docs: convert DESIGN.md into wiki landing + add wiki draft pages

.github/ISSUE_TEMPLATE/config.yml

@@ -1,5 +1,5 @@
 blank_issues_enabled: true
 contact_links:
   - name: "📖 Architecture Reference"
-    url: https://github.com/devlux76/cortex/blob/main/DESIGN.md
-    about: Review DESIGN.md before proposing architectural changes.
+    url: https://github.com/devlux76/cortex/wiki
+    about: Review the architecture wiki before proposing architectural changes.

.github/copilot-instructions.md

@@ -14,11 +14,12 @@ The engine models three biological brain regions:
 | File | Purpose |
 |---|---|
 | `README.md` | Product vision and quick start |
-| `DESIGN.md` | Complete architecture specification and design principles |
+| **CORTEX Wiki** | Canonical architecture specification and design principles |
+| `DESIGN.md` | Repo landing page / TOC into the wiki |
 | `PLAN.md` | Module-by-module implementation status and development phases |
 | `TODO.md` | Prioritized actionable tasks to ship v1.0 |
 
-Keep `DESIGN.md` synchronized with the real code state after every implementation pass.
+Keep the wiki and `DESIGN.md` synchronized with the real code state after every implementation pass.
 
 ## Project Management
 

README.md

@@ -113,7 +113,8 @@ bun run dev:harness # start the browser runtime harness at http://127.0.0.1:4173
 
 | Document | Purpose |
 |---|---|
-| [`DESIGN.md`](DESIGN.md) | Architecture specification and core design principles |
+| [CORTEX Wiki](https://github.com/devlux76/cortex/wiki) | Canonical design documentation (architecture, algorithms, and math). |
+| [`DESIGN.md`](DESIGN.md) | Static repo landing page / TOC into the wiki |
 | [`PLAN.md`](PLAN.md) | Module-by-module implementation status and development phases |
 | [`TODO.md`](TODO.md) | Prioritized actionable tasks to ship v1.0 |
 | [`docs/api.md`](docs/api.md) | API reference for developers integrating with CORTEX |

docs/development.md

@@ -170,10 +170,11 @@ This command will fail the build if it detects numeric literals that are likely
 
 At the end of every implementation pass, update documents in this order:
 
-1. **`DESIGN.md`** — update if architecture changes.
-2. **`README.md`** — confirm the project description still reflects reality.
-3. **`docs/api.md`** — update if new public APIs are added or existing ones change.
-4. **GitHub Issues** — close completed tasks, create new ones as needed via `gh` CLI or the web UI.
+1. **`DESIGN.md`** — update if the design landing/TOC changes.
+2. **Wiki** — update the relevant wiki page(s) for any architecture or algorithm changes.
+3. **`README.md`** — confirm the project description still reflects reality.
+4. **`docs/api.md`** — update if new public APIs are added or existing ones change.
+5. **GitHub Issues** — close completed tasks, create new ones as needed via `gh` CLI or the web UI.
 
 > Numeric examples in design docs are illustrative unless explicitly sourced from model metadata.
 

docs/wiki-draft/Architecture.md

@@ -0,0 +1,30 @@
+# Architecture Overview
+
+This page describes the high-level architecture of CORTEX and the major subsystems.
+
+## The Three Living Regions
+
+CORTEX models three biological brain regions working in concert:
+
+- **Hippocampus** — Fast associative encoding and incremental prototype construction.
+- **Cortex** — Intelligent routing, dialectical retrieval, and coherence.
+- **Daydreamer** — Background consolidation and maintenance.
+
+Each region is responsible for a distinct phase of the memory lifecycle. Together they form a pipeline from ingestion through retrieval.
+
+## Core Concepts
+
+### Medoid vs. Centroid vs. Metroid
+
+- **Medoid** — An actual memory node (page) selected as the representative of a cluster.
+- **Centroid** — A computed geometric average (never stored as a real node).
+- **Metroid** — A transient, structured dialectical search probe (`{ m1, m2, c }`) used at query time.
+
+### How the subsystems interact
+
+1. **Ingestion:** Hippocampus embeds content and creates/update prototypes.
+2. **Retrieval:** Cortex constructs Metroids and performs dialectical search for coherent context.
+3. **Consolidation:** Daydreamer updates prototypes, prunes edges, and maintains stability.
+
+
+> For the full algorithmic detail, see **Retrieval & Metroid Algorithm**.

docs/wiki-draft/Consolidation.md

@@ -0,0 +1,14 @@
+# Consolidation (Daydreamer)
+
+This page covers background consolidation and maintenance mechanisms.
+
+## Daydreamer Responsibilities
+
+- **Long-term potentiation (LTP):** strengthen important connections.
+- **Long-term depression (LTD):** decay and prune weak edges.
+- **Medoid/centroid recomputation:** keep prototypes coherent as the graph evolves.
+- **Experience replay:** rehearse recent data in background when idle.
+
+## Stability & Throttling
+
+The Daydreamer is designed to run opportunistically without blocking foreground query performance. Its work is throttled and batch-sized according to the current memory graph complexity.

docs/wiki-draft/Home.md

@@ -0,0 +1,38 @@
+# CORTEX Design Wiki
+
+This wiki is the **canonical home for CORTEX architecture and design documentation**.
+
+> The repository includes `DESIGN.md` as a small **TOC/landing page** that points here. Use this wiki for all deep dives, algorithm descriptions, and mathematical reasoning.
+
+## Where to start
+
+- **If you’re writing an issue or PR that affects the architecture:** start with **Architecture Overview**.
+- **If you need to understand retrieval behavior:** see **Retrieval & Metroid Algorithm**.
+- **If you’re changing ingestion or indexing:** see **Ingestion (Hippocampus)**.
+- **If you’re optimizing or debugging consolidation:** see **Consolidation (Daydreamer)**.
+- **If you’re changing storage formats or persistence:** see **Storage Architecture**.
+- **If you’re tuning performance budgets:** see **Performance Model & Constraints**.
+- **If you need definitions or constant values:** see **Terminology + Numerics**.
+- **If you need the math behind the design:** see **Math Appendix**.
+
+---
+
+## Wiki Pages (Table of Contents)
+
+- [Architecture Overview](Architecture.md)
+- [Retrieval & Metroid Algorithm](Retrieval.md)
+- [Ingestion (Hippocampus)](Ingestion.md)
+- [Consolidation (Daydreamer)](Consolidation.md)
+- [Storage Architecture](Storage.md)
+- [Performance Model & Constraints](Performance.md)
+- [Security & Trust](Security.md)
+- [Terminology + Numerics](Terminology.md)
+- [Math Appendix](Math-Appendix.md)
+
+---
+
+## How to use this wiki
+
+- **Edit on GitHub**: Edit the markdown directly in the wiki repo (`cortex.wiki`) and push.
+- **Linking from issues/PRs**: Link to the relevant wiki page (e.g., `https://github.com/devlux76/cortex/wiki/Retrieval-&-Metroid-Algorithm`).
+- **Keeping it up to date**: When the code changes, update the relevant wiki page; include the wiki link in the PR description.

docs/wiki-draft/Ingestion.md

@@ -0,0 +1,16 @@
+# Ingestion (Hippocampus)
+
+This page describes how CORTEX ingests new observations and integrates them into memory.
+
+## Ingest Path
+
+1. **Chunking/Parsing** — Raw inputs are segmented into pages/blocks.
+2. **Embedding** — Each chunk is embedded using a Matryoshka-capable model.
+3. **Fast Neighbor Insert** — New vectors are connected into the semantic neighbor graph.
+4. **Hierarchical Prototypes** — Pages are organized into Books, Volumes, and Shelves.
+
+## Hierarchy & Promotion
+
+CORTEX manages a hierarchical prototype structure to keep hot (frequently-accessed) concepts in memory while relying on disk-backed storage for the long tail.
+
+> For implementation details, see the code in `hippocampus/` and the `HierarchyBuilder` design notes.

docs/wiki-draft/Math-Appendix.md

@@ -0,0 +1,37 @@
+# Math Appendix
+
+This appendix contains the mathematical background that motivates several of CORTEX’s key design decisions.
+
+## Curse of Dimensionality
+
+In high-dimensional spaces, the volume of a unit ball collapses rapidly. For even dimension `n = 2m`: 
+
+```
+V_n = π^m / m!
+```
+
+Stirling’s approximation shows this shrinks exponentially with `n`, meaning nearly all the volume is concentrated near the surface.
+
+## Hypersphere Volume and the Hollow Sphere
+
+CORTEX leverages this “hollow sphere” phenomenon: in high dimensions, the interior of a ball is essentially empty, so nearest-neighbor search can focus on the surface shell.
+
+## Williams 2025 Sublinear Bound
+
+CORTEX applies the result:
+
+```
+S = O(√(t · log t))
+```
+
+to bound space requirements (hotpath capacity, fanout limits, maintenance budgets) in a way that maintains on-device performance.
+
+## Why This Matters
+
+These mathematical observations drive several design decisions in CORTEX:
+
+- Matryoshka dimension protection (to prevent domain drift)
+- Sublinear fanout quotas (to avoid explosion in edge counts)
+- The Metroid dialectical search pattern (to avoid confirmation bias in high-D retrieval)
+
+> For full details, see the source code and the other wiki pages.

docs/wiki-draft/Performance.md

@@ -0,0 +1,28 @@
+# Performance Model & Constraints
+
+This page explains the performance budget model and the key formulas that keep CORTEX sublinear.
+
+## Williams Sublinear Bound
+
+CORTEX uses the Williams 2025 result:
+
+> **S = O(√(t · log t))**
+
+This bound is applied to multiple budgets (hotpath index size, hierarchy fanout, neighbor degrees, maintenance batch sizes) to ensure the system stays efficient as the graph grows.
+
+## Hotpath Capacity
+
+The resident hotpath index is capped to a sublinear growth function, often expressed as:
+
+```
+H(t) = ⌈c · √(t · log₂(1 + t))⌉
+```
+
+## Budgeting & Fanout Limits
+
+The same sublinear law is used for:
+- Hierarchy fanout limits
+- Semantic neighbor degree caps
+- Daydreamer maintenance batch sizing
+
+> See the code in `core/HotpathPolicy.ts` and `hippocampus/HierarchyBuilder.ts` for the concrete implementations.

docs/wiki-draft/Retrieval.md

@@ -0,0 +1,29 @@
+# Retrieval & Metroid Algorithm
+
+This page explains the retrieval pipeline and the Metroid-based dialectical search mechanism.
+
+## Metroid Overview
+
+A **Metroid** is a structured search primitive: it contains a thesis (`m1`), an antithesis (`m2`), and a frozen centroid (`c`).
+
+- `m1` is the medoid closest to the query.
+- `m2` is an opposite medoid found via cosine-opposite medoid search.
+- `c` is the frozen centroid between `m1` and `m2`.
+
+## Dialectical Search Zones
+
+From the centroid `c`, the system classifies candidates into three zones:
+
+- **Thesis zone:** closer to `m1` than to `c`.
+- **Antithesis zone:** closer to `m2` than to `c`.
+- **Synthesis zone:** near `c`, balanced between both poles.
+
+## Matryoshka Dimensional Unwinding
+
+CORTEX uses Matryoshka embeddings with protected dimensions (lower dimensions that anchor domain context). The retrieval algorithm progressively frees dimensions to explore antithesis candidates while keeping the centroid frozen.
+
+## Knowledge Gap Detection
+
+When no suitable `m2` can be found within constraints, the system flags a **knowledge gap** and may broadcast a P2P curiosity request.
+
+> See the **Math Appendix** for the geometric intuition behind why this approach is necessary in high-dimensional spaces.

docs/wiki-draft/Security.md

@@ -0,0 +1,16 @@
+# Security & Trust
+
+This page covers trust assumptions, cryptographic integrity, and smart sharing guardrails.
+
+## Cryptographic Integrity
+
+CORTEX supports cryptographic signing (and optional verification) for stored vectors and metadata to help detect tampering and integrity issues.
+
+## Smart Sharing Guardrails
+
+When sharing memory fragments over P2P, CORTEX enforces:
+- MIME type validation
+- Model URN compatibility checks
+- Eligibility filtering (to avoid leaking sensitive or irrelevant data)
+
+> See `sharing/` for the implementation details of peer exchange and eligibility classification.

docs/wiki-draft/Storage.md

@@ -0,0 +1,19 @@
+# Storage Architecture
+
+This page describes how CORTEX stores vectors and metadata in the browser.
+
+## Vector Storage (OPFS)
+
+- Vectors are stored in an append-only OPFS file for fast writes.
+- The OPFS backend is designed to be zero-copy for WebGPU and WebGL consumption.
+
+## Metadata Storage (IndexedDB)
+
+- Metadata (nodes, edges, schema) is stored in IndexedDB.
+- IndexedDB is used for fast subgraph retrieval and persistence across sessions.
+
+## Maintenance & Corruption Resistance
+
+Today, CORTEX relies on the browser’s OPFS and IndexedDB durability guarantees, with limited, optional integrity checks (for example, content-hash verification on incoming peer fragments).
+
+Planned: a broader integrity verification and corruption-detection/recovery flow for OPFS/IndexedDB-backed data, including cryptographic integrity validation of stored payloads and automated remediation of partial failures.

docs/wiki-draft/Terminology.md

@@ -0,0 +1,23 @@
+# Terminology & Numerics
+
+This page collects key terms, model-derived numeric constants, and policy-derived constants.
+
+## Key Terms
+
+- **Medoid** — an existing memory node selected as a cluster representative.
+- **Centroid** — a computed average vector (not necessarily a real node).
+- **Metroid** — a transient search construct `{ m1, m2, c }` used during retrieval.
+- **Hotpath** — the in-memory resident index of active nodes.
+
+## Model-Derived Numerics
+
+These values are derived from the embedding model profile (not hardcoded):
+- Embedding dimensionality
+- Matryoshka protected dimension boundary
+- Query context length limits
+
+## Policy-Derived Constants
+
+Policy constants (e.g. fanout caps, quota ratios) are defined in the code and kept in sync with the design.
+
+> For the authoritative source of policy constants, see `core/HotpathPolicy.ts`.