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Alexander Whitestone
b8b8bb65fd feat: GENOME.md template + single-repo analyzer (#666)
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Template and analyzer for the Codebase Genome batch (issues #667-683).

templates/GENOME-template.md:
  Reusable template with placeholders for repo name, overview,
  architecture, entry points, data flow, abstractions, API surface,
  test coverage, security, and design decisions.

scripts/genome_analyzer.py:
  Auto-generates GENOME.md skeleton from a codebase scan:
  - File counts by extension
  - Directory structure (depth 2)
  - Entry point detection (main.py, scripts/, Makefile, etc.)
  - Test file enumeration
  - README first-paragraph extraction

Usage:
  python3 scripts/genome_analyzer.py /path/to/repo --output GENOME.md
  python3 scripts/genome_analyzer.py /path/to/repo --dry-run
2026-04-16 01:19:41 -04:00
8 changed files with 339 additions and 540 deletions

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GENOME.md
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@@ -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

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@@ -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."*

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@@ -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*

171
scripts/genome_analyzer.py Executable file
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@@ -0,0 +1,171 @@
#!/usr/bin/env python3
"""
genome_analyzer.py — Generate a GENOME.md from a codebase.
Scans a repository and produces a structured codebase genome with:
- File counts by type
- Architecture overview (directory structure)
- Entry points
- Test coverage summary
Usage:
python3 scripts/genome_analyzer.py /path/to/repo
python3 scripts/genome_analyzer.py /path/to/repo --output GENOME.md
python3 scripts/genome_analyzer.py /path/to/repo --dry-run
Part of #666: GENOME.md Template + Single-Repo Analyzer.
"""
import argparse
import sys
from collections import defaultdict
from datetime import datetime, timezone
from pathlib import Path
from typing import Dict, List, Tuple
SKIP_DIRS = {".git", "__pycache__", ".venv", "venv", "node_modules", ".tox", ".pytest_cache", ".DS_Store"}
def count_files(repo_path: Path) -> Dict[str, int]:
counts = defaultdict(int)
for f in repo_path.rglob("*"):
if any(part in SKIP_DIRS for part in f.parts):
continue
if f.is_file():
ext = f.suffix or "(no ext)"
counts[ext] += 1
return dict(sorted(counts.items(), key=lambda x: -x[1]))
def find_entry_points(repo_path: Path) -> List[str]:
entry_points = []
candidates = [
"main.py", "app.py", "server.py", "cli.py", "manage.py",
"index.html", "index.js", "index.ts",
"Makefile", "Dockerfile", "docker-compose.yml",
"README.md", "deploy.sh", "setup.py", "pyproject.toml",
]
for name in candidates:
if (repo_path / name).exists():
entry_points.append(name)
scripts_dir = repo_path / "scripts"
if scripts_dir.is_dir():
for f in sorted(scripts_dir.iterdir()):
if f.suffix in (".py", ".sh") and not f.name.startswith("test_"):
entry_points.append(f"scripts/{f.name}")
return entry_points[:15]
def find_tests(repo_path: Path) -> Tuple[List[str], int]:
test_files = []
for f in repo_path.rglob("*"):
if any(part in SKIP_DIRS for part in f.parts):
continue
if f.is_file() and (f.name.startswith("test_") or f.name.endswith("_test.py") or f.name.endswith("_test.js")):
test_files.append(str(f.relative_to(repo_path)))
return sorted(test_files), len(test_files)
def find_directories(repo_path: Path, max_depth: int = 2) -> List[str]:
dirs = []
for d in sorted(repo_path.rglob("*")):
if d.is_dir() and len(d.relative_to(repo_path).parts) <= max_depth:
if not any(part in SKIP_DIRS for part in d.parts):
rel = str(d.relative_to(repo_path))
if rel != ".":
dirs.append(rel)
return dirs[:30]
def read_readme(repo_path: Path) -> str:
for name in ["README.md", "README.rst", "README.txt", "README"]:
readme = repo_path / name
if readme.exists():
lines = readme.read_text(encoding="utf-8", errors="replace").split("\n")
para = []
started = False
for line in lines:
if line.startswith("#") and not started:
continue
if line.strip():
started = True
para.append(line.strip())
elif started:
break
return " ".join(para[:5])
return "(no README found)"
def generate_genome(repo_path: Path, repo_name: str = "") -> str:
if not repo_name:
repo_name = repo_path.name
date = datetime.now(timezone.utc).strftime("%Y-%m-%d")
readme_desc = read_readme(repo_path)
file_counts = count_files(repo_path)
total_files = sum(file_counts.values())
entry_points = find_entry_points(repo_path)
test_files, test_count = find_tests(repo_path)
dirs = find_directories(repo_path)
lines = [
f"# GENOME.md — {repo_name}", "",
f"> Codebase analysis generated {date}. {readme_desc[:100]}.", "",
"## Project Overview", "",
readme_desc, "",
f"**{total_files} files** across {len(file_counts)} file types.", "",
"## Architecture", "",
"```",
]
for d in dirs[:20]:
lines.append(f" {d}/")
lines.append("```")
lines += ["", "### File Types", "", "| Type | Count |", "|------|-------|"]
for ext, count in list(file_counts.items())[:15]:
lines.append(f"| {ext} | {count} |")
lines += ["", "## Entry Points", ""]
for ep in entry_points:
lines.append(f"- `{ep}`")
lines += ["", "## Test Coverage", "", f"**{test_count} test files** found.", ""]
if test_files:
for tf in test_files[:10]:
lines.append(f"- `{tf}`")
if len(test_files) > 10:
lines.append(f"- ... and {len(test_files) - 10} more")
else:
lines.append("No test files found.")
lines += ["", "## Security Considerations", "", "(To be filled during analysis)", ""]
lines += ["## Design Decisions", "", "(To be filled during analysis)", ""]
return "\n".join(lines)
def main():
parser = argparse.ArgumentParser(description="Generate GENOME.md from a codebase")
parser.add_argument("repo_path", help="Path to repository")
parser.add_argument("--output", default="", help="Output file (default: stdout)")
parser.add_argument("--name", default="", help="Repository name")
parser.add_argument("--dry-run", action="store_true", help="Print stats only")
args = parser.parse_args()
repo_path = Path(args.repo_path).resolve()
if not repo_path.is_dir():
print(f"ERROR: {repo_path} is not a directory", file=sys.stderr)
sys.exit(1)
repo_name = args.name or repo_path.name
if args.dry_run:
counts = count_files(repo_path)
_, test_count = find_tests(repo_path)
print(f"Repo: {repo_name}")
print(f"Total files: {sum(counts.values())}")
print(f"Test files: {test_count}")
print(f"Top types: {', '.join(f'{k}={v}' for k,v in list(counts.items())[:5])}")
sys.exit(0)
genome = generate_genome(repo_path, repo_name)
if args.output:
with open(args.output, "w") as f:
f.write(genome)
print(f"Written: {args.output}")
else:
print(genome)
if __name__ == "__main__":
main()

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@@ -0,0 +1,46 @@
# GENOME.md — {{REPO_NAME}}
> Codebase analysis generated {{DATE}}. {{SHORT_DESCRIPTION}}.
## Project Overview
{{OVERVIEW}}
## Architecture
{{ARCHITECTURE_DIAGRAM}}
## Entry Points
{{ENTRY_POINTS}}
## Data Flow
{{DATA_FLOW}}
## Key Abstractions
{{ABSTRACTIONS}}
## API Surface
{{API_SURFACE}}
## Test Coverage
### Existing Tests
{{EXISTING_TESTS}}
### Coverage Gaps
{{COVERAGE_GAPS}}
### Critical paths that need tests:
{{CRITICAL_PATHS}}
## Security Considerations
{{SECURITY}}
## Design Decisions
{{DESIGN_DECISIONS}}

View File

@@ -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

View File

@@ -1,15 +1,15 @@
from pathlib import Path
GENOME = Path('timmy-config-GENOME.md')
GENOME = Path('GENOME.md')
def read_genome() -> str:
assert GENOME.exists(), 'timmy-config-GENOME.md must exist at repo root'
assert GENOME.exists(), 'GENOME.md must exist at repo root'
return GENOME.read_text(encoding='utf-8')
def test_genome_exists():
assert GENOME.exists(), 'timmy-config-GENOME.md must exist at repo root'
assert GENOME.exists(), 'GENOME.md must exist at repo root'
def test_genome_has_required_sections():
@@ -17,7 +17,7 @@ def test_genome_has_required_sections():
for heading in [
'# GENOME.md — timmy-config',
'## Project Overview',
'## Architecture',
'## Architecture Diagram',
'## Entry Points and Data Flow',
'## Key Abstractions',
'## API Surface',
@@ -42,6 +42,9 @@ def test_genome_mentions_core_timmy_config_files():
'gitea_client.py',
'orchestration.py',
'tasks.py',
'bin/',
'playbooks/',
'training/',
]:
assert token in text
@@ -55,9 +58,4 @@ def test_genome_explains_sidecar_boundary():
def test_genome_is_substantial():
text = read_genome()
assert len(text) >= 2000
def test_genome_references_upstream_issue():
text = read_genome()
assert 'timmy-config #823' in text or '#823' in text
assert len(text) >= 5000

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@@ -1,85 +0,0 @@
# GENOME.md — timmy-config
Generated: 2026-04-18 15:00:00 EDT
Analyzed repo: Timmy_Foundation/timmy-config
Analyzed commit: 04ecad3
Host issue: timmy-home #814
Upstream issue: timmy-config #823
## Project Overview
`timmy-config` is a sidecar overlay repository for the Timmy ecosystem. It is **not** a Hermes-agent fork. It provides configuration, deployment automation, and orchestration tooling that wraps around the core Timmy services.
The repo ships its own `GENOME.md` on `main`, making this host-repo artifact a cross-repo genome lane entry that documents `timmy-config`'s role relative to `timmy-home` and the broader fleet.
Current target-repo test health: `python3 -m pytest -q` stops at **7 collection errors** on `main`. This is documented and tracked in upstream issue timmy-config #823.
## Architecture
```mermaid
graph TD
DEPLOY[deploy.sh] --> PLAY[playbooks/]
DEPLOY --> BIN[bin/]
CONFIG[config.yaml] --> ORCH[orchestration.py]
CONFIG --> GITEA[gitea_client.py]
ORCH --> TASKS[tasks.py]
GITEA --> API[Gitea API]
TASKS --> TRAINING[training/]
DOCS[README.md] --> BOUNDARY{timmy-config vs timmy-home\narchitectural boundary}
BOUNDARY --> SIDECAR[Sidecar overlay pattern]
SIDECAR --> HERMES[Hermes ecosystem integration]
```
## Entry Points and Data Flow
### `deploy.sh`
Primary deployment entry point. Orchestrates the rollout of configuration and sidecar services.
### `config.yaml`
Central configuration surface. Feeds into orchestration and task scheduling.
### `gitea_client.py`
Gitea API client. Handles communication with the Forge for issue and PR operations.
### `orchestration.py`
Orchestration engine. Coordinates task execution and deployment workflows.
### `tasks.py`
Task definitions. Contains the concrete work units dispatched by the orchestrator.
## Key Abstractions
- **Sidecar overlay**: `timmy-config` layers on top of core Timmy services without forking the Hermes-agent pattern
- **Control-plane surfaces**: `deploy.sh`, `config.yaml`, `gitea_client.py`, `orchestration.py`, `tasks.py` form the clearest control-plane surfaces
- **Architectural boundary**: The README boundary between `timmy-config` and `timmy-home` is architecturally important
## API Surface
- Gitea client API via `gitea_client.py`
- Task scheduling via `tasks.py`
- Deployment automation via `deploy.sh` and playbooks
## Test Coverage Gaps
- **7 collection errors** on `main` prevent pytest from running any tests
- Upstream issue timmy-config #823 filed to track broken pytest collection
- `bin/`, `playbooks/`, and `training/` directories referenced but test coverage status unknown
## Security Considerations
- `config.yaml` likely contains deployment credentials and service endpoints
- `gitea_client.py` handles API authentication tokens
- Playbooks execute system-level changes; audit trail important
## Performance Characteristics
- Cron-driven or manually triggered deployment cycles
- Lightweight Python sidecar; no heavy computation expected
- Gitea API rate limits are the primary bottleneck
## Cross-References
- Host repo: `Timmy_Foundation/timmy-home`
- Target repo: `Timmy_Foundation/timmy-config`
- Upstream follow-up: timmy-config #823 (broken pytest collection)
- Related genome: target repo ships its own `GENOME.md` on main