Compare commits

..

1 Commits

Author SHA1 Message Date
Alexander Payne
6595a82afb MATH-001: Add shadow-maths triage rubric and no-crank guardrails
Some checks failed
Self-Healing Smoke / self-healing-smoke (pull_request) Failing after 25s
Smoke Test / smoke (pull_request) Failing after 25s
Agent PR Gate / gate (pull_request) Failing after 48s
Agent PR Gate / report (pull_request) Successful in 24s
2026-04-26 15:46:44 -04:00
5 changed files with 354 additions and 148 deletions

299
GENOME.md
View File

@@ -1,144 +1,209 @@
# GENOME.md — Timmy_Foundation/timmy-home
Generated by `pipelines/codebase_genome.py`.
# GENOME.md — the-nexus
## Project Overview
Timmy Foundation's home repository for development operations and configurations.
`the-nexus` is a hybrid repo that combines three layers in one codebase:
- Text files indexed: 3181
- Source and script files: 231
- Test files: 95
- Documentation files: 755
1. A browser-facing world shell rooted in `index.html`, `boot.js`, `bootstrap.mjs`, `app.js`, `style.css`, `portals.json`, `vision.json`, `manifest.json`, and `gofai_worker.js`
2. A Python realtime bridge centered on `server.py` plus harness code under `nexus/`
3. A memory / fleet / operator layer spanning `mempalace/`, `mcp_servers/`, `multi_user_bridge.py`, and supporting scripts
## Architecture
The repo is not a clean single-purpose frontend and not just a backend harness. It is a mixed world/runtime/ops repository where browser rendering, WebSocket telemetry, MCP-driven game harnesses, and fleet memory tooling coexist.
Grounded repo facts from this checkout:
- Browser shell files exist at repo root: `index.html`, `app.js`, `style.css`, `manifest.json`, `gofai_worker.js`
- Data/config files also live at repo root: `portals.json`, `vision.json`
- Realtime bridge exists in `server.py`
- Game harnesses exist in `nexus/morrowind_harness.py` and `nexus/bannerlord_harness.py`
- Memory/fleet sync exists in `mempalace/tunnel_sync.py`
- Desktop/game automation MCP servers exist in `mcp_servers/desktop_control_server.py` and `mcp_servers/steam_info_server.py`
- Validation exists in `tests/test_browser_smoke.py`, `tests/test_portals_json.py`, `tests/test_index_html_integrity.py`, and `tests/test_repo_truth.py`
The current architecture is best understood as a sovereign world shell plus operator/game harness backend, with accumulated documentation drift from multiple restoration and migration efforts.
## Architecture Diagram
```mermaid
graph TD
repo_root["repo"]
angband["angband"]
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
browser[Index HTML Shell\nindex.html -> boot.js -> bootstrap.mjs -> app.js]
assets[Root Assets\nstyle.css\nmanifest.json\ngofai_worker.js]
data[World Data\nportals.json\nvision.json]
ws[Realtime Bridge\nserver.py\nWebSocket broadcast hub]
gofai[In-browser GOFAI\nSymbolicEngine\nNeuroSymbolicBridge\nsetupGOFAI/updateGOFAI]
harnesses[Python Harnesses\nnexus/morrowind_harness.py\nnexus/bannerlord_harness.py]
mcp[MCP Adapters\nmcp_servers/desktop_control_server.py\nmcp_servers/steam_info_server.py]
memory[Memory + Fleet\nmempalace/tunnel_sync.py\nmempalace.js]
bridge[Operator / MUD Bridge\nmulti_user_bridge.py\ncommands/timmy_commands.py]
tests[Verification\ntests/test_browser_smoke.py\ntests/test_portals_json.py\ntests/test_repo_truth.py]
docs[Contracts + Drift Docs\nBROWSER_CONTRACT.md\nREADME.md\nCLAUDE.md\nINVESTIGATION_ISSUE_1145.md]
browser --> assets
browser --> data
browser --> gofai
browser --> ws
harnesses --> mcp
harnesses --> ws
bridge --> ws
memory --> ws
tests --> browser
tests --> data
tests --> docs
docs --> browser
```
## Entry Points
## Entry Points and Data Flow
- `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/audit_trail.py` — operational script (`python3 scripts/audit_trail.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`)
### Primary entry points
## Data Flow
- `index.html` — root browser entry point
- `boot.js` — startup selector; `tests/boot.test.js` shows it chooses file-mode vs HTTP/module-mode and injects `bootstrap.mjs` when served over HTTP
- `bootstrap.mjs` — module bootstrap for the browser shell
- `app.js` — main browser runtime; owns world state, GOFAI wiring, metrics polling, and portal/UI logic
- `server.py` — WebSocket broadcast bridge on `ws://0.0.0.0:8765`
- `nexus/morrowind_harness.py` — GamePortal/MCP harness for OpenMW Morrowind
- `nexus/bannerlord_harness.py` — GamePortal/MCP harness for Bannerlord
- `mempalace/tunnel_sync.py` — pulls remote fleet closets into the local palace over HTTP
- `multi_user_bridge.py` — HTTP bridge for multi-user chat/session integration
- `mcp_servers/desktop_control_server.py` — stdio MCP server exposing screenshots/mouse/keyboard control
1. Operators enter through `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.
### Data flow
1. Browser startup begins at `index.html`
2. `boot.js` decides whether the page is being served correctly; in HTTP mode it injects `bootstrap.mjs`
3. `bootstrap.mjs` hands off to `app.js`
4. `app.js` loads world configuration from `portals.json` and `vision.json`
5. `app.js` constructs the Three.js scene and in-browser reasoning components, including `SymbolicEngine`, `NeuroSymbolicBridge`, `setupGOFAI()`, and `updateGOFAI()`
6. Browser state and external runtimes connect through `server.py`, which broadcasts messages between connected clients
7. Python harnesses (`nexus/morrowind_harness.py`, `nexus/bannerlord_harness.py`) spawn MCP subprocesses for desktop control / Steam metadata, capture state, execute actions, and feed telemetry into the Nexus bridge
8. Memory/fleet tools like `mempalace/tunnel_sync.py` import remote palace data into local closets, extending what the operator/runtime layers can inspect
9. Tests validate both the static browser contract and the higher-level repo-truth/memory contracts
### Important repo-specific runtime facts
- `portals.json` is a JSON array of portal/world/operator entries; examples in this checkout include `morrowind`, `bannerlord`, `workshop`, `archive`, `chapel`, and `courtyard`
- `server.py` is a plain broadcast hub: clients send messages, the server forwards them to other connected clients
- `nexus/morrowind_harness.py` and `nexus/bannerlord_harness.py` both implement a GamePortal pattern with MCP subprocess clients over stdio and WebSocket telemetry uplink
- `mempalace/tunnel_sync.py` is not speculative; it is a real client that discovers remote wings, searches remote rooms, and writes `.closet.json` payloads locally
## Key Abstractions
- `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
### Browser runtime
- `app.js`
- Defines in-browser reasoning/state machinery, including `class SymbolicEngine`, `class NeuroSymbolicBridge`, `setupGOFAI()`, and `updateGOFAI()`
- Couples rendering, local symbolic reasoning, metrics polling, and portal/UI logic in one very large root module
- `BROWSER_CONTRACT.md`
- Acts like an executable architecture contract for the browser surface
- Declares required files, DOM IDs, Three.js expectations, provenance rules, and WebSocket expectations
### Realtime bridge
- `server.py`
- Single hub abstraction: a WebSocket broadcast server maintaining a `clients` set and forwarding messages from one client to the others
- This is the seam between browser shell, harnesses, and external telemetry producers
### GamePortal harness layer
- `nexus/morrowind_harness.py`
- `nexus/bannerlord_harness.py`
- Both define MCP client wrappers, `GameState` / `ActionResult`-style data classes, and an Observe-Decide-Act telemetry loop
- The harnesses are symmetric enough to be understood as reusable portal adapters with game-specific context injected on top
### Memory / fleet layer
- `mempalace/tunnel_sync.py`
- Encodes the fleet-memory sync client contract: discover wings, pull broad room queries, write closet files, support dry-run
- `mempalace.js`
- Minimal browser/Electron bridge to MemPalace commands via `window.electronAPI.execPython(...)`
- Important because it shows a second memory integration surface distinct from the Python fleet sync path
### Operator / interaction bridge
- `multi_user_bridge.py`
- `commands/timmy_commands.py`
- These bridge user-facing conversations or MUD/Evennia interactions back into Timmy/Nexus services
## API Surface
- CLI: `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: `python3 scripts/audit_trail.py` — operational script (`scripts/audit_trail.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`)
- 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`
### Browser / static surface
## Test Coverage Report
- `index.html` served over HTTP
- `boot.js` exports `bootPage()`; verified by `node --test tests/boot.test.js`
- Data APIs are file-based inside the repo: `portals.json`, `vision.json`, `manifest.json`
- Source and script files inspected: 231
- Test files inspected: 95
- 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
- `scripts/sovereignty_audit.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
### Network/runtime surface
## Security Audit Findings
- `python3 server.py`
- Starts the WebSocket bridge on port `8765`
- `python3 l402_server.py`
- Local HTTP microservice for cost-estimate style responses
- `python3 multi_user_bridge.py`
- Multi-user HTTP/chat bridge
- [medium] `briefings/briefing_20260325.json:37` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `"gitea_error": "Gitea 404: {\"errors\":null,\"message\":\"not found\",\"url\":\"http://143.198.27.163:3000/api/swagger\"}\n [http://143.198.27.163:3000/api/v1/repos/Timmy_Foundation/sovereign-orchestration/issues?state=open&type=issues&sort=created&direction=desc&limit=1&page=1]",`
- [medium] `briefings/briefing_20260328.json:11` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `"provider_base_url": "http://localhost:8081/v1",`
- [medium] `briefings/briefing_20260329.json:11` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `"provider_base_url": "http://localhost:8081/v1",`
- [medium] `config.yaml:37` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `summary_base_url: http://localhost:11434/v1`
- [medium] `config.yaml:47` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
- [medium] `config.yaml:52` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
- [medium] `config.yaml:57` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
- [medium] `config.yaml:62` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
- [medium] `config.yaml:67` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
- [medium] `config.yaml:77` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
- [medium] `config.yaml:82` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: 'http://localhost:11434/v1'`
- [medium] `config.yaml:174` — hardcoded http endpoint: plaintext or fixed HTTP endpoints can drift or leak across environments. Evidence: `base_url: http://localhost:11434/v1`
### Harness / operator CLI surfaces
## Dead Code Candidates
- `python3 nexus/morrowind_harness.py`
- `python3 nexus/bannerlord_harness.py`
- `python3 mempalace/tunnel_sync.py --peer <url> [--dry-run] [--n N]`
- `python3 mcp_servers/desktop_control_server.py`
- `python3 mcp_servers/steam_info_server.py`
- `wizards/allegro/home/skills/red-teaming/godmode/scripts/auto_jailbreak.py` — not imported by indexed Python modules and not referenced by tests
- `timmy-local/cache/agent_cache.py` — not imported by indexed Python modules and not referenced by tests
- `wizards/allegro/home/skills/red-teaming/godmode/scripts/parseltongue.py` — not imported by indexed Python modules and not referenced by tests
- `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
- `scripts/sovereignty_audit.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
### Validation surface
## Performance Bottleneck Analysis
- `python3 -m pytest tests/test_portals_json.py tests/test_index_html_integrity.py tests/test_repo_truth.py -q`
- `node --test tests/boot.test.js`
- `python3 -m py_compile server.py nexus/morrowind_harness.py nexus/bannerlord_harness.py mempalace/tunnel_sync.py mcp_servers/desktop_control_server.py`
- `tests/test_browser_smoke.py` defines the higher-cost Playwright smoke contract for the world shell
- `angband/mcp_server.py` — large module (353 lines) likely hides multiple responsibilities
- `evennia/timmy_world/game.py` — large module (1541 lines) likely hides multiple responsibilities
- `evennia/timmy_world/world/game.py` — large module (1345 lines) likely hides multiple responsibilities
- `morrowind/mcp_server.py` — large module (451 lines) likely hides multiple responsibilities
- `morrowind/pilot.py` — large module (459 lines) likely hides multiple responsibilities
- `pipelines/codebase_genome.py` — large module (557 lines) likely hides multiple responsibilities
- `scripts/fleet_progression.py` — large module (361 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
## 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.

View File

@@ -1,14 +0,0 @@
---
- name: Codebase Genome Nightly
schedule: '30 2 * * *' # Daily at 02:30 local time
tasks:
- name: Ensure output and log directories exist
shell: "mkdir -p ~/.timmy/codebase-genomes ~/.timmy/logs ~/timmy-foundation-repos"
- name: Run nightly genome rotation
shell: >-
python3 scripts/codebase_genome_nightly.py
--org Timmy_Foundation
--workspace-root ~/timmy-foundation-repos
--output-root ~/.timmy/codebase-genomes
--state-path ~/.timmy/codebase_genome_state.json
>> ~/.timmy/logs/codebase_genome_nightly.log 2>&1

View File

@@ -10,8 +10,6 @@ This pipeline gives Timmy a repeatable way to generate a deterministic `GENOME.m
- `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
- `scripts/codebase_test_generator.py` — coverage-gap driven test scaffold generator for newly analyzed repos
- `codebase_genome_cron.yml` — checked-in nightly cron spec for the rotating genome pass
- `GENOME.md` — generated analysis for `timmy-home` itself
## Genome output

View File

@@ -0,0 +1,172 @@
# Shadow Maths Triage Rubric (MATH-001)
**Status**: Draft v1.0 **Date**: 2026-04-26 **Author**: Timmy
**Milestone**: Contribute to Mathematics — Shadow Maths Search
**Parent**: #876 — [MATH][EPIC] Shadow Maths
---
## Purpose
Timmy's mathematics contribution program targets *bounded, verifiable, useful* problems hiding in plain sight. This rubric operationalizes "shadow maths" — distinguishing legitimate first-crack contributions from crank Grand Unified Theories.
The rubric serves two roles:
1. **Triage gate** — filter submissions and scout list candidates worth pursuing.
2. **No-crank guardrail** — explicitly reject unfalsifiable, unscoped, or unsourced claims.
---
## Candidate Categories (Positive Types)
| Category | Description | Verification Path | Useful Because |
|----------|-------------|-------------------|---------------|
| **Small lemma** | Missing but straightforward piece in an active area (e.g., "Proposition 3.2 in Smith 2021 needs this case analysis") | Check paper + 12 related references; prove or give counterexample | Clarifies existing theory, removes ambiguity |
| **Counterexample search** | Find explicit counterexample to a claimed-but-unproven statement (often from MO/SE) | Compute/construct + cite the original claim | Prevents propagation of errors |
| **Computational classification** | Exhaustive enumeration/classification of a small infinite family (e.g., "all groups of order < 200 with property X") | Code is verifiable; results match known data | Creates reference data, spotlights patterns |
| **Formalization gap** | Statement already believed true but missing from Lean/mathlib/Isabelle | Formal proof artifact; merges to mainline library | Makes mathematics machine-checkable |
| **OEIS sequence note** | New sequence entry or correction to an existing entry with proof/algorithm | OEIS A-number + formula/generation code | Public archival, enables further work |
| **Exposition repair** | Fix an unclear proof, fill a gap, simplify an argument in an existing paper | Side-by-side diff + justification for each change | Improves pedagogy, reduces confusion |
| **MathOverflow-quality answer** | Answer to a specific, bounded, research-level question on MO/SE that has no accepted answer | Cite question + self-contained proof/computation | Serves the community directly |
---
## Rejection Criteria (No-Crank Guardrails)
> Any candidate that triggers one or more of these is **rejected outright** — no scoring needed.
| Rule | What to look for | Why it's crank |
|------|------------------|----------------|
| **Unsourced grand theory** | Claim introduces new "framework"/"paradigm" without citing specific bounded problem it solves | Mathematics advances by solving problems, not proposing frameworks |
| **Impossible scope** | "I will prove/disprove the Riemann Hypothesis", "classify all finite simple groups" | Demonstrably beyond single-attack capability |
| **No verification path** | No way for a third party to check the work (no code, no formalization, no explicit examples) | Cannot be wrong if it cannot be checked |
| **Novelty claim without literature search** | States "I believe this is new" without checking MathSciNet/arXiv/Google Scholar | Almost certainly reinvention or known result |
| **Vague mathematical objects** | Uses undefined or ambiguous terminology ("energy", "resonance", "harmonic" in non-standard ways) | Not mathematics |
| **Secrecy or paywall** | Key definition or proof behind a paywall or withheld | Not sovereign; not verifiable |
| **Symbolic overloading without definition** | Repurposes standard notation in non-standard ways without explicit redefinition | Creates confusion, not clarity |
| **Invariance violations** | Claims "up to isomorphism" or "modulo equivalence" without defining the equivalence relation | Not mathematically precise |
| **Cherry-picked examples as proof** | Proves only easy special cases and claims the general case follows | Example ≠ theorem |
| **Circular citation chains** | Relies on unpublished/preprint work that itself cites the candidate as motivation | Not a foundation |
| **No clear problem statement** | Cannot write a one-sentence problem statement in standard mathematical English | Not a problem; just musings |
| **Claims of "obvious" or "clear" for non-trivial steps** | Uses "obviously" or "it is clear that" where a proof requires >2 lines | Evasion |
| **References only popular science / non-technical sources** | Cites Penrose, Hawking, Tegmark for technical claims | Wrong tier of source |
| **All notation defined in non-standard way** | Redefines basic operators (+, ×, ≤) without explicit warning | Not mathematics |
| **No engagement with existing literature** | Zero citations to relevant peer-reviewed work or established preprints | scholarship was not done |
| **Claims of "disproof" of widely-accepted theorems** | Without finding a peer-reviewed error in the existing proof | Almost certainly wrong |
---
## Evidence Tiers
| Tier | Artifact | What it Proves |
|------|----------|----------------|
| **T3 — Literature** | MathSciNet / Zentralblatt / Google Scholar citations showing the problem is real and open | Problem exists in the literature |
| **T2 — Executable** | Python/Sage/Lean code that others can run to verify computation/formalization | Result is reproducible |
| **T1 — Human-reviewed** | MO answer with upvotes, referee report, or explicit external review | Independent verification |
| **T0 — Self-contained** | Clear statement + proof/computation in a single document, all definitions explicit | Standalone correctness |
A valid candidate must have at least **one** T3 citation (shows the problem is real) AND a verification artifact (T0 minimum; T2 ideal).
---
## Scoring Rubric
Score each candidate on **4 dimensions**, each 03. Maximum 12 points.
| Dimension | 3 (excellent) | 2 (good) | 1 (minimal) | 0 (absent) |
|-----------|---------------|----------|-------------|------------|
| **Boundedness** | Scope is explicitly finite/small (single lemma, finite classification < N, one SE question) | Scope is implied bounded but not quantified | Scope is large/vague but attackable | Unbounded or impossible scope |
| **Verifiability** | T2 artifact (code/formalization) + T3 citation | T0 proof + T3 citation | Proof/computation only, no citations | No way to check independently |
| **Usefulness** | Solves problem others actively need (cites known difficulty, fills formalization gap) | Solves a clean exercise or interesting special case | Interesting but no clear audience | Pointless or self-referential |
| **Discipline** | No crank flags; explicit rejection criteria cleanly passed | Minor crank flags (vague wording) but overall sound | Some crank flags but bounded scope rescues it | Triggers multiple rejection rules |
**Thresholds**:
- **812**: Legitimate shadow maths candidate — queue for work
- **47**: Needs refinement — reject unless strong disciplinary context
- **03**: Reject as crank / out-of-scope
---
## Three Worked Examples
### Example 1: Small Lemma — Bounded
**Candidate**: "Proposition 3.2 in 'Coarse Geometry and Coarse Embeddings' (Lang-Schlichenmaier 2005) states that every finite CW-complex has Markov property. The proof gives 'it follows by induction on skeleta' without handling the attaching map case. Fill the gap."
**Triage**:
- **Category**: Small lemma (exposition repair + proof gap fill)
- **Boundedness**: 3 — single proposition in a specific paper, 23 pages max
- **Verifiability**: 3 — paper is cited (T3), self-contained proof in 20 lines (T0), can formalize in Lean (T2 possible)
- **Usefulness**: 3 — readers of this paper hit this gap; Lean formalization needed for mathlib
- **Discipline**: 3 — no crank flags; scoped, sourced, technical
- **Total**: **12/12** → YES
**Action**: File ticket "MATH-LEMMA-001"; assign to formalization lane + human review.
---
### Example 2: Grand Unified Theory — CRANK
**Candidate**: "I have discovered the Energy-Conscious Riemann Hypothesis framework. The zeros of ζ(s) correspond to harmonic resonance frequencies in prime-number energy manifolds. Uses my new Operator-Weight theory."
**Triage**:
- **Category**: N/A
- **Rejection triggers**:
- ✗ Unsourced grand theory (introduces "Energy-Conscious", "Operator-Weight" with no definition in standard math)
- ✗ No verification path (no computation, no reference to known data)
- ✗ No literature engagement (zero citations)
- ✗ Vague mathematical objects ("energy", "resonance", "harmonic")
- ✗ Claims new framework
- **Score**: 0 — **REJECT**
**Action**: Close with reason "crank: unsourced grand theory + no verification path".
---
### Example 3: Computational Classification — Bounded
**Candidate**: "Compute all 3-headed Turing machines with 3 states that halt within 100 steps on the blank tape. There are 9 such machines. This fills an OEIS gap: A327000 only lists up to 2-state 2-symbol."
**Triage**:
- **Category**: Computational classification + OEIS sequence
- **Boundedness**: 3 — finite exhaustive enumeration (3^6 = 729 machines, filter to 9)
- **Verifiability**: 2 — code is executable (T2), but no T3 citation of why this sequence matters yet
- **Usefulness**: 2 — plugs a gap in the Busy Beaver frontier; OEIS entry gets concrete data
- **Discipline**: 3 — explicit scope, reproducible, submits to OEIS (external review path)
- **Total**: **10/12** → YES (minor fix: add motivation/references)
**Action**: Accept; write exhaustive script; submit OEIS draft with code + results; file MATH-COMP-001.
---
## Operational Use
### Triage Workflow
1. **Read candidate** (issue, email, self-generated idea).
2. **Check rejection criteria first** — if any trigger → **REJECT** immediately, cite rule.
3. If passes rejection gate, **score 4 dimensions**.
4. **Score ≥8** → mark as `shadow-maths-candidate`, route to appropriate lane:
- Lemma/exposition → `formalization-lane`
- Computation → `compute-lane`
- MO/SE answer → `answer-lane`
- OEIS → `oeis-lane`
5. **Score 47** → requires refinement; ask for:
- Explicit scope bound
- T3 citation
- Verification artifact
6. **Score ≤3** → reject with specific rule(s) triggered.
### Guardrail Enforcement
The following prompts/agents **must refuse** to work on any candidate that:
- Triggers any rejection criterion (before any code/proof work)
- Has no T3 citation (real problem statement from literature)
- Has no bounded scope (cannot write ≤1-sentence problem statement)
Enforcement is a **pre-flight check** in the task intake pipeline.
---
## Revision History
- v1.0 — 2026-04-26 — initial rubric + 3 scored examples

View File

@@ -8,7 +8,6 @@ ROOT = Path(__file__).resolve().parents[1]
PIPELINE_PATH = ROOT / "pipelines" / "codebase_genome.py"
NIGHTLY_PATH = ROOT / "scripts" / "codebase_genome_nightly.py"
GENOME_PATH = ROOT / "GENOME.md"
CRON_PATH = ROOT / "codebase_genome_cron.yml"
def _load_module(path: Path, name: str):
@@ -114,17 +113,3 @@ def test_repo_contains_generated_timmy_home_genome() -> None:
"## Performance Bottleneck Analysis",
):
assert snippet in text
def test_repo_contains_nightly_cron_spec_for_genome_rotation() -> None:
assert CRON_PATH.exists(), "missing codebase_genome_cron.yml"
text = CRON_PATH.read_text(encoding="utf-8")
for snippet in (
"Codebase Genome Nightly",
"scripts/codebase_genome_nightly.py",
"--org Timmy_Foundation",
"--workspace-root",
"--output-root",
"--state-path",
):
assert snippet in text