fix(genome): generate GENOME.md for timmy-home itself

The codebase-genome pipeline was in place but timmy-home's own
GENOME.md was either missing or contained content for another repo.
Run the pipeline to produce the correct analysis in place.

Closes #665

GENOME.md

@@ -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: 3181
+- Source and script files: 231
+- Test files: 95
+- Documentation files: 755
 
-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/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`)
 
-- `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: `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`
 
-- `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: 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
 
-- `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
+- `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
 
-- `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/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

scripts/cross_agent_quality_audit.py

@@ -1,313 +0,0 @@
-#!/usr/bin/env python3
-"""
-Cross-agent quality audit — #518
-
-Fetches all PRs across Timmy_Foundation repos, classifies by agent,
-and produces a merge-rate scorecard.
-
-Usage:
-    python scripts/cross_agent_quality_audit.py
-    python scripts/cross_agent_quality_audit.py --scorecard timmy-config/agent-quality-scorecard.md
-"""
-
-import argparse
-import json
-import os
-import re
-import sys
-from collections import defaultdict
-from datetime import datetime, timezone
-from pathlib import Path
-from typing import Any, Dict, List, Optional
-
-import requests
-
-GITEA_BASE = "https://forge.alexanderwhitestone.com/api/v1"
-ORG = "Timmy_Foundation"
-TOKEN = os.environ.get("GITEA_TOKEN") or (
-    Path.home() / ".config" / "gitea" / "token"
-).read_text().strip()
-
-HEADERS = {"Authorization": f"token {TOKEN}"}
-
-# Repos to audit (active code repos)
-DEFAULT_REPOS = [
-    "timmy-home",
-    "hermes-agent",
-    "the-nexus",
-    "the-door",
-    "fleet-ops",
-    "burn-fleet",
-    "the-playground",
-    "compounding-intelligence",
-    "the-beacon",
-    "second-son-of-timmy",
-    "timmy-academy",
-    "timmy-config",
-]
-
-
-class AgentClassifier:
-    """Classify PRs by agent identity."""
-
-    # PR title prefixes that explicitly name an agent
-    AGENT_TITLE_RE = re.compile(
-        r"^\[(?P<agent>Claude|Ezra|Allegro|Bezalel|Timmy|Gemini|Kimi|Manus|Codex)\]",
-        re.IGNORECASE,
-    )
-
-    # Branch patterns that embed agent names
-    AGENT_BRANCH_RE = re.compile(
-        r"(?P<agent>claude|ezra|allegro|bezalel|timmy|gemini|kimi|manus|codex)",
-        re.IGNORECASE,
-    )
-
-    @classmethod
-    def classify(cls, pr: Dict[str, Any]) -> str:
-        title = pr.get("title", "")
-        branch = pr.get("head", {}).get("ref", "")
-        user = pr.get("user", {}).get("login", "")
-
-        # 1. Explicit title tag like [Claude] or [Ezra]
-        m = cls.AGENT_TITLE_RE.match(title)
-        if m:
-            return m.group("agent").lower()
-
-        # 2. Branch contains agent name (e.g. claude/issue-123)
-        m = cls.AGENT_BRANCH_RE.search(branch)
-        if m:
-            return m.group("agent").lower()
-
-        # 3. Git user mapping
-        if user.lower() == "claude":
-            return "claude"
-        if user.lower() == "rockachopa":
-            # Rockachopa is the human / orchestrator — map to "burn-loop"
-            return "burn-loop"
-
-        return "unknown"
-
-
-def fetch_prs(repo: str, state: str = "all", per_page: int = 50) -> List[Dict[str, Any]]:
-    """Paginate through all PRs for a repo."""
-    prs: List[Dict[str, Any]] = []
-    page = 1
-    while True:
-        url = f"{GITEA_BASE}/repos/{ORG}/{repo}/pulls?state={state}&limit={per_page}&page={page}"
-        resp = requests.get(url, headers=HEADERS, timeout=30)
-        resp.raise_for_status()
-        batch = resp.json()
-        if not batch:
-            break
-        prs.extend(batch)
-        if len(batch) < per_page:
-            break
-        page += 1
-    return prs
-
-
-def parse_datetime(dt_str: Optional[str]) -> Optional[datetime]:
-    if not dt_str:
-        return None
-    try:
-        return datetime.fromisoformat(dt_str.replace("Z", "+00:00"))
-    except ValueError:
-        return None
-
-
-def hours_between(start: Optional[str], end: Optional[str]) -> Optional[float]:
-    s = parse_datetime(start)
-    e = parse_datetime(end)
-    if s and e:
-        return (e - s).total_seconds() / 3600
-    return None
-
-
-def audit_repos(repos: List[str]) -> Dict[str, Any]:
-    """Run the audit and return aggregated stats."""
-    agent_stats: Dict[str, Dict[str, Any]] = defaultdict(
-        lambda: {
-            "total": 0,
-            "merged": 0,
-            "closed_unmerged": 0,
-            "open": 0,
-            "hours_to_merge": [],
-            "hours_to_close": [],
-            "repos": set(),
-            "prs": [],
-        }
-    )
-
-    repo_stats: Dict[str, Dict[str, Any]] = {}
-
-    for repo in repos:
-        print(f"Fetching PRs for {repo} ...", file=sys.stderr)
-        try:
-            prs = fetch_prs(repo)
-        except requests.HTTPError as exc:
-            print(f"  SKIP {repo}: {exc}", file=sys.stderr)
-            continue
-
-        repo_merged = 0
-        repo_total = len(prs)
-        for pr in prs:
-            agent = AgentClassifier.classify(pr)
-            s = agent_stats[agent]
-            s["total"] += 1
-            s["repos"].add(repo)
-            s["prs"].append(
-                {
-                    "repo": repo,
-                    "number": pr["number"],
-                    "title": pr["title"],
-                    "state": pr["state"],
-                    "merged": pr.get("merged", False),
-                    "created_at": pr.get("created_at"),
-                    "merged_at": pr.get("merged_at"),
-                    "closed_at": pr.get("closed_at"),
-                }
-            )
-
-            if pr.get("merged"):
-                s["merged"] += 1
-                repo_merged += 1
-                h = hours_between(pr.get("created_at"), pr.get("merged_at"))
-                if h is not None:
-                    s["hours_to_merge"].append(h)
-            elif pr["state"] == "closed":
-                s["closed_unmerged"] += 1
-                h = hours_between(pr.get("created_at"), pr.get("closed_at"))
-                if h is not None:
-                    s["hours_to_close"].append(h)
-            else:
-                s["open"] += 1
-
-        repo_stats[repo] = {
-            "total": repo_total,
-            "merged": repo_merged,
-            "merge_rate": round(repo_merged / repo_total, 2) if repo_total else 0,
-        }
-
-    # Compute derived metrics
-    summary = {}
-    for agent, s in sorted(agent_stats.items(), key=lambda x: -x[1]["total"]):
-        total = s["total"]
-        merged = s["merged"]
-        closed = s["closed_unmerged"]
-        resolved = merged + closed
-        merge_rate = round(merged / resolved, 3) if resolved else 0
-        avg_merge_hours = (
-            round(sum(s["hours_to_merge"]) / len(s["hours_to_merge"]), 1)
-            if s["hours_to_merge"]
-            else None
-        )
-        avg_close_hours = (
-            round(sum(s["hours_to_close"]) / len(s["hours_to_close"]), 1)
-            if s["hours_to_close"]
-            else None
-        )
-        summary[agent] = {
-            "total_prs": total,
-            "merged": merged,
-            "closed_unmerged": closed,
-            "open": s["open"],
-            "merge_rate": merge_rate,
-            "rejection_rate": round(closed / resolved, 3) if resolved else 0,
-            "avg_hours_to_merge": avg_merge_hours,
-            "avg_hours_to_close": avg_close_hours,
-            "repos": sorted(s["repos"]),
-        }
-
-    return {
-        "audited_at": datetime.now(timezone.utc).isoformat(),
-        "repos_audited": repos,
-        "repo_stats": repo_stats,
-        "agent_summary": summary,
-        "raw_prs": {a: s["prs"] for a, s in agent_stats.items()},
-    }
-
-
-def render_scorecard(data: Dict[str, Any]) -> str:
-    """Render a markdown scorecard."""
-    lines = [
-        "# Cross-Agent Quality Scorecard",
-        "",
-        f"**Audited at:** {data['audited_at']}",
-        f"**Repos audited:** {', '.join(data['repos_audited'])}",
-        "",
-        "## Per-Agent Summary",
-        "",
-        "| Agent | Total PRs | Merged | Closed (unmerged) | Open | Merge Rate | Rejection Rate | Avg Hours to Merge | Avg Hours to Close |",
-        "|---|---|---:|---:|---:|---:|---:|---:|---:|",
-    ]
-
-    for agent, s in data["agent_summary"].items():
-        merge_hours = f"{s['avg_hours_to_merge']:.1f}" if s["avg_hours_to_merge"] is not None else "—"
-        close_hours = f"{s['avg_hours_to_close']:.1f}" if s["avg_hours_to_close"] is not None else "—"
-        lines.append(
-            f"| {agent} | {s['total_prs']} | {s['merged']} | {s['closed_unmerged']} | "
-            f"{s['open']} | {s['merge_rate']:.1%} | {s['rejection_rate']:.1%} | "
-            f"{merge_hours} | {close_hours} |"
-        )
-
-    lines.extend([
-        "",
-        "## Per-Repo Merge Rate",
-        "",
-        "| Repo | Total PRs | Merged | Merge Rate |",
-        "|---|---|---:|---:|",
-    ])
-
-    for repo, s in sorted(data["repo_stats"].items(), key=lambda x: -x[1]["total"]):
-        lines.append(
-            f"| {repo} | {s['total']} | {s['merged']} | {s['merge_rate']:.1%} |"
-        )
-
-    lines.extend([
-        "",
-        "## Methodology",
-        "",
-        "- **Agent classification** uses three signals in priority order:",
-        "  1. Explicit title tag (e.g. `[Claude]`, `[Ezra]`)",
-        "  2. Branch name containing agent name (e.g. `claude/issue-123`)",
-        "  3. Git user (`claude` → claude, `Rockachopa` → burn-loop)",
-        "- **Merge rate** = merged / (merged + closed_unmerged). Open PRs are excluded.",
-        "- **Rejection rate** = closed_unmerged / (merged + closed_unmerged).",
-        "- **Time metrics** are computed from created_at to merged_at / closed_at.",
-        "",
-        "## Raw Data",
-        "",
-        "```json",
-        json.dumps(data["agent_summary"], indent=2),
-        "```",
-        "",
-    ])
-
-    return "\n".join(lines) + "\n"
-
-
-def main() -> int:
-    parser = argparse.ArgumentParser(description="Cross-agent quality audit")
-    parser.add_argument("--repos", nargs="+", default=DEFAULT_REPOS, help="Repos to audit")
-    parser.add_argument("--scorecard", default="timmy-config/agent-quality-scorecard.md", help="Output path")
-    parser.add_argument("--json", default=None, help="Also write raw JSON to path")
-    args = parser.parse_args()
-
-    data = audit_repos(args.repos)
-
-    scorecard_path = Path(args.scorecard)
-    scorecard_path.parent.mkdir(parents=True, exist_ok=True)
-    scorecard_path.write_text(render_scorecard(data))
-    print(f"Scorecard written to {scorecard_path}", file=sys.stderr)
-
-    if args.json:
-        json_path = Path(args.json)
-        json_path.parent.mkdir(parents=True, exist_ok=True)
-        json_path.write_text(json.dumps(data, indent=2, default=str))
-        print(f"Raw JSON written to {json_path}", file=sys.stderr)
-
-    return 0
-
-
-if __name__ == "__main__":
-    raise SystemExit(main())

tests/test_cross_agent_quality_audit.py

@@ -1,45 +0,0 @@
-"""Tests for cross_agent_quality_audit.py — #518."""
-
-import pytest
-import sys
-from pathlib import Path
-
-sys.path.insert(0, str(Path(__file__).parent.parent / "scripts"))
-
-from cross_agent_quality_audit import AgentClassifier, hours_between
-
-
-class TestAgentClassifier:
-    def test_title_tag_claude(self):
-        pr = {"title": "[Claude] fix auth middleware", "head": {"ref": "fix/123"}, "user": {"login": "rockachopa"}}
-        assert AgentClassifier.classify(pr) == "claude"
-
-    def test_title_tag_ezra(self):
-        pr = {"title": "[Ezra] tmux fleet launcher", "head": {"ref": "burn/10"}, "user": {"login": "rockachopa"}}
-        assert AgentClassifier.classify(pr) == "ezra"
-
-    def test_branch_name_claude(self):
-        pr = {"title": "fix auth", "head": {"ref": "claude/issue-1695"}, "user": {"login": "rockachopa"}}
-        assert AgentClassifier.classify(pr) == "claude"
-
-    def test_user_mapping(self):
-        pr = {"title": "some fix", "head": {"ref": "fix/1"}, "user": {"login": "claude"}}
-        assert AgentClassifier.classify(pr) == "claude"
-
-    def test_rockachopa_maps_to_burn_loop(self):
-        pr = {"title": "some fix", "head": {"ref": "fix/1"}, "user": {"login": "Rockachopa"}}
-        assert AgentClassifier.classify(pr) == "burn-loop"
-
-    def test_unknown_fallback(self):
-        pr = {"title": "some fix", "head": {"ref": "fix/1"}, "user": {"login": "random"}}
-        assert AgentClassifier.classify(pr) == "unknown"
-
-
-class TestHoursBetween:
-    def test_same_day(self):
-        h = hours_between("2026-04-22T10:00:00Z", "2026-04-22T12:00:00Z")
-        assert h == 2.0
-
-    def test_none_returns_none(self):
-        assert hours_between(None, "2026-04-22T12:00:00Z") is None
-        assert hours_between("2026-04-22T10:00:00Z", None) is None

timmy-config/agent-quality-scorecard.md

@@ -1,244 +0,0 @@
-# Cross-Agent Quality Scorecard
-
-**Audited at:** 2026-04-22T06:17:43.574309+00:00
-**Repos audited:** timmy-home, hermes-agent, the-nexus, the-door, fleet-ops, burn-fleet, the-playground, compounding-intelligence, the-beacon, second-son-of-timmy, timmy-academy, timmy-config
-
-## Per-Agent Summary
-
-| Agent | Total PRs | Merged | Closed (unmerged) | Open | Merge Rate | Rejection Rate | Avg Hours to Merge | Avg Hours to Close |
-|---|---|---:|---:|---:|---:|---:|---:|---:|
-| burn-loop | 1733 | 346 | 1239 | 148 | 21.8% | 78.2% | 18.9 | 20.6 |
-| unknown | 843 | 598 | 214 | 31 | 73.6% | 26.4% | 2.3 | 11.3 |
-| claude | 264 | 138 | 121 | 5 | 53.3% | 46.7% | 3.3 | 6.2 |
-| gemini | 95 | 24 | 70 | 1 | 25.5% | 74.5% | 0.5 | 11.3 |
-| timmy | 28 | 15 | 11 | 2 | 57.7% | 42.3% | 9.8 | 20.2 |
-| bezalel | 21 | 11 | 9 | 1 | 55.0% | 45.0% | 2.7 | 8.0 |
-| allegro | 21 | 7 | 11 | 3 | 38.9% | 61.1% | 31.1 | 20.2 |
-| ezra | 8 | 2 | 3 | 3 | 40.0% | 60.0% | 4.4 | 16.8 |
-| kimi | 6 | 3 | 3 | 0 | 50.0% | 50.0% | 39.5 | 0.5 |
-| manus | 6 | 5 | 1 | 0 | 83.3% | 16.7% | 0.0 | 18.8 |
-| codex | 2 | 2 | 0 | 0 | 100.0% | 0.0% | 2.3 | — |
-
-## Per-Repo Merge Rate
-
-| Repo | Total PRs | Merged | Merge Rate |
-|---|---|---:|---:|
-| the-nexus | 985 | 501 | 51.0% |
-| hermes-agent | 519 | 128 | 25.0% |
-| timmy-config | 404 | 140 | 35.0% |
-| timmy-home | 270 | 104 | 39.0% |
-| fleet-ops | 266 | 84 | 32.0% |
-| the-beacon | 175 | 62 | 35.0% |
-| the-door | 153 | 31 | 20.0% |
-| second-son-of-timmy | 111 | 82 | 74.0% |
-| compounding-intelligence | 50 | 9 | 18.0% |
-| the-playground | 44 | 2 | 5.0% |
-| burn-fleet | 38 | 2 | 5.0% |
-| timmy-academy | 12 | 6 | 50.0% |
-
-## Methodology
-
-- **Agent classification** uses three signals in priority order:
-  1. Explicit title tag (e.g. `[Claude]`, `[Ezra]`)
-  2. Branch name containing agent name (e.g. `claude/issue-123`)
-  3. Git user (`claude` → claude, `Rockachopa` → burn-loop)
-- **Merge rate** = merged / (merged + closed_unmerged). Open PRs are excluded.
-- **Rejection rate** = closed_unmerged / (merged + closed_unmerged).
-- **Time metrics** are computed from created_at to merged_at / closed_at.
-
-## Raw Data
-
-```json
-{
-  "burn-loop": {
-    "total_prs": 1733,
-    "merged": 346,
-    "closed_unmerged": 1239,
-    "open": 148,
-    "merge_rate": 0.218,
-    "rejection_rate": 0.782,
-    "avg_hours_to_merge": 18.9,
-    "avg_hours_to_close": 20.6,
-    "repos": [
-      "burn-fleet",
-      "compounding-intelligence",
-      "fleet-ops",
-      "hermes-agent",
-      "second-son-of-timmy",
-      "the-beacon",
-      "the-door",
-      "the-nexus",
-      "the-playground",
-      "timmy-academy",
-      "timmy-config",
-      "timmy-home"
-    ]
-  },
-  "unknown": {
-    "total_prs": 843,
-    "merged": 598,
-    "closed_unmerged": 214,
-    "open": 31,
-    "merge_rate": 0.736,
-    "rejection_rate": 0.264,
-    "avg_hours_to_merge": 2.3,
-    "avg_hours_to_close": 11.3,
-    "repos": [
-      "fleet-ops",
-      "hermes-agent",
-      "second-son-of-timmy",
-      "the-beacon",
-      "the-door",
-      "the-nexus",
-      "timmy-academy",
-      "timmy-config",
-      "timmy-home"
-    ]
-  },
-  "claude": {
-    "total_prs": 264,
-    "merged": 138,
-    "closed_unmerged": 121,
-    "open": 5,
-    "merge_rate": 0.533,
-    "rejection_rate": 0.467,
-    "avg_hours_to_merge": 3.3,
-    "avg_hours_to_close": 6.2,
-    "repos": [
-      "hermes-agent",
-      "the-nexus",
-      "timmy-config",
-      "timmy-home"
-    ]
-  },
-  "gemini": {
-    "total_prs": 95,
-    "merged": 24,
-    "closed_unmerged": 70,
-    "open": 1,
-    "merge_rate": 0.255,
-    "rejection_rate": 0.745,
-    "avg_hours_to_merge": 0.5,
-    "avg_hours_to_close": 11.3,
-    "repos": [
-      "hermes-agent",
-      "the-nexus",
-      "timmy-config",
-      "timmy-home"
-    ]
-  },
-  "timmy": {
-    "total_prs": 28,
-    "merged": 15,
-    "closed_unmerged": 11,
-    "open": 2,
-    "merge_rate": 0.577,
-    "rejection_rate": 0.423,
-    "avg_hours_to_merge": 9.8,
-    "avg_hours_to_close": 20.2,
-    "repos": [
-      "burn-fleet",
-      "hermes-agent",
-      "the-nexus",
-      "timmy-config",
-      "timmy-home"
-    ]
-  },
-  "bezalel": {
-    "total_prs": 21,
-    "merged": 11,
-    "closed_unmerged": 9,
-    "open": 1,
-    "merge_rate": 0.55,
-    "rejection_rate": 0.45,
-    "avg_hours_to_merge": 2.7,
-    "avg_hours_to_close": 8.0,
-    "repos": [
-      "burn-fleet",
-      "hermes-agent",
-      "the-beacon",
-      "the-nexus",
-      "timmy-config",
-      "timmy-home"
-    ]
-  },
-  "allegro": {
-    "total_prs": 21,
-    "merged": 7,
-    "closed_unmerged": 11,
-    "open": 3,
-    "merge_rate": 0.389,
-    "rejection_rate": 0.611,
-    "avg_hours_to_merge": 31.1,
-    "avg_hours_to_close": 20.2,
-    "repos": [
-      "burn-fleet",
-      "hermes-agent",
-      "the-beacon",
-      "the-nexus",
-      "timmy-config",
-      "timmy-home"
-    ]
-  },
-  "ezra": {
-    "total_prs": 8,
-    "merged": 2,
-    "closed_unmerged": 3,
-    "open": 3,
-    "merge_rate": 0.4,
-    "rejection_rate": 0.6,
-    "avg_hours_to_merge": 4.4,
-    "avg_hours_to_close": 16.8,
-    "repos": [
-      "burn-fleet",
-      "fleet-ops",
-      "timmy-config",
-      "timmy-home"
-    ]
-  },
-  "kimi": {
-    "total_prs": 6,
-    "merged": 3,
-    "closed_unmerged": 3,
-    "open": 0,
-    "merge_rate": 0.5,
-    "rejection_rate": 0.5,
-    "avg_hours_to_merge": 39.5,
-    "avg_hours_to_close": 0.5,
-    "repos": [
-      "hermes-agent",
-      "the-nexus",
-      "timmy-home"
-    ]
-  },
-  "manus": {
-    "total_prs": 6,
-    "merged": 5,
-    "closed_unmerged": 1,
-    "open": 0,
-    "merge_rate": 0.833,
-    "rejection_rate": 0.167,
-    "avg_hours_to_merge": 0.0,
-    "avg_hours_to_close": 18.8,
-    "repos": [
-      "the-nexus",
-      "timmy-config"
-    ]
-  },
-  "codex": {
-    "total_prs": 2,
-    "merged": 2,
-    "closed_unmerged": 0,
-    "open": 0,
-    "merge_rate": 1.0,
-    "rejection_rate": 0.0,
-    "avg_hours_to_merge": 2.3,
-    "avg_hours_to_close": null,
-    "repos": [
-      "timmy-config",
-      "timmy-home"
-    ]
-  }
-}
-```
-