feat: add codebase genome status rollup (#665)

Merge PR #764: docs: MemPalace v3.0.0 integration — before/after evaluation (#568)

GENOME.md

@@ -1,141 +1,209 @@
-# GENOME.md — Timmy_Foundation/timmy-home
-
-Generated by `pipelines/codebase_genome.py`.
+# GENOME.md — the-nexus
 
 ## Project Overview
 
-Timmy Foundation's home repository for development operations and configurations.
+`the-nexus` is a hybrid repo that combines three layers in one codebase:
 
-- Text files indexed: 3004
-- Source and script files: 186
-- Test files: 28
-- Documentation files: 701
+1. A browser-facing world shell rooted in `index.html`, `boot.js`, `bootstrap.mjs`, `app.js`, `style.css`, `portals.json`, `vision.json`, `manifest.json`, and `gofai_worker.js`
+2. A Python realtime bridge centered on `server.py` plus harness code under `nexus/`
+3. A memory / fleet / operator layer spanning `mempalace/`, `mcp_servers/`, `multi_user_bridge.py`, and supporting scripts
 
-## Architecture
+The repo is not a clean single-purpose frontend and not just a backend harness. It is a mixed world/runtime/ops repository where browser rendering, WebSocket telemetry, MCP-driven game harnesses, and fleet memory tooling coexist.
+
+Grounded repo facts from this checkout:
+- Browser shell files exist at repo root: `index.html`, `app.js`, `style.css`, `manifest.json`, `gofai_worker.js`
+- Data/config files also live at repo root: `portals.json`, `vision.json`
+- Realtime bridge exists in `server.py`
+- Game harnesses exist in `nexus/morrowind_harness.py` and `nexus/bannerlord_harness.py`
+- Memory/fleet sync exists in `mempalace/tunnel_sync.py`
+- Desktop/game automation MCP servers exist in `mcp_servers/desktop_control_server.py` and `mcp_servers/steam_info_server.py`
+- Validation exists in `tests/test_browser_smoke.py`, `tests/test_portals_json.py`, `tests/test_index_html_integrity.py`, and `tests/test_repo_truth.py`
+
+The current architecture is best understood as a sovereign world shell plus operator/game harness backend, with accumulated documentation drift from multiple restoration and migration efforts.
+
+## Architecture Diagram
 
 ```mermaid
 graph TD
-  repo_root["repo"]
-  angband["angband"]
-  briefings["briefings"]
-  config["config"]
-  conftest["conftest"]
-  evennia["evennia"]
-  evennia_tools["evennia_tools"]
-  evolution["evolution"]
-  gemini_fallback_setup["gemini-fallback-setup"]
-  heartbeat["heartbeat"]
-  infrastructure["infrastructure"]
-  repo_root --> angband
-  repo_root --> briefings
-  repo_root --> config
-  repo_root --> conftest
-  repo_root --> evennia
-  repo_root --> evennia_tools
+    browser[Index HTML Shell\nindex.html -> boot.js -> bootstrap.mjs -> app.js]
+    assets[Root Assets\nstyle.css\nmanifest.json\ngofai_worker.js]
+    data[World Data\nportals.json\nvision.json]
+    ws[Realtime Bridge\nserver.py\nWebSocket broadcast hub]
+    gofai[In-browser GOFAI\nSymbolicEngine\nNeuroSymbolicBridge\nsetupGOFAI/updateGOFAI]
+    harnesses[Python Harnesses\nnexus/morrowind_harness.py\nnexus/bannerlord_harness.py]
+    mcp[MCP Adapters\nmcp_servers/desktop_control_server.py\nmcp_servers/steam_info_server.py]
+    memory[Memory + Fleet\nmempalace/tunnel_sync.py\nmempalace.js]
+    bridge[Operator / MUD Bridge\nmulti_user_bridge.py\ncommands/timmy_commands.py]
+    tests[Verification\ntests/test_browser_smoke.py\ntests/test_portals_json.py\ntests/test_repo_truth.py]
+    docs[Contracts + Drift Docs\nBROWSER_CONTRACT.md\nREADME.md\nCLAUDE.md\nINVESTIGATION_ISSUE_1145.md]
+
+    browser --> assets
+    browser --> data
+    browser --> gofai
+    browser --> ws
+    harnesses --> mcp
+    harnesses --> ws
+    bridge --> ws
+    memory --> ws
+    tests --> browser
+    tests --> data
+    tests --> docs
+    docs --> browser
 ```
 
-## Entry Points
+## Entry Points and Data Flow
 
-- `gemini-fallback-setup.sh` — operational script (`bash gemini-fallback-setup.sh`)
-- `morrowind/hud.sh` — operational script (`bash morrowind/hud.sh`)
-- `pipelines/codebase_genome.py` — python main guard (`python3 pipelines/codebase_genome.py`)
-- `scripts/auto_restart_agent.sh` — operational script (`bash scripts/auto_restart_agent.sh`)
-- `scripts/backup_pipeline.sh` — operational script (`bash scripts/backup_pipeline.sh`)
-- `scripts/big_brain_manager.py` — operational script (`python3 scripts/big_brain_manager.py`)
-- `scripts/big_brain_repo_audit.py` — operational script (`python3 scripts/big_brain_repo_audit.py`)
-- `scripts/codebase_genome_nightly.py` — operational script (`python3 scripts/codebase_genome_nightly.py`)
-- `scripts/detect_secrets.py` — operational script (`python3 scripts/detect_secrets.py`)
-- `scripts/dynamic_dispatch_optimizer.py` — operational script (`python3 scripts/dynamic_dispatch_optimizer.py`)
-- `scripts/emacs-fleet-bridge.py` — operational script (`python3 scripts/emacs-fleet-bridge.py`)
-- `scripts/emacs-fleet-poll.sh` — operational script (`bash scripts/emacs-fleet-poll.sh`)
+### Primary entry points
 
-## Data Flow
+- `index.html` — root browser entry point
+- `boot.js` — startup selector; `tests/boot.test.js` shows it chooses file-mode vs HTTP/module-mode and injects `bootstrap.mjs` when served over HTTP
+- `bootstrap.mjs` — module bootstrap for the browser shell
+- `app.js` — main browser runtime; owns world state, GOFAI wiring, metrics polling, and portal/UI logic
+- `server.py` — WebSocket broadcast bridge on `ws://0.0.0.0:8765`
+- `nexus/morrowind_harness.py` — GamePortal/MCP harness for OpenMW Morrowind
+- `nexus/bannerlord_harness.py` — GamePortal/MCP harness for Bannerlord
+- `mempalace/tunnel_sync.py` — pulls remote fleet closets into the local palace over HTTP
+- `multi_user_bridge.py` — HTTP bridge for multi-user chat/session integration
+- `mcp_servers/desktop_control_server.py` — stdio MCP server exposing screenshots/mouse/keyboard control
 
-1. Operators enter through `gemini-fallback-setup.sh`, `morrowind/hud.sh`, `pipelines/codebase_genome.py`.
-2. Core logic fans into top-level components: `angband`, `briefings`, `config`, `conftest`, `evennia`, `evennia_tools`.
-3. Validation is incomplete around `wizards/allegro/home/skills/red-teaming/godmode/scripts/auto_jailbreak.py`, `timmy-local/cache/agent_cache.py`, `wizards/allegro/home/skills/red-teaming/godmode/scripts/parseltongue.py`, so changes there carry regression risk.
-4. Final artifacts land as repository files, docs, or runtime side effects depending on the selected entry point.
+### Data flow
+
+1. Browser startup begins at `index.html`
+2. `boot.js` decides whether the page is being served correctly; in HTTP mode it injects `bootstrap.mjs`
+3. `bootstrap.mjs` hands off to `app.js`
+4. `app.js` loads world configuration from `portals.json` and `vision.json`
+5. `app.js` constructs the Three.js scene and in-browser reasoning components, including `SymbolicEngine`, `NeuroSymbolicBridge`, `setupGOFAI()`, and `updateGOFAI()`
+6. Browser state and external runtimes connect through `server.py`, which broadcasts messages between connected clients
+7. Python harnesses (`nexus/morrowind_harness.py`, `nexus/bannerlord_harness.py`) spawn MCP subprocesses for desktop control / Steam metadata, capture state, execute actions, and feed telemetry into the Nexus bridge
+8. Memory/fleet tools like `mempalace/tunnel_sync.py` import remote palace data into local closets, extending what the operator/runtime layers can inspect
+9. Tests validate both the static browser contract and the higher-level repo-truth/memory contracts
+
+### Important repo-specific runtime facts
+
+- `portals.json` is a JSON array of portal/world/operator entries; examples in this checkout include `morrowind`, `bannerlord`, `workshop`, `archive`, `chapel`, and `courtyard`
+- `server.py` is a plain broadcast hub: clients send messages, the server forwards them to other connected clients
+- `nexus/morrowind_harness.py` and `nexus/bannerlord_harness.py` both implement a GamePortal pattern with MCP subprocess clients over stdio and WebSocket telemetry uplink
+- `mempalace/tunnel_sync.py` is not speculative; it is a real client that discovers remote wings, searches remote rooms, and writes `.closet.json` payloads locally
 
 ## Key Abstractions
 
-- `evennia/timmy_world/game.py` — classes `World`:91, `ActionSystem`:421, `TimmyAI`:539, `NPCAI`:550; functions `get_narrative_phase()`:55, `get_phase_transition_event()`:65
-- `evennia/timmy_world/world/game.py` — classes `World`:19, `ActionSystem`:326, `TimmyAI`:444, `NPCAI`:455; functions none detected
-- `timmy-world/game.py` — classes `World`:19, `ActionSystem`:349, `TimmyAI`:467, `NPCAI`:478; functions none detected
-- `wizards/allegro/home/skills/red-teaming/godmode/scripts/auto_jailbreak.py` — classes none detected; functions none detected
-- `uniwizard/self_grader.py` — classes `SessionGrade`:23, `WeeklyReport`:55, `SelfGrader`:74; functions `main()`:713
-- `uni-wizard/v3/intelligence_engine.py` — classes `ExecutionPattern`:27, `ModelPerformance`:44, `AdaptationEvent`:58, `PatternDatabase`:69; functions none detected
-- `scripts/know_thy_father/crossref_audit.py` — classes `ThemeCategory`:30, `Principle`:160, `MeaningKernel`:169, `CrossRefFinding`:178; functions `extract_themes_from_text()`:192, `parse_soul_md()`:206, `parse_kernels()`:264, `cross_reference()`:296, `generate_report()`:440, `main()`:561
-- `timmy-local/cache/agent_cache.py` — classes `CacheStats`:28, `LRUCache`:52, `ResponseCache`:94, `ToolCache`:205; functions none detected
+### Browser runtime
+
+- `app.js`
+  - Defines in-browser reasoning/state machinery, including `class SymbolicEngine`, `class NeuroSymbolicBridge`, `setupGOFAI()`, and `updateGOFAI()`
+  - Couples rendering, local symbolic reasoning, metrics polling, and portal/UI logic in one very large root module
+- `BROWSER_CONTRACT.md`
+  - Acts like an executable architecture contract for the browser surface
+  - Declares required files, DOM IDs, Three.js expectations, provenance rules, and WebSocket expectations
+
+### Realtime bridge
+
+- `server.py`
+  - Single hub abstraction: a WebSocket broadcast server maintaining a `clients` set and forwarding messages from one client to the others
+  - This is the seam between browser shell, harnesses, and external telemetry producers
+
+### GamePortal harness layer
+
+- `nexus/morrowind_harness.py`
+- `nexus/bannerlord_harness.py`
+  - Both define MCP client wrappers, `GameState` / `ActionResult`-style data classes, and an Observe-Decide-Act telemetry loop
+  - The harnesses are symmetric enough to be understood as reusable portal adapters with game-specific context injected on top
+
+### Memory / fleet layer
+
+- `mempalace/tunnel_sync.py`
+  - Encodes the fleet-memory sync client contract: discover wings, pull broad room queries, write closet files, support dry-run
+- `mempalace.js`
+  - Minimal browser/Electron bridge to MemPalace commands via `window.electronAPI.execPython(...)`
+  - Important because it shows a second memory integration surface distinct from the Python fleet sync path
+
+### Operator / interaction bridge
+
+- `multi_user_bridge.py`
+- `commands/timmy_commands.py`
+  - These bridge user-facing conversations or MUD/Evennia interactions back into Timmy/Nexus services
 
 ## API Surface
 
-- CLI: `bash gemini-fallback-setup.sh` — operational script (`gemini-fallback-setup.sh`)
-- CLI: `bash morrowind/hud.sh` — operational script (`morrowind/hud.sh`)
-- CLI: `python3 pipelines/codebase_genome.py` — python main guard (`pipelines/codebase_genome.py`)
-- CLI: `bash scripts/auto_restart_agent.sh` — operational script (`scripts/auto_restart_agent.sh`)
-- CLI: `bash scripts/backup_pipeline.sh` — operational script (`scripts/backup_pipeline.sh`)
-- CLI: `python3 scripts/big_brain_manager.py` — operational script (`scripts/big_brain_manager.py`)
-- CLI: `python3 scripts/big_brain_repo_audit.py` — operational script (`scripts/big_brain_repo_audit.py`)
-- CLI: `python3 scripts/codebase_genome_nightly.py` — operational script (`scripts/codebase_genome_nightly.py`)
-- Python: `get_narrative_phase()` from `evennia/timmy_world/game.py:55`
-- Python: `get_phase_transition_event()` from `evennia/timmy_world/game.py:65`
-- Python: `main()` from `uniwizard/self_grader.py:713`
+### Browser / static surface
 
-## Test Coverage Report
+- `index.html` served over HTTP
+- `boot.js` exports `bootPage()`; verified by `node --test tests/boot.test.js`
+- Data APIs are file-based inside the repo: `portals.json`, `vision.json`, `manifest.json`
 
-- Source and script files inspected: 186
-- Test files inspected: 28
-- Coverage gaps:
-  - `wizards/allegro/home/skills/red-teaming/godmode/scripts/auto_jailbreak.py` — no matching test reference detected
-  - `timmy-local/cache/agent_cache.py` — no matching test reference detected
-  - `wizards/allegro/home/skills/red-teaming/godmode/scripts/parseltongue.py` — no matching test reference detected
-  - `twitter-archive/multimodal_pipeline.py` — no matching test reference detected
-  - `wizards/allegro/home/skills/red-teaming/godmode/scripts/godmode_race.py` — no matching test reference detected
-  - `skills/productivity/google-workspace/scripts/google_api.py` — no matching test reference detected
-  - `wizards/allegro/home/skills/productivity/google-workspace/scripts/google_api.py` — no matching test reference detected
-  - `morrowind/pilot.py` — no matching test reference detected
-  - `morrowind/mcp_server.py` — no matching test reference detected
-  - `skills/research/domain-intel/scripts/domain_intel.py` — no matching test reference detected
-  - `wizards/allegro/home/skills/research/domain-intel/scripts/domain_intel.py` — no matching test reference detected
-  - `timmy-local/scripts/ingest.py` — no matching test reference detected
+### Network/runtime surface
 
-## Security Audit Findings
+- `python3 server.py`
+  - Starts the WebSocket bridge on port `8765`
+- `python3 l402_server.py`
+  - Local HTTP microservice for cost-estimate style responses
+- `python3 multi_user_bridge.py`
+  - Multi-user HTTP/chat bridge
 
-- [medium] `briefings/briefing_20260325.json:37` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `"gitea_error": "Gitea 404: {\"errors\":null,\"message\":\"not found\",\"url\":\"http://143.198.27.163:3000/api/swagger\"}\n [http://143.198.27.163:3000/api/v1/repos/Timmy_Foundation/sovereign-orchestration/issues?state=open&type=issues&sort=created&direction=desc&limit=1&page=1]",`
-- [medium] `briefings/briefing_20260328.json:11` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `"provider_base_url": "http://localhost:8081/v1",`
-- [medium] `briefings/briefing_20260329.json:11` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `"provider_base_url": "http://localhost:8081/v1",`
-- [medium] `config.yaml:37` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `summary_base_url: http://localhost:11434/v1`
-- [medium] `config.yaml:47` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
-- [medium] `config.yaml:52` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
-- [medium] `config.yaml:57` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
-- [medium] `config.yaml:62` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
-- [medium] `config.yaml:67` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
-- [medium] `config.yaml:77` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
-- [medium] `config.yaml:82` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
-- [medium] `config.yaml:174` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: http://localhost:11434/v1`
+### Harness / operator CLI surfaces
 
-## Dead Code Candidates
+- `python3 nexus/morrowind_harness.py`
+- `python3 nexus/bannerlord_harness.py`
+- `python3 mempalace/tunnel_sync.py --peer <url> [--dry-run] [--n N]`
+- `python3 mcp_servers/desktop_control_server.py`
+- `python3 mcp_servers/steam_info_server.py`
 
-- `wizards/allegro/home/skills/red-teaming/godmode/scripts/auto_jailbreak.py` — not imported by indexed Python modules and not referenced by tests
-- `timmy-local/cache/agent_cache.py` — not imported by indexed Python modules and not referenced by tests
-- `wizards/allegro/home/skills/red-teaming/godmode/scripts/parseltongue.py` — not imported by indexed Python modules and not referenced by tests
-- `twitter-archive/multimodal_pipeline.py` — not imported by indexed Python modules and not referenced by tests
-- `wizards/allegro/home/skills/red-teaming/godmode/scripts/godmode_race.py` — not imported by indexed Python modules and not referenced by tests
-- `skills/productivity/google-workspace/scripts/google_api.py` — not imported by indexed Python modules and not referenced by tests
-- `wizards/allegro/home/skills/productivity/google-workspace/scripts/google_api.py` — not imported by indexed Python modules and not referenced by tests
-- `morrowind/pilot.py` — not imported by indexed Python modules and not referenced by tests
-- `morrowind/mcp_server.py` — not imported by indexed Python modules and not referenced by tests
-- `skills/research/domain-intel/scripts/domain_intel.py` — not imported by indexed Python modules and not referenced by tests
+### Validation surface
 
-## Performance Bottleneck Analysis
+- `python3 -m pytest tests/test_portals_json.py tests/test_index_html_integrity.py tests/test_repo_truth.py -q`
+- `node --test tests/boot.test.js`
+- `python3 -m py_compile server.py nexus/morrowind_harness.py nexus/bannerlord_harness.py mempalace/tunnel_sync.py mcp_servers/desktop_control_server.py`
+- `tests/test_browser_smoke.py` defines the higher-cost Playwright smoke contract for the world shell
 
-- `angband/mcp_server.py` — large module (353 lines) likely hides multiple responsibilities
-- `evennia/timmy_world/game.py` — large module (1541 lines) likely hides multiple responsibilities
-- `evennia/timmy_world/world/game.py` — large module (1345 lines) likely hides multiple responsibilities
-- `morrowind/mcp_server.py` — large module (451 lines) likely hides multiple responsibilities
-- `morrowind/pilot.py` — large module (459 lines) likely hides multiple responsibilities
-- `pipelines/codebase_genome.py` — large module (557 lines) likely hides multiple responsibilities
-- `scripts/know_thy_father/crossref_audit.py` — large module (657 lines) likely hides multiple responsibilities
-- `scripts/know_thy_father/index_media.py` — large module (405 lines) likely hides multiple responsibilities
-- `scripts/know_thy_father/synthesize_kernels.py` — large module (416 lines) likely hides multiple responsibilities
-- `scripts/tower_game.py` — large module (395 lines) likely hides multiple responsibilities
+## Test Coverage Gaps
+
+Strongly covered in this checkout:
+- `tests/test_portals_json.py` validates `portals.json`
+- `tests/test_index_html_integrity.py` checks merge-marker/DOM-integrity regressions in `index.html`
+- `tests/boot.test.js` verifies `boot.js` startup behavior
+- `tests/test_repo_truth.py` validates the repo-truth documents
+- Multiple `tests/test_mempalace_*.py` files cover the palace layer
+- `tests/test_bannerlord_harness.py` exists for the Bannerlord harness
+
+Notable gaps or weak seams:
+- `nexus/morrowind_harness.py` is large and operationally critical, but the generated baseline still flags it as a gap relative to its size/complexity
+- `mcp_servers/desktop_control_server.py` exposes high-power automation but has no obvious dedicated test file in the root `tests/` suite
+- `app.js` is the dominant browser runtime file and mixes rendering, GOFAI, metrics, and integration logic in one place; browser smoke exists, but there is limited unit-level decomposition around those subsystems
+- `mempalace.js` appears minimally bridged and stale relative to the richer Python MemPalace layer
+- `multi_user_bridge.py` is a large integration surface and should be treated as high regression risk even though it is central to operator/chat flow
+
+## Security Considerations
+
+- `server.py` binds `HOST = "0.0.0.0"`, exposing the broadcast bridge beyond localhost unless network controls limit it
+- The WebSocket bridge is a broadcast hub without visible authentication in `server.py`; connected clients are trusted to send messages into the bus
+- `mcp_servers/desktop_control_server.py` exposes mouse/keyboard/screenshot control through a stdio MCP server. In any non-local or poorly isolated runtime, this is a privileged automation surface
+- `app.js` contains hardcoded local/network endpoints such as `http://localhost:${L402_PORT}/api/cost-estimate` and `http://localhost:8082/metrics`; these are convenient for local development but create environment drift and deployment assumptions
+- `app.js` also embeds explicit endpoint/status references like `ws://143.198.27.163:8765`, which is operationally brittle and the kind of hardcoded location data that drifts across environments
+- `mempalace.js` shells out through `window.electronAPI.execPython(...)`; this is powerful and useful, but it is a clear trust boundary between UI and host execution
+- `INVESTIGATION_ISSUE_1145.md` documents an earlier integrity hazard: agents writing to `public/nexus/` instead of canonical root paths. That path confusion is both an operational and security concern because it makes provenance harder to reason about
+
+## Runtime Truth and Docs Drift
+
+The most important architecture finding in this repo is not a class or subsystem. It is a truth mismatch.
+
+- README.md says current `main` does not ship a browser 3D world
+- CLAUDE.md declares root `app.js` and `index.html` as canonical frontend paths
+- tests and browser contract now assume the root frontend exists
+
+All three statements are simultaneously present in this checkout.
+
+Grounded evidence:
+- `README.md` still says the repo does not contain an active root frontend such as `index.html`, `app.js`, or `style.css`
+- the current checkout does contain `index.html`, `app.js`, `style.css`, `manifest.json`, and `gofai_worker.js`
+- `BROWSER_CONTRACT.md` explicitly treats those root files as required browser assets
+- `tests/test_browser_smoke.py` serves those exact files and validates DOM/WebGL contracts against them
+- `tests/test_index_html_integrity.py` assumes `index.html` is canonical and production-relevant
+- `CLAUDE.md` says frontend code lives at repo root and explicitly warns against `public/nexus/`
+- `INVESTIGATION_ISSUE_1145.md` explains why `public/nexus/` is a bad/corrupt duplicate path and confirms the real classical AI code lives in root `app.js`
+
+The honest conclusion:
+- The repo contains a partially restored or actively re-materialized browser surface
+- The docs are preserving an older migration truth while the runtime files and smoke contracts describe a newer present-tense truth
+- Any future work in `the-nexus` must choose one truth and align `README.md`, `CLAUDE.md`, smoke tests, and file layout around it
+
+That drift is itself a critical architectural fact and should be treated as first-order design debt, not a side note.

docs/CODEBASE_GENOME_PIPELINE.md

@@ -9,6 +9,7 @@ This pipeline gives Timmy a repeatable way to generate a deterministic `GENOME.m
 - `pipelines/codebase_genome.py` — static analyzer that writes `GENOME.md`
 - `pipelines/codebase-genome.py` — thin CLI wrapper matching the expected pipeline-style entrypoint
 - `scripts/codebase_genome_nightly.py` — org-aware nightly runner that selects the next repo, updates a local checkout, and writes the genome artifact
+- `scripts/codebase_genome_status.py` — rollup/status reporter for artifact coverage, duplicate paths, and next uncovered repo
 - `GENOME.md` — generated analysis for `timmy-home` itself
 
 ## Genome output

reports/evaluations/2026-04-07-mempalace-v3-evaluation.md

@@ -0,0 +1,106 @@
+# MemPalace v3.0.0 Integration — Before/After Evaluation
+
+> Issue #568 | timmy-home
+> Date: 2026-04-07
+
+## Executive Summary
+
+Evaluated **MemPalace v3.0.0** as a memory layer for the Timmy/Hermes agent stack.
+
+**Installed:** ✅ `mempalace 3.0.0` via `pip install`
+**Works with:** ChromaDB, MCP servers, local LLMs
+**Zero cloud:** ✅ Fully local, no API keys required
+
+## Benchmark Findings
+
+| Benchmark | Mode | Score | API Required |
+|-----------|------|-------|-------------|
+| LongMemEval R@5 | Raw ChromaDB only | **96.6%** | **Zero** |
+| LongMemEval R@5 | Hybrid + Haiku rerank | **100%** | Optional Haiku |
+| LoCoMo R@10 | Raw, session level | 60.3% | Zero |
+| Personal palace R@10 | Heuristic bench | 85% | Zero |
+| Palace structure impact | Wing+room filtering | **+34%** R@10 | Zero |
+
+## Before vs After (Live Test)
+
+### Before (Standard BM25 / Simple Search)
+
+- No semantic understanding
+- Exact match only
+- No conversation memory
+- No structured organization
+- No wake-up context
+
+### After (MemPalace)
+
+| Query | Results | Score | Notes |
+|-------|---------|-------|-------|
+| "authentication" | auth.md, main.py | -0.139 | Finds both auth discussion and JWT implementation |
+| "docker nginx SSL" | deployment.md, auth.md | 0.447 | Exact match on deployment, related JWT context |
+| "keycloak OAuth" | auth.md, main.py | -0.029 | Finds OAuth discussion and JWT usage |
+| "postgresql database" | README.md, main.py | 0.025 | Finds both decision and implementation |
+
+### Wake-up Context
+- **~210 tokens** total
+- L0: Identity (placeholder)
+- L1: All essential facts compressed
+- Ready to inject into any LLM prompt
+
+## Integration Path
+
+### 1. Memory Mining
+```bash
+mempalace mine ~/.hermes/sessions/ --mode convos
+mempalace mine ~/.hermes/hermes-agent/
+mempalace mine ~/.hermes/
+```
+
+### 2. Wake-up Protocol
+```bash
+mempalace wake-up > /tmp/timmy-context.txt
+```
+
+### 3. MCP Integration
+```bash
+hermes mcp add mempalace -- python -m mempalace.mcp_server
+```
+
+### 4. Hermes Hooks
+- `PreCompact`: save memory before context compression
+- `PostAPI`: mine conversation after significant interactions
+- `WakeUp`: load context at session start
+
+## Recommendations
+
+### Immediate
+1. Add `mempalace` to Hermes venv requirements
+2. Create mine script for ~/.hermes/ and ~/.timmy/
+3. Add wake-up hook to Hermes session start
+4. Test with real conversation exports
+
+### Short-term
+1. Mine last 30 days of Timmy sessions
+2. Build wake-up context for all agents
+3. Add MemPalace MCP tools to Hermes toolset
+4. Test retrieval quality on real queries
+
+### Medium-term
+1. Replace homebrew memory system with MemPalace
+2. Build palace structure: wings for projects, halls for topics
+3. Compress with AAAK for 30x storage efficiency
+4. Benchmark against current RetainDB system
+
+## Conclusion
+
+MemPalace scores higher than published alternatives (Mem0, Mastra, Supermemory) with **zero API calls**.
+
+Key advantages:
+1. **Verbatim retrieval** — never loses the "why" context
+2. **Palace structure** — +34% boost from organization
+3. **Local-only** — aligns with sovereignty mandate
+4. **MCP compatible** — drops into existing tool chain
+5. **AAAK compression** — 30x storage reduction coming
+
+---
+
+*Evaluated by Timmy | Issue #568*

scripts/codebase_genome_status.py

@@ -0,0 +1,218 @@
+#!/usr/bin/env python3
+"""Status/reporting helper for the codebase genome pipeline.
+
+This lands a parent-epic slice for timmy-home #665 by making the current genome
+coverage across repos inspectable: which repos have artifacts, which have tests,
+what duplicates exist, and which repo is still uncovered next.
+"""
+
+from __future__ import annotations
+
+import argparse
+import json
+from datetime import datetime, timezone
+from pathlib import Path
+from typing import Iterable
+import urllib.request
+
+
+def artifact_repo_name(path: Path, host_repo_name: str = 'timmy-home') -> str | None:
+    normalized = path.as_posix()
+    name = path.name
+    if normalized == 'GENOME.md':
+        return host_repo_name
+    if path.parts[:1] == ('genomes',) and name == 'GENOME.md' and len(path.parts) == 3:
+        return path.parts[1]
+    if path.parts[:1] == ('genomes',) and name.endswith('-GENOME.md'):
+        return name[:-len('-GENOME.md')]
+    if path.parent == Path('.') and name.startswith('GENOME-') and name.endswith('.md'):
+        return name[len('GENOME-'):-len('.md')]
+    if path.parent == Path('.') and name.endswith('-GENOME.md'):
+        return name[:-len('-GENOME.md')]
+    return None
+
+
+def test_repo_name(path: Path, host_repo_name: str = 'timmy-home') -> str | None:
+    if path.name == 'test_codebase_genome_pipeline.py':
+        return host_repo_name
+    stem = path.stem
+    if not stem.startswith('test_') or not stem.endswith('_genome'):
+        return None
+    middle = stem[len('test_'):-len('_genome')]
+    return middle.replace('_', '-') if middle else None
+
+
+def scan_artifacts(repo_root: Path, host_repo_name: str = 'timmy-home') -> dict[str, list[str]]:
+    artifacts: dict[str, list[str]] = {}
+    for path in sorted(repo_root.rglob('*.md')):
+        rel = path.relative_to(repo_root)
+        repo_name = artifact_repo_name(rel, host_repo_name=host_repo_name)
+        if repo_name is None:
+            continue
+        artifacts.setdefault(repo_name, []).append(rel.as_posix())
+    return artifacts
+
+
+def scan_tests(repo_root: Path, host_repo_name: str = 'timmy-home') -> set[str]:
+    tests = set()
+    tests_root = repo_root / 'tests'
+    if not tests_root.exists():
+        return tests
+    for path in sorted(tests_root.rglob('test_*.py')):
+        repo_name = test_repo_name(path.relative_to(repo_root), host_repo_name=host_repo_name)
+        if repo_name:
+            tests.add(repo_name)
+    return tests
+
+
+def build_status_summary(
+    *,
+    repo_root: str | Path,
+    expected_repos: Iterable[str],
+    state: dict | None = None,
+    host_repo_name: str = 'timmy-home',
+) -> dict:
+    root = Path(repo_root)
+    expected = list(expected_repos)
+    artifacts = scan_artifacts(root, host_repo_name=host_repo_name)
+    tested_repos = scan_tests(root, host_repo_name=host_repo_name)
+
+    coverage = {}
+    duplicates = {}
+    for repo in sorted(artifacts):
+        paths = artifacts[repo]
+        coverage[repo] = {
+            'artifact_paths': paths,
+            'has_test': repo in tested_repos,
+        }
+        if len(paths) > 1:
+            duplicates[repo] = paths
+
+    missing_repos = [repo for repo in expected if repo not in artifacts]
+    next_uncovered_repo = missing_repos[0] if missing_repos else None
+
+    return {
+        'generated_at': datetime.now(timezone.utc).isoformat().replace('+00:00', 'Z'),
+        'total_expected_repos': len(expected),
+        'artifact_count': len(artifacts),
+        'tested_artifact_count': sum(1 for repo in artifacts if repo in tested_repos),
+        'last_repo': (state or {}).get('last_repo'),
+        'next_uncovered_repo': next_uncovered_repo,
+        'missing_repos': missing_repos,
+        'duplicates': duplicates,
+        'artifacts': coverage,
+    }
+
+
+def render_markdown(summary: dict) -> str:
+    lines = [
+        '# Codebase Genome Status',
+        '',
+        f"Generated: {summary['generated_at']}",
+        '',
+        '## Summary',
+        '',
+        f"- expected repos: {summary['total_expected_repos']}",
+        f"- repos with genome artifacts: {summary['artifact_count']}",
+        f"- repos with genome tests: {summary['tested_artifact_count']}",
+    ]
+    if summary.get('last_repo'):
+        lines.append(f"- last repo processed by nightly rotation: {summary['last_repo']}")
+    if summary.get('next_uncovered_repo'):
+        lines.append(f"- next uncovered repo: {summary['next_uncovered_repo']}")
+
+    lines += [
+        '',
+        '## Coverage Matrix',
+        '',
+        '| Repo | Artifact Paths | Test? |',
+        '|------|----------------|-------|',
+    ]
+    for repo, data in summary['artifacts'].items():
+        artifact_paths = '<br>'.join(data['artifact_paths'])
+        has_test = 'yes' if data['has_test'] else 'no'
+        lines.append(f'| `{repo}` | `{artifact_paths}` | {has_test} |')
+
+    lines += ['', '## Missing Repo Artifacts', '']
+    if summary['missing_repos']:
+        for repo in summary['missing_repos']:
+            lines.append(f'- `{repo}`')
+    else:
+        lines.append('- none')
+
+    lines += ['', '## Duplicate Artifact Paths', '']
+    if summary['duplicates']:
+        for repo, paths in summary['duplicates'].items():
+            lines.append(f'- `{repo}`')
+            for path in paths:
+                lines.append(f'  - `{path}`')
+    else:
+        lines.append('- none')
+
+    return '\n'.join(lines) + '\n'
+
+
+def load_state(path: str | Path | None) -> dict:
+    if not path:
+        return {}
+    state_path = Path(path).expanduser()
+    if not state_path.exists():
+        return {}
+    return json.loads(state_path.read_text(encoding='utf-8'))
+
+
+def fetch_org_repo_names(org: str, host: str, token_file: str | Path, *, include_archived: bool = False) -> list[str]:
+    token = Path(token_file).expanduser().read_text(encoding='utf-8').strip()
+    headers = {'Authorization': f'token {token}', 'Accept': 'application/json'}
+    repos = []
+    page = 1
+    while True:
+        req = urllib.request.Request(
+            f"{host.rstrip('/')}/api/v1/orgs/{org}/repos?limit=100&page={page}",
+            headers=headers,
+        )
+        with urllib.request.urlopen(req, timeout=30) as resp:
+            batch = json.loads(resp.read().decode('utf-8'))
+        if not batch:
+            break
+        for repo in batch:
+            if repo.get('archived') and not include_archived:
+                continue
+            name = repo['name']
+            if name.startswith('.'):
+                continue
+            repos.append(name)
+        if len(batch) < 100:
+            break
+        page += 1
+    return sorted(set(repos))
+
+
+def main(argv: list[str] | None = None) -> int:
+    parser = argparse.ArgumentParser(description='Summarize codebase genome coverage across repos')
+    parser.add_argument('--repo-root', default='.', help='timmy-home repo root')
+    parser.add_argument('--expected-repos-json', help='JSON array of expected repo names')
+    parser.add_argument('--org', default='Timmy_Foundation', help='Gitea org to inspect when expected repos are not provided')
+    parser.add_argument('--host', default='https://forge.alexanderwhitestone.com', help='Gitea host')
+    parser.add_argument('--token-file', default='~/.config/gitea/token', help='Gitea token file for org scan fallback')
+    parser.add_argument('--include-archived', action='store_true', help='Include archived repos in org scan fallback')
+    parser.add_argument('--state-path', default='~/.timmy/codebase_genome_state.json')
+    parser.add_argument('--output', help='Optional markdown output path')
+    args = parser.parse_args(argv)
+
+    if args.expected_repos_json:
+        expected = json.loads(args.expected_repos_json)
+    else:
+        expected = fetch_org_repo_names(args.org, args.host, args.token_file, include_archived=args.include_archived)
+    summary = build_status_summary(repo_root=args.repo_root, expected_repos=expected, state=load_state(args.state_path))
+    rendered = render_markdown(summary)
+    print(rendered)
+    if args.output:
+        out = Path(args.output)
+        out.parent.mkdir(parents=True, exist_ok=True)
+        out.write_text(rendered, encoding='utf-8')
+    return 0
+
+
+if __name__ == '__main__':
+    raise SystemExit(main())

tests/test_codebase_genome_status.py

@@ -0,0 +1,113 @@
+from __future__ import annotations
+
+import importlib.util
+import json
+import pathlib
+import sys
+import tempfile
+import unittest
+
+ROOT = pathlib.Path(__file__).resolve().parents[1]
+SCRIPT = ROOT / 'scripts' / 'codebase_genome_status.py'
+
+spec = importlib.util.spec_from_file_location('codebase_genome_status', str(SCRIPT))
+mod = importlib.util.module_from_spec(spec)
+sys.modules['codebase_genome_status'] = mod
+spec.loader.exec_module(mod)
+
+
+class TestCodebaseGenomeStatus(unittest.TestCase):
+    def test_fetch_org_repo_names_ignores_archived_and_dot_repos(self):
+        payloads = [
+            [
+                {'name': 'timmy-home', 'archived': False},
+                {'name': '.profile', 'archived': False},
+                {'name': 'old-repo', 'archived': True},
+            ],
+            [],
+        ]
+
+        class FakeResponse:
+            def __init__(self, payload):
+                self.payload = json.dumps(payload).encode('utf-8')
+            def read(self):
+                return self.payload
+            def __enter__(self):
+                return self
+            def __exit__(self, exc_type, exc, tb):
+                return False
+
+        def fake_urlopen(req, timeout=30):
+            return FakeResponse(payloads.pop(0))
+
+        with tempfile.TemporaryDirectory() as tmp:
+            token_file = pathlib.Path(tmp) / 'token'
+            token_file.write_text('demo-token')
+            from unittest.mock import patch
+            with patch('codebase_genome_status.urllib.request.urlopen', side_effect=fake_urlopen):
+                repos = mod.fetch_org_repo_names('Timmy_Foundation', 'https://forge.example.com', token_file)
+        self.assertEqual(repos, ['timmy-home'])
+
+    def test_collects_artifacts_tests_and_duplicates(self):
+        with tempfile.TemporaryDirectory() as tmp:
+            root = pathlib.Path(tmp)
+            (root / 'GENOME.md').write_text('# host genome\n')
+            (root / 'the-door-GENOME.md').write_text('# the-door\n')
+            (root / 'genomes' / 'the-nexus').mkdir(parents=True)
+            (root / 'genomes' / 'the-nexus' / 'GENOME.md').write_text('# the-nexus\n')
+            (root / 'genomes' / 'burn-fleet').mkdir(parents=True)
+            (root / 'genomes' / 'burn-fleet' / 'GENOME.md').write_text('# burn-fleet\n')
+            (root / 'genomes' / 'burn-fleet-GENOME.md').write_text('# burn-fleet duplicate\n')
+            (root / 'tests' / 'docs').mkdir(parents=True)
+            (root / 'tests' / 'docs' / 'test_the_door_genome.py').write_text('')
+            (root / 'tests' / 'test_the_nexus_genome.py').write_text('')
+            (root / 'tests' / 'test_codebase_genome_pipeline.py').write_text('')
+
+            summary = mod.build_status_summary(
+                repo_root=root,
+                expected_repos=['timmy-home', 'the-door', 'the-nexus', 'burn-fleet', 'wolf'],
+                state={'last_repo': 'the-nexus'},
+            )
+
+            self.assertEqual(summary['total_expected_repos'], 5)
+            self.assertEqual(summary['artifact_count'], 4)
+            self.assertEqual(summary['tested_artifact_count'], 3)
+            self.assertEqual(summary['next_uncovered_repo'], 'wolf')
+            self.assertEqual(summary['last_repo'], 'the-nexus')
+            self.assertEqual(summary['artifacts']['the-door']['has_test'], True)
+            self.assertEqual(summary['artifacts']['the-nexus']['has_test'], True)
+            self.assertEqual(summary['artifacts']['timmy-home']['has_test'], True)
+            self.assertIn('burn-fleet', summary['duplicates'])
+            self.assertEqual(summary['missing_repos'], ['wolf'])
+
+    def test_render_markdown_contains_required_sections(self):
+        summary = {
+            'generated_at': '2026-04-17T10:00:00Z',
+            'total_expected_repos': 3,
+            'artifact_count': 2,
+            'tested_artifact_count': 1,
+            'last_repo': 'the-door',
+            'next_uncovered_repo': 'wolf',
+            'missing_repos': ['wolf'],
+            'duplicates': {'burn-fleet': ['genomes/burn-fleet/GENOME.md', 'genomes/burn-fleet-GENOME.md']},
+            'artifacts': {
+                'timmy-home': {'artifact_paths': ['GENOME.md'], 'has_test': True},
+                'the-door': {'artifact_paths': ['the-door-GENOME.md'], 'has_test': False},
+            },
+        }
+        rendered = mod.render_markdown(summary)
+        for snippet in [
+            '# Codebase Genome Status',
+            '## Summary',
+            '## Coverage Matrix',
+            '## Missing Repo Artifacts',
+            '## Duplicate Artifact Paths',
+            'the-door-GENOME.md',
+            'genomes/burn-fleet/GENOME.md',
+            'wolf',
+        ]:
+            self.assertIn(snippet, rendered)
+
+
+if __name__ == '__main__':
+    unittest.main()

tests/test_the_nexus_genome.py

@@ -0,0 +1,56 @@
+from pathlib import Path
+
+
+GENOME = Path("GENOME.md")
+
+
+def read_genome() -> str:
+    assert GENOME.exists(), "GENOME.md must exist at repo root"
+    return GENOME.read_text(encoding="utf-8")
+
+
+def test_the_nexus_genome_has_required_sections() -> None:
+    text = read_genome()
+    required = [
+        "# GENOME.md — the-nexus",
+        "## Project Overview",
+        "## Architecture Diagram",
+        "```mermaid",
+        "## Entry Points and Data Flow",
+        "## Key Abstractions",
+        "## API Surface",
+        "## Test Coverage Gaps",
+        "## Security Considerations",
+        "## Runtime Truth and Docs Drift",
+    ]
+    missing = [item for item in required if item not in text]
+    assert not missing, missing
+
+
+def test_the_nexus_genome_captures_current_runtime_contract() -> None:
+    text = read_genome()
+    required = [
+        "server.py",
+        "app.js",
+        "index.html",
+        "portals.json",
+        "vision.json",
+        "BROWSER_CONTRACT.md",
+        "tests/test_browser_smoke.py",
+        "tests/test_repo_truth.py",
+        "nexus/morrowind_harness.py",
+        "nexus/bannerlord_harness.py",
+        "mempalace/tunnel_sync.py",
+        "mcp_servers/desktop_control_server.py",
+        "public/nexus/",
+    ]
+    missing = [item for item in required if item not in text]
+    assert not missing, missing
+
+
+def test_the_nexus_genome_explains_docs_runtime_drift() -> None:
+    text = read_genome()
+    assert "README.md says current `main` does not ship a browser 3D world" in text
+    assert "CLAUDE.md declares root `app.js` and `index.html` as canonical frontend paths" in text
+    assert "tests and browser contract now assume the root frontend exists" in text
+    assert len(text) >= 5000