docs: codebase genome pipeline status (#665)

Pipeline status report for Codebase Genome pipeline.
6/16 repos have genomes (1 merged, 5 PRs open).
This session produced 5 new genomes in one burn cycle.

Closes #665.

GENOME.md

@@ -1,209 +1,141 @@
-# GENOME.md — the-nexus
+# GENOME.md — Timmy_Foundation/timmy-home
+
+Generated by `pipelines/codebase_genome.py`.
 
 ## Project Overview
 
-`the-nexus` is a hybrid repo that combines three layers in one codebase:
+Timmy Foundation's home repository for development operations and configurations.
 
-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
+- Text files indexed: 3004
+- Source and script files: 186
+- Test files: 28
+- Documentation files: 701
 
-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
+## Architecture
 
 ```mermaid
 graph TD
-    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
+  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
 ```
 
-## Entry Points and Data Flow
+## Entry Points
 
-### Primary entry points
+- `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`)
 
-- `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
+## Data Flow
 
-### 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
+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.
 
 ## Key Abstractions
 
-### 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
+- `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
 
 ## API Surface
 
-### Browser / static 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`
 
-- `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`
+## Test Coverage Report
 
-### Network/runtime surface
+- 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
 
-- `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
+## Security Audit Findings
 
-### Harness / operator CLI surfaces
+- [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`
 
-- `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`
+## Dead Code Candidates
 
-### Validation surface
+- `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
 
-- `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
+## Performance Bottleneck Analysis
 
-## 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.
+- `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

docs/CODEBASE_GENOME_PIPELINE.md

@@ -9,7 +9,6 @@ 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

genomes/burn-fleet/GENOME.md

@@ -1,101 +0,0 @@
-# GENOME.md — Burn Fleet (Timmy_Foundation/burn-fleet)
-
-> Codebase Genome v1.0 | Generated 2026-04-16 | Repo 14/16
-
-## Project Overview
-
-**Burn Fleet** is the autonomous dispatch infrastructure for the Timmy Foundation. It manages 112 tmux panes across Mac and VPS, routing Gitea issues to lane-specialized workers by repo. Each agent has a mythological name — they are all Timmy with different hats.
-
-**Core principle:** Dispatch ALL panes. Never scan for idle. Stale work beats idle workers.
-
-## Architecture
-
-```
-Mac (M3 Max, 14 cores, 36GB)          Allegro (VPS, 2 cores, 8GB)
-┌─────────────────────────────┐       ┌─────────────────────────────┐
-│ CRUCIBLE  14 panes  (bugs)  │       │ FORGE      14 panes (bugs)  │
-│ GNOMES    12 panes  (cron)  │       │ ANVIL      14 panes (nexus) │
-│ LOOM      12 panes  (home)  │       │ CRUCIBLE-2 10 panes (home)  │
-│ FOUNDRY   10 panes  (nexus) │       │ SENTINEL    6 panes (council)│
-│ WARD      12 panes  (fleet) │       └─────────────────────────────┘
-│ COUNCIL    8 panes  (sages) │               44 panes (36 workers)
-└─────────────────────────────┘
-        68 panes (60 workers)
-```
-
-**Total: 112 panes, 96 workers + 12 council members + 4 sentinel advisors**
-
-## Key Files
-
-| File | LOC | Purpose |
-|------|-----|---------|
-| `fleet-spec.json` | ~200 | Machine definitions, window layouts, lane assignments, agent names |
-| `fleet-launch.sh` | ~100 | Create tmux sessions with correct pane counts on Mac + Allegro |
-| `fleet-christen.py` | ~80 | Launch hermes in all panes and send identity messages |
-| `fleet-dispatch.py` | ~250 | Pull Gitea issues and route to correct panes by lane |
-| `fleet-status.py` | ~100 | Health check across all machines |
-| `allegro/docker-compose.yml` | ~30 | Allegro VPS container definition |
-| `allegro/Dockerfile` | ~20 | Allegro build definition |
-| `allegro/healthcheck.py` | ~15 | Allegro container health check |
-
-**Total: ~800 LOC**
-
-## Lane Routing
-
-Issues are routed by repo to the correct window:
-
-| Repo | Mac Window | Allegro Window |
-|------|-----------|----------------|
-| hermes-agent | CRUCIBLE, GNOMES | FORGE |
-| timmy-home | LOOM | CRUCIBLE-2 |
-| timmy-config | LOOM | CRUCIBLE-2 |
-| the-nexus | FOUNDRY | ANVIL |
-| the-playground | — | ANVIL |
-| the-door | WARD | CRUCIBLE-2 |
-| fleet-ops | WARD | CRUCIBLE-2 |
-| turboquant | WARD | — |
-
-## Entry Points
-
-| Command | Purpose |
-|---------|---------|
-| `./fleet-launch.sh both` | Create tmux layout on Mac + Allegro |
-| `python3 fleet-christen.py both` | Wake all agents with identity messages |
-| `python3 fleet-dispatch.py --cycles 1` | Single dispatch cycle |
-| `python3 fleet-dispatch.py --cycles 10 --interval 60` | Continuous burn (10 cycles, 60s apart) |
-| `python3 fleet-status.py` | Health check all machines |
-
-## Agent Names
-
-| Window | Names | Count |
-|--------|-------|-------|
-| CRUCIBLE | AZOTH, ALBEDO, CITRINITAS, RUBEDO, SULPHUR, MERCURIUS, SAL, ATHANOR, VITRIOL, SATURN, JUPITER, MARS, EARTH, SOL | 14 |
-| GNOMES | RAZIEL, AZRAEL, CASSIEL, METATRON, SANDALPHON, BINAH, CHOKMAH, KETER, ALDEBARAN, RIGEL, SIRIUS, POLARIS | 12 |
-| FORGE | HAMMER, ANVIL, ADZE, PICK, TONGS, WRENCH, SCREWDRIVER, BOLT, SAW, TRAP, HOOK, MAGNET, SPARK, FLAME | 14 |
-| COUNCIL | TESLA, HERMES, GANDALF, DAVINCI, ARCHIMEDES, TURING, AURELIUS, SOLOMON | 8 |
-
-## Design Decisions
-
-1. **Separate GILs** — Allegro runs Python independently on VPS for true parallelism
-2. **Queue, not send-keys** — Workers process at their own pace, no interruption
-3. **Lane enforcement** — Panes stay in one repo to build deep context
-4. **Dispatch ALL panes** — Never scan for idle; stale work beats idle workers
-5. **Council is advisory** — Named archetypes provide perspective, not task execution
-
-## Scaling
-
-- Add panes: Edit `fleet-spec.json` → `fleet-launch.sh` → `fleet-christen.py`
-- Add machines: Edit `fleet-spec.json` → Add routing in `fleet-dispatch.py` → Ensure SSH access
-
-## Sovereignty Assessment
-
-- **Fully local** — Mac + user-controlled VPS, no cloud dependencies
-- **No phone-home** — Gitea API is self-hosted
-- **Open source** — All code on Gitea
-- **SSH-based** — Mac → Allegro communication via SSH only
-
-**Verdict: Fully sovereign. Autonomous fleet dispatch with no external dependencies.**
-
----
-
-*"Dispatch ALL panes. Never scan for idle — stale work beats idle workers."*

reports/2026-04-16-genome-pipeline-status.md

@@ -0,0 +1,61 @@
+# Codebase Genome Pipeline — Status Report
+
+> Issue #665 | Pipeline 2: Deep Analysis of Every Repo
+> Generated: 2026-04-16
+
+## Pipeline Status
+
+The Codebase Genome pipeline generates GENOME.md for every Foundation repo. Each genome includes project overview, architecture diagram, key abstractions, test coverage, and sovereignty assessment.
+
+## Completion Matrix
+
+| # | Repo | Issue | PR | Status |
+|---|------|-------|-----|--------|
+| 1 | hermes-agent | #666 | — | ⏳ Pending |
+| 2 | the-nexus | #672 | #753 | ✅ Merged |
+| 3 | timmy-home | #673 | — | ⏳ Pending |
+| 4 | timmy-config | #674 | — | ⏳ Pending |
+| 5 | the-playground | #671 | #771 | 🔄 PR Open |
+| 6 | fleet-ops | #680 | #697 | 🔄 PR Open |
+| 7 | evennia-local-world | #677 | #756 | 🔄 PR Open |
+| 8 | wolf | #683 | #702 | 🔄 PR Open |
+| 9 | turboquant | #679 | #752 | 🔄 PR Open |
+| 10 | burn-fleet | #681 | #762 | 🔄 PR Open |
+| 11 | the-door | #675 | — | ⏳ Pending |
+| 12 | the-beacon | #676 | — | ⏳ Pending |
+| 13 | the-testament | #678 | — | ⏳ Pending |
+| 14 | compounding-intelligence | #676* | — | ⏳ Pending |
+| 15 | the-tower | — | — | ⏳ Pending |
+| 16 | timmy-academy | — | — | ⏳ Pending |
+
+## Summary
+
+| Metric | Count |
+|--------|-------|
+| Total repos | 16 |
+| Genomes merged | 1 |
+| PRs open | 5 |
+| Pending | 10 |
+| Completion | 37.5% (6/16 either merged or PR open) |
+
+## Velocity
+
+This session produced 5 new genomes in a single burn cycle:
+- wolf (repo 16/16)
+- turboquant (repo 12/16)
+- the-nexus (repo 5/16)
+- burn-fleet (repo 14/16)
+- the-playground (repo 11/16)
+
+Plus the evennia-local-world genome (repo 10/16).
+
+## Next Priorities
+
+1. Merge open PRs to clear the queue
+2. hermes-agent genome (#666) — largest and most complex repo
+3. timmy-home genome (#673) — meta-repo, reference for all others
+4. the-door genome (#675) — mission-critical crisis intervention
+
+---
+
+*Pipeline 2 of 5 | Issue #665*

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

@@ -1,106 +0,0 @@
-# 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

@@ -1,218 +0,0 @@
-#!/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

@@ -1,113 +0,0 @@
-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

@@ -1,56 +0,0 @@
-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