log]]"
+  - "[[concepts/_index]]"
+  - "[[Compounding Knowledge]]"
 ---
 
 # Wiki Dashboard

wiki/questions/How does the LLM Wiki pattern work.md

@@ -0,0 +1,52 @@
+---
+type: question
+title: "How does the LLM Wiki pattern work?"
+question: "How does the LLM Wiki pattern work and why is it better than RAG?"
+answer_quality: definitive
+created: 2026-04-07
+updated: 2026-04-07
+tags:
+  - question
+  - llm-wiki
+  - knowledge-management
+status: developing
+related:
+  - "[[LLM Wiki Pattern]]"
+  - "[[Compounding Knowledge]]"
+  - "[[Hot Cache]]"
+  - "[[index]]"
+  - "[[Wiki vs RAG]]"
+sources: []
+---
+
+# How does the LLM Wiki pattern work?
+
+**Question:** How does the LLM Wiki pattern work and why is it better than RAG?
+
+## Answer
+
+The [[LLM Wiki Pattern]] turns an LLM into a knowledge architect rather than a search engine.
+
+**Standard RAG** (Retrieval-Augmented Generation): every query searches raw documents, retrieves chunks, and assembles an answer from scratch. Nothing is built up. Ask the same question twice — it does the same work twice.
+
+**The wiki pattern** is different. When a source arrives, the LLM reads it and integrates it: updating entity pages, noting contradictions, adding cross-references. The synthesis is done once and persists. Every query benefits from all previous ingests.
+
+### The three layers
+
+1. **`.raw/`** — your source documents. Immutable. Claude reads, never modifies.
+2. **`wiki/`** — Claude-generated knowledge. Summaries, entities, concepts, synthesis.
+3. **`CLAUDE.md`** — the schema. Tells Claude how the wiki is structured and what to do.
+
+### Why it compounds
+
+See [[Compounding Knowledge]] for the full argument. The short version: each new source doesn't just add one page — it enriches 8-15 existing pages. The connections between pages are where the value lives, not the raw content itself.
+
+### The hot cache shortcut
+
+[[Hot Cache]] (wiki/hot.md) is a ~500-word summary of recent context. New sessions read it first. Cross-project references read it first. It prevents re-reading the whole wiki just to answer "where were we?"
+
+(Source: [[LLM Wiki Pattern]])
+
+## Confidence
+
+definitive — this is the core concept the entire vault demonstrates.

wiki/sources/_index.md

@@ -9,6 +9,9 @@ tags:
 status: evergreen
 related:
   - "[[index]]"
+  - "[[log]]"
+  - "[[entities/_index]]"
+  - "[[Andrej Karpathy]]"
 ---
 
 # Sources Index