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Alexander Whitestone
aad1b0e652 docs: add GENOME template and refresh root genome (#666)
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2026-04-17 03:09:59 -04:00
Alexander Whitestone
e47e6506b4 test: cover GENOME template surface for #666 2026-04-17 03:05:53 -04:00
7 changed files with 230 additions and 611 deletions

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GENOME.md
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@@ -1,209 +1,144 @@
# 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: 3133
- Source and script files: 219
- Test files: 73
- Documentation files: 743
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"]
ansible["ansible"]
briefings["briefings"]
codebase_genome["codebase_genome"]
config["config"]
configs["configs"]
conftest["conftest"]
dns_records["dns-records"]
evennia["evennia"]
evennia_tools["evennia_tools"]
repo_root --> angband
repo_root --> ansible
repo_root --> briefings
repo_root --> codebase_genome
repo_root --> config
repo_root --> configs
```
## Entry Points and Data Flow
## Entry Points
### Primary entry points
- `codebase_genome.py` — python main guard (`python3 codebase_genome.py`)
- `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/agent_pr_gate.py` — operational script (`python3 scripts/agent_pr_gate.py`)
- `scripts/auto_restart_agent.sh` — operational script (`bash scripts/auto_restart_agent.sh`)
- `scripts/autonomous_issue_creator.py` — operational script (`python3 scripts/autonomous_issue_creator.py`)
- `scripts/backlog_cleanup.py` — operational script (`python3 scripts/backlog_cleanup.py`)
- `scripts/backlog_triage.py` — operational script (`python3 scripts/backlog_triage.py`)
- `scripts/backlog_triage_cron.sh` — operational script (`bash scripts/backlog_triage_cron.sh`)
- `scripts/backup_pipeline.sh` — operational script (`bash scripts/backup_pipeline.sh`)
- `scripts/bezalel_gemma4_vps.py` — operational script (`python3 scripts/bezalel_gemma4_vps.py`)
- `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 `codebase_genome.py`, `gemini-fallback-setup.sh`, `morrowind/hud.sh`.
2. Core logic fans into top-level components: `angband`, `ansible`, `briefings`, `codebase_genome`, `config`, `configs`.
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
- `codebase_genome.py` — classes `FunctionInfo`:19; functions `extract_functions()`:58, `generate_test()`:116, `scan_repo()`:191, `find_existing_tests()`:209, `main()`:231
- `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
## API Surface
### Browser / static surface
- CLI: `python3 codebase_genome.py` — python main guard (`codebase_genome.py`)
- 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: `python3 scripts/agent_pr_gate.py` — operational script (`scripts/agent_pr_gate.py`)
- CLI: `bash scripts/auto_restart_agent.sh` — operational script (`scripts/auto_restart_agent.sh`)
- CLI: `python3 scripts/autonomous_issue_creator.py` — operational script (`scripts/autonomous_issue_creator.py`)
- CLI: `python3 scripts/backlog_cleanup.py` — operational script (`scripts/backlog_cleanup.py`)
- Python: `extract_functions()` from `codebase_genome.py:58`
- Python: `generate_test()` from `codebase_genome.py:116`
- Python: `scan_repo()` from `codebase_genome.py:191`
- Python: `find_existing_tests()` from `codebase_genome.py:209`
- Python: `main()` from `codebase_genome.py:231`
- Python: `get_narrative_phase()` from `evennia/timmy_world/game.py:55`
- `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: 219
- Test files inspected: 73
- 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
- `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
- `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
- `uni-wizard/scripts/generate_scorecard.py` — no matching test reference detected
- `morrowind/local_brain.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
- `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
- `skills/research/domain-intel/scripts/domain_intel.py` — not imported by indexed Python modules and not referenced by tests
- `wizards/allegro/home/skills/research/domain-intel/scripts/domain_intel.py` — not imported by indexed Python modules and not referenced by tests
- `timmy-local/scripts/ingest.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/predictive_resource_allocator.py` — large module (410 lines) likely hides multiple responsibilities

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@@ -8,6 +8,7 @@ This pipeline gives Timmy a repeatable way to generate a deterministic `GENOME.m
- `pipelines/codebase_genome.py` — static analyzer that writes `GENOME.md`
- `pipelines/codebase-genome.py` — thin CLI wrapper matching the expected pipeline-style entrypoint
- `templates/GENOME-template.md` — reusable review scaffold with the exact sections the generator emits
- `scripts/codebase_genome_nightly.py` — org-aware nightly runner that selects the next repo, updates a local checkout, and writes the genome artifact
- `GENOME.md` — generated analysis for `timmy-home` itself
@@ -40,6 +41,14 @@ The hyphenated wrapper also works:
python3 pipelines/codebase-genome.py --repo-root /path/to/repo --repo Timmy_Foundation/some-repo
```
If an agent or human wants to review or hand-edit the artifact before publishing it, start from:
```text
templates/GENOME-template.md
```
The template uses the same section names as the generator output, so issue-specific verification can lock the structure without depending on one repo's exact contents.
## Nightly org rotation
Dry-run the next selection:

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@@ -1,74 +0,0 @@
# LAB-003 — Truck Battery Disconnect Install Packet
No battery disconnect switch has been purchased or installed yet.
This packet turns the issue into a field-ready purchase / install / validation checklist while preserving what still requires live work.
## Candidate Store Run
- AutoZone — Newport or Claremont
- Advance Auto Parts — Newport or Claremont
- O'Reilly Auto Parts — Newport or Claremont
## Required Items
- battery terminal disconnect switch
- terminal shim/post riser if needed
## Selection Criteria
- Fits the truck battery post without forcing the clamp
- Mounts on the negative battery terminal
- Physically secure once tightened
- no special tools required to operate
## Live Purchase State
- Store selected: pending
- Part selected: pending
- Part cost: pending purchase
## Installation Target
- Install location: negative battery terminal
- Ready to operate without tools: yes
## Install Checklist
- [ ] Verify the truck is off and keys are removed before touching the battery
- [ ] Confirm the disconnect fits the negative battery terminal before final tightening
- [ ] Install the disconnect on the negative battery terminal
- [ ] Tighten until physically secure with no terminal wobble
- [ ] Verify the disconnect can be opened and closed by hand
## Validation Checklist
- [ ] Leave the truck parked with the disconnect opened for at least 24 hours
- [ ] Reconnect the switch by hand the next day
- [ ] Truck starts reliably after sitting 24+ hours with switch disconnected
- [ ] Receipt or photo of installed switch uploaded to this issue
## Overnight Verification Log
- Install completed: False
- Physically secure: False
- Overnight disconnect duration: pending
- Truck started after disconnect: pending
- Receipt / photo path: pending
## Battery Replacement Fallback
If the truck still fails the overnight test after the disconnect install, replace battery and re-run the 24-hour validation.
## Missing Live Fields
- store_selected
- part_name
- install_completed
- physically_secure
- overnight_test_hours
- truck_started_after_disconnect
- receipt_or_photo_path
## Honest next step
Buy the disconnect switch, install it on the negative battery terminal, leave the truck disconnected for 24+ hours, and only close the issue after receipt/photo evidence and the overnight start result are attached.

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@@ -1,267 +0,0 @@
#!/usr/bin/env python3
"""Prepare a field-ready install packet for LAB-003 truck battery disconnect work."""
from __future__ import annotations
import argparse
import json
from pathlib import Path
from typing import Any
CANDIDATE_STORES = [
"AutoZone — Newport or Claremont",
"Advance Auto Parts — Newport or Claremont",
"O'Reilly Auto Parts — Newport or Claremont",
]
REQUIRED_ITEMS = [
"battery terminal disconnect switch",
"terminal shim/post riser if needed",
]
SELECTION_CRITERIA = [
"Fits the truck battery post without forcing the clamp",
"Mounts on the negative battery terminal",
"Physically secure once tightened",
"no special tools required to operate",
]
INSTALL_CHECKLIST = [
"Verify the truck is off and keys are removed before touching the battery",
"Confirm the disconnect fits the negative battery terminal before final tightening",
"Install the disconnect on the negative battery terminal",
"Tighten until physically secure with no terminal wobble",
"Verify the disconnect can be opened and closed by hand",
]
VALIDATION_CHECKLIST = [
"Leave the truck parked with the disconnect opened for at least 24 hours",
"Reconnect the switch by hand the next day",
"Truck starts reliably after sitting 24+ hours with switch disconnected",
"Receipt or photo of installed switch uploaded to this issue",
]
BATTERY_REPLACEMENT_FOLLOWUP = (
"If the truck still fails the overnight test after the disconnect install, "
"replace battery and re-run the 24-hour validation."
)
def _as_bool(value: Any) -> bool | None:
if value is None:
return None
if isinstance(value, bool):
return value
text = str(value).strip().lower()
if text in {"1", "true", "yes", "y"}:
return True
if text in {"0", "false", "no", "n"}:
return False
return None
def build_packet(details: dict[str, Any]) -> dict[str, Any]:
store_selected = (details.get("store_selected") or "").strip()
part_name = (details.get("part_name") or "").strip()
receipt_or_photo_path = (details.get("receipt_or_photo_path") or "").strip()
install_completed = _as_bool(details.get("install_completed"))
physically_secure = _as_bool(details.get("physically_secure"))
truck_started = _as_bool(details.get("truck_started_after_disconnect"))
replacement_needed = _as_bool(details.get("replacement_battery_needed"))
overnight_test_hours = details.get("overnight_test_hours")
part_cost_usd = details.get("part_cost_usd")
try:
overnight_test_hours = int(overnight_test_hours) if overnight_test_hours is not None else None
except (TypeError, ValueError):
overnight_test_hours = None
try:
part_cost_usd = float(part_cost_usd) if part_cost_usd is not None else None
except (TypeError, ValueError):
part_cost_usd = None
missing_fields: list[str] = []
if not store_selected:
missing_fields.append("store_selected")
if not part_name:
missing_fields.append("part_name")
if install_completed is not True:
missing_fields.append("install_completed")
if physically_secure is not True:
missing_fields.append("physically_secure")
if overnight_test_hours is None:
missing_fields.append("overnight_test_hours")
if truck_started is None:
missing_fields.append("truck_started_after_disconnect")
if not receipt_or_photo_path:
missing_fields.append("receipt_or_photo_path")
ready_to_operate_without_tools = True
if replacement_needed is True or truck_started is False:
status = "battery_replace_candidate"
elif not store_selected or not part_name:
status = "pending_parts_run"
elif install_completed is not True:
status = "pending_install"
elif physically_secure is not True or overnight_test_hours is None or truck_started is None or not receipt_or_photo_path:
status = "overnight_validation"
elif overnight_test_hours >= 24 and truck_started is True:
status = "verified"
else:
status = "overnight_validation"
return {
"candidate_stores": list(CANDIDATE_STORES),
"required_items": list(REQUIRED_ITEMS),
"selection_criteria": list(SELECTION_CRITERIA),
"install_target": "negative battery terminal",
"install_checklist": list(INSTALL_CHECKLIST),
"validation_checklist": list(VALIDATION_CHECKLIST),
"store_selected": store_selected,
"part_name": part_name,
"part_cost_usd": part_cost_usd,
"install_completed": install_completed,
"physically_secure": physically_secure,
"overnight_test_hours": overnight_test_hours,
"truck_started_after_disconnect": truck_started,
"receipt_or_photo_path": receipt_or_photo_path,
"ready_to_operate_without_tools": ready_to_operate_without_tools,
"missing_fields": missing_fields,
"battery_replacement_followup": BATTERY_REPLACEMENT_FOLLOWUP,
"status": status,
}
def render_markdown(packet: dict[str, Any]) -> str:
part_cost = packet["part_cost_usd"]
cost_line = f"${part_cost:.2f}" if isinstance(part_cost, (int, float)) else "pending purchase"
overnight = packet["overnight_test_hours"]
overnight_line = f"{overnight} hours" if overnight is not None else "pending"
started = packet["truck_started_after_disconnect"]
if started is True:
started_line = "yes"
elif started is False:
started_line = "no"
else:
started_line = "pending"
lines = [
"# LAB-003 — Truck Battery Disconnect Install Packet",
"",
"No battery disconnect switch has been purchased or installed yet.",
"This packet turns the issue into a field-ready purchase / install / validation checklist while preserving what still requires live work.",
"",
"## Candidate Store Run",
"",
]
lines.extend(f"- {store}" for store in packet["candidate_stores"])
lines.extend([
"",
"## Required Items",
"",
])
lines.extend(f"- {item}" for item in packet["required_items"])
lines.extend([
"",
"## Selection Criteria",
"",
])
lines.extend(f"- {item}" for item in packet["selection_criteria"])
lines.extend([
"",
"## Live Purchase State",
"",
f"- Store selected: {packet['store_selected'] or 'pending'}",
f"- Part selected: {packet['part_name'] or 'pending'}",
f"- Part cost: {cost_line}",
"",
"## Installation Target",
"",
f"- Install location: {packet['install_target']}",
f"- Ready to operate without tools: {'yes' if packet['ready_to_operate_without_tools'] else 'no'}",
"",
"## Install Checklist",
"",
])
lines.extend(f"- [ ] {item}" for item in packet["install_checklist"])
lines.extend([
"",
"## Validation Checklist",
"",
])
lines.extend(f"- [ ] {item}" for item in packet["validation_checklist"])
lines.extend([
"",
"## Overnight Verification Log",
"",
f"- Install completed: {packet['install_completed'] if packet['install_completed'] is not None else 'pending'}",
f"- Physically secure: {packet['physically_secure'] if packet['physically_secure'] is not None else 'pending'}",
f"- Overnight disconnect duration: {overnight_line}",
f"- Truck started after disconnect: {started_line}",
f"- Receipt / photo path: {packet['receipt_or_photo_path'] or 'pending'}",
"",
"## Battery Replacement Fallback",
"",
packet['battery_replacement_followup'],
"",
"## Missing Live Fields",
"",
])
if packet["missing_fields"]:
lines.extend(f"- {field}" for field in packet["missing_fields"])
else:
lines.append("- none")
lines.extend([
"",
"## Honest next step",
"",
"Buy the disconnect switch, install it on the negative battery terminal, leave the truck disconnected for 24+ hours, and only close the issue after receipt/photo evidence and the overnight start result are attached.",
"",
])
return "\n".join(lines)
def main() -> None:
parser = argparse.ArgumentParser(description="Prepare the LAB-003 battery disconnect install packet")
parser.add_argument("--store-selected", default="")
parser.add_argument("--part-name", default="")
parser.add_argument("--part-cost-usd", type=float, default=None)
parser.add_argument("--install-completed", action="store_true")
parser.add_argument("--physically-secure", action="store_true")
parser.add_argument("--overnight-test-hours", type=int, default=None)
parser.add_argument("--truck-started-after-disconnect", choices=["yes", "no"], default=None)
parser.add_argument("--receipt-or-photo-path", default="")
parser.add_argument("--replacement-battery-needed", action="store_true")
parser.add_argument("--output", default=None)
parser.add_argument("--json", action="store_true")
args = parser.parse_args()
packet = build_packet(
{
"store_selected": args.store_selected,
"part_name": args.part_name,
"part_cost_usd": args.part_cost_usd,
"install_completed": args.install_completed,
"physically_secure": args.physically_secure,
"overnight_test_hours": args.overnight_test_hours,
"truck_started_after_disconnect": args.truck_started_after_disconnect,
"receipt_or_photo_path": args.receipt_or_photo_path,
"replacement_battery_needed": args.replacement_battery_needed,
}
)
rendered = json.dumps(packet, indent=2) if args.json else render_markdown(packet)
if args.output:
output_path = Path(args.output).expanduser()
output_path.parent.mkdir(parents=True, exist_ok=True)
output_path.write_text(rendered, encoding="utf-8")
print(f"Battery disconnect packet written to {output_path}")
else:
print(rendered)
if __name__ == "__main__":
main()

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@@ -0,0 +1,67 @@
# GENOME.md — [org/repo]
Generated by `pipelines/codebase_genome.py` or used as a manual review scaffold when a human is curating the final artifact.
## Project Overview
[One paragraph: what the repo does, why it exists, and what outcome it creates.]
- Text files indexed: [count]
- Source and script files: [count]
- Test files: [count]
- Documentation files: [count]
## Architecture
```mermaid
graph TD
repo_root["repo"] --> component_a["component-a"]
repo_root --> component_b["component-b"]
component_a --> component_b
```
## Entry Points
- `[path/to/entrypoint]` — [why it matters] (`python3 path/to/entrypoint.py`)
- `[path/to/other-entrypoint]` — [why it matters] (`bash path/to/script.sh`)
## Data Flow
1. [How operators or callers enter the system.]
2. [Which modules or directories fan out from the entrypoint.]
3. [Where validation or test gaps create risk.]
4. [What artifact, state change, or runtime side effect is produced.]
## Key Abstractions
- `[module.py]` — classes `[ClassName]:line`; functions `[function_name()]:line`
- `[another_module.py]` — classes `[AnotherClass]:line`; functions `[run()]:line`
## API Surface
- CLI: `python3 [entrypoint] --help` — [what it exposes]
- Python: `[public_function]()` from `[module.py:line]`
- HTTP/WebSocket/other: `[surface]` — [contract summary]
## Test Coverage Report
- Source and script files inspected: [count]
- Test files inspected: [count]
- Coverage gaps:
- `[path/to/file]` — [missing coverage detail]
- `[path/to/other]` — [missing coverage detail]
## Security Audit Findings
- `[severity]` `[path:line]` — [risk category]: [detail]. Evidence: `[snippet]`
- `[severity]` `[path:line]` — [risk category]: [detail]. Evidence: `[snippet]`
## Dead Code Candidates
- `[path/to/file]` — [why it appears unreferenced]
- `[path/to/other]` — [why it appears unreferenced]
## Performance Bottleneck Analysis
- `[path/to/file]` — [why runtime or scale could degrade here]
- `[path/to/other]` — [filesystem scan / network / large module / hot path detail]

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@@ -0,0 +1,37 @@
from __future__ import annotations
from pathlib import Path
ROOT = Path(__file__).resolve().parents[1]
TEMPLATE_PATH = ROOT / "templates" / "GENOME-template.md"
DOC_PATH = ROOT / "docs" / "CODEBASE_GENOME_PIPELINE.md"
REQUIRED_HEADINGS = (
"# GENOME.md — [org/repo]",
"## Project Overview",
"## Architecture",
"## Entry Points",
"## Data Flow",
"## Key Abstractions",
"## API Surface",
"## Test Coverage Report",
"## Security Audit Findings",
"## Dead Code Candidates",
"## Performance Bottleneck Analysis",
)
def test_issue_666_template_exists_and_covers_required_sections() -> None:
assert TEMPLATE_PATH.exists(), "missing templates/GENOME-template.md"
text = TEMPLATE_PATH.read_text(encoding="utf-8")
for heading in REQUIRED_HEADINGS:
assert heading in text
def test_issue_666_docs_reference_template_and_single_repo_entrypoint() -> None:
text = DOC_PATH.read_text(encoding="utf-8")
assert "templates/GENOME-template.md" in text
assert "python3 pipelines/codebase_genome.py" in text
assert "python3 pipelines/codebase-genome.py" in text

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@@ -1,88 +0,0 @@
from pathlib import Path
import importlib.util
import unittest
ROOT = Path(__file__).resolve().parent.parent
SCRIPT_PATH = ROOT / "scripts" / "lab_003_battery_disconnect_packet.py"
DOC_PATH = ROOT / "docs" / "LAB_003_BATTERY_DISCONNECT_PACKET.md"
def load_module(path: Path, name: str):
assert path.exists(), f"missing {path.relative_to(ROOT)}"
spec = importlib.util.spec_from_file_location(name, path)
assert spec and spec.loader
module = importlib.util.module_from_spec(spec)
spec.loader.exec_module(module)
return module
class TestLab003BatteryDisconnectPacket(unittest.TestCase):
def test_packet_defaults_to_parts_run_and_tracks_issue_specific_requirements(self):
mod = load_module(SCRIPT_PATH, "lab_003_battery_disconnect_packet")
packet = mod.build_packet({})
self.assertEqual(packet["status"], "pending_parts_run")
self.assertEqual(packet["install_target"], "negative battery terminal")
self.assertIn("battery terminal disconnect switch", packet["required_items"])
self.assertIn("terminal shim/post riser if needed", packet["required_items"])
self.assertIn("AutoZone", packet["candidate_stores"][0])
self.assertIn("no special tools required to operate", packet["selection_criteria"])
self.assertIn("overnight_test_hours", packet["missing_fields"])
self.assertIn("receipt_or_photo_path", packet["missing_fields"])
def test_packet_marks_verified_after_successful_24h_validation_with_proof(self):
mod = load_module(SCRIPT_PATH, "lab_003_battery_disconnect_packet")
packet = mod.build_packet(
{
"store_selected": "AutoZone - Newport",
"part_name": "Knob-style battery disconnect switch",
"part_cost_usd": 24.99,
"install_completed": True,
"physically_secure": True,
"overnight_test_hours": 26,
"truck_started_after_disconnect": True,
"receipt_or_photo_path": "evidence/lab-003-installed-switch.jpg",
}
)
self.assertEqual(packet["status"], "verified")
self.assertEqual(packet["missing_fields"], [])
self.assertTrue(packet["ready_to_operate_without_tools"])
def test_packet_flags_battery_replace_candidate_when_overnight_test_fails(self):
mod = load_module(SCRIPT_PATH, "lab_003_battery_disconnect_packet")
packet = mod.build_packet(
{
"store_selected": "O'Reilly - Claremont",
"part_name": "Knob-style battery disconnect switch",
"install_completed": True,
"physically_secure": True,
"overnight_test_hours": 24,
"truck_started_after_disconnect": False,
}
)
self.assertEqual(packet["status"], "battery_replace_candidate")
self.assertIn("battery_replacement_followup", packet)
self.assertIn("replace battery", packet["battery_replacement_followup"].lower())
def test_repo_contains_grounded_lab_003_packet_doc(self):
self.assertTrue(DOC_PATH.exists(), "missing committed LAB-003 packet doc")
text = DOC_PATH.read_text(encoding="utf-8")
for snippet in (
"# LAB-003 — Truck Battery Disconnect Install Packet",
"No battery disconnect switch has been purchased or installed yet.",
"negative battery terminal",
"AutoZone",
"Advance",
"O'Reilly",
"terminal shim/post riser if needed",
"Truck starts reliably after sitting 24+ hours with switch disconnected",
"Receipt or photo of installed switch uploaded to this issue",
):
self.assertIn(snippet, text)
if __name__ == "__main__":
unittest.main()