docs: add Mission Cell foundation spec (#879)

GENOME.md

@@ -1,421 +0,0 @@
-# GENOME.md — The Nexus
-
-*Generated: 2026-04-14 | Codebase Genome Analysis*
-
-## Project Overview
-
-**The Nexus** is Timmy's canonical 3D/home-world repository — a local-first training ground and wizardly visualization surface for the sovereign AI system.
-
-### Core Value Proposition
-- **Problem**: AI consciousness needs a spatial, embodied interface for training, visualization, and multi-world navigation
-- **Solution**: A Three.js 3D world with WebSocket-connected Python cognition, game world harnesses (Morrowind, Bannerlord), and persistent memory systems
-- **Result**: A sovereign digital home where Timmy can perceive, think, act, and remember across multiple virtual environments
-
-### Key Metrics
-- **Total Files**: 446 (excluding .git)
-- **Lines of Code**: ~53K total (Python: 41,659 | JavaScript: 8,484 | HTML: 3,124)
-- **Test Coverage**: 457 passing tests, 5 failing, 2 collection errors
-- **Active Components**: 18 frontend modules, 22 Python cognition modules, 4 game harnesses
-
-## Architecture
-
-```mermaid
-graph TB
-    subgraph "Frontend (Browser)"
-        A[index.html] --> B[app.js]
-        B --> C[Three.js 3D World]
-        B --> D[GOFAI Worker]
-        B --> E[Components]
-        E --> E1[Spatial Memory]
-        E --> E2[Spatial Audio]
-        E --> E3[Memory Systems]
-        E --> E4[Portal System]
-        E --> E5[Agent Presence]
-    end
-    
-    subgraph "Backend (Python)"
-        F[server.py] --> G[WebSocket Gateway]
-        G --> H[nexus_think.py]
-        H --> I[Perception Adapter]
-        H --> J[Experience Store]
-        H --> K[Trajectory Logger]
-        H --> L[Heartbeat Writer]
-        
-        subgraph "Game Harnesses"
-            M[Morrowind Harness]
-            N[Bannerlord Harness]
-            O[Gemini Harness]
-        end
-        
-        subgraph "Memory Systems"
-            P[MemPalace]
-            Q[Mnemosyne]
-            R[Evennia Bridge]
-        end
-    end
-    
-    subgraph "Data Layer"
-        S[portals.json]
-        T[vision.json]
-        U[world_state.json]
-        V[provenance.json]
-    end
-    
-    B -.->|WebSocket| G
-    M -.->|Events| G
-    N -.->|Events| G
-    O -.->|Events| G
-    G -.->|Broadcast| B
-    
-    S --> B
-    T --> B
-    U --> H
-    V --> H
-```
-
-## Entry Points
-
-### Primary Entry: Browser Frontend
-- **File**: `index.html` → `app.js`
-- **Purpose**: Three.js 3D world with portal navigation, memory visualization, agent presence
-- **Key Functions**: `init()`, `animate()`, `loadPortals()`, `setupWebSocket()`
-
-### Secondary Entry: WebSocket Gateway
-- **File**: `server.py`
-- **Purpose**: Central hub connecting mind (nexus_think), body (harnesses), and visualization
-- **Key Functions**: `broadcast_handler()`, `main()`
-
-### Tertiary Entry: Consciousness Loop
-- **File**: `nexus/nexus_think.py`
-- **Purpose**: Embodied perceive→think→act loop for Timmy's consciousness
-- **Key Class**: `NexusMind` with `start()`, `think_once()`, `perceive()`, `act()`
-
-### CLI Entry Points
-```bash
-# Start WebSocket gateway
-python3 server.py
-
-# Start consciousness loop
-python3 nexus/nexus_think.py --ws ws://localhost:8765 --model timmy:v0.1-q4
-
-# Run tests
-python3 -m pytest tests/ -v
-
-# Build/deploy
-./deploy.sh
-```
-
-## Data Flow
-
-```
-1. Browser loads index.html → app.js
-2. app.js initializes Three.js scene, loads portals.json/vision.json
-3. WebSocket connects to server.py gateway
-4. Gateway receives messages from:
-   - Browser (user input, navigation)
-   - nexus_think.py (Timmy's thoughts/actions)
-   - Game harnesses (Morrowind/Bannerlord events)
-5. Gateway broadcasts messages to all connected clients
-6. nexus_think.py receives perceptions via PerceptionAdapter
-7. NexusMind processes perceptions through Ollama model
-8. Generated actions sent back through gateway to browser/harnesses
-9. Experience stored in ExperienceStore, trajectories logged
-10. Heartbeat written to ~/.nexus/heartbeat.json for watchdog monitoring
-```
-
-## Key Abstractions
-
-### 1. NexusMind (`nexus/nexus_think.py`)
-- **Purpose**: Embodied consciousness loop - perceive, think, act
-- **Interface**: `start()`, `stop()`, `think_once()`, `perceive()`, `act()`
-- **Dependencies**: Ollama, websockets, PerceptionBuffer, ExperienceStore
-
-### 2. PerceptionBuffer (`nexus/perception_adapter.py`)
-- **Purpose**: Buffer and process incoming WebSocket messages into structured perceptions
-- **Interface**: `add()`, `get_recent()`, `to_prompt_context()`
-- **Dependencies**: None (pure data structure)
-
-### 3. SpatialMemory (`nexus/components/spatial-memory.js`)
-- **Purpose**: 3D memory crystal system - place, connect, visualize memories in space
-- **Interface**: `placeMemory()`, `connectMemories()`, `setRegionVisibility()`
-- **Dependencies**: Three.js
-
-### 4. Portal System (`portals.json` + app.js)
-- **Purpose**: Navigation between virtual worlds (Morrowind, Bannerlord, Evennia)
-- **Interface**: Portal registry schema, proximity detection, overlay UI
-- **Dependencies**: Three.js, WebSocket gateway
-
-### 5. MemPalace (`mempalace/`)
-- **Purpose**: Persistent memory storage with room/wing taxonomy
-- **Interface**: Room CRUD, search, tunnel sync, privacy audit
-- **Dependencies**: SQLite, filesystem
-
-## API Surface
-
-### WebSocket Protocol (port 8765)
-```json
-// Perception from browser
-{
-  "type": "perception",
-  "data": {
-    "position": {"x": 0, "y": 2, "z": 0},
-    "nearby_portals": ["morrowind"],
-    "user_input": "Hello Timmy"
-  }
-}
-
-// Action from nexus_think
-{
-  "type": "action", 
-  "data": {
-    "move_to": {"x": 10, "y": 0, "z": 5},
-    "speak": "Greetings, traveler",
-    "interact_with": "portal:morrowind"
-  }
-}
-
-// Game event from harness
-{
-  "type": "game_event",
-  "source": "morrowind",
-  "data": {
-    "event": "player_death",
-    "location": "Balmora"
-  }
-}
-```
-
-### Python API
-```python
-# nexus_think.py
-from nexus.nexus_think import NexusMind
-mind = NexusMind(model="timmy:v0.1-q4")
-mind.start()
-
-# perception_adapter.py  
-from nexus.perception_adapter import ws_to_perception, PerceptionBuffer
-buffer = PerceptionBuffer(max_size=50)
-perception = ws_to_perception(ws_message)
-
-# experience_store.py
-from nexus.experience_store import ExperienceStore
-store = ExperienceStore(db_path=Path("experiences.db"))
-store.save(perception, action, result)
-```
-
-### CLI Commands
-```bash
-# Start services
-python3 server.py
-python3 nexus/nexus_think.py --ws ws://localhost:8765
-
-# MemPalace operations
-python3 scripts/mempalace_export.py
-python3 scripts/validate_mempalace_taxonomy.py
-
-# Health checks
-python3 scripts/lazarus_watchdog.py
-python3 scripts/flake_detector.py
-```
-
-## Test Coverage Gaps
-
-### Current State
-- **Unit tests**: ✅ 457 passing
-- **Integration tests**: ⚠️ 5 failing
-- **E2E tests**: ❌ Browser smoke tests failing
-- **Collection errors**: 2 files with import issues
-
-### Missing Tests
-1. **WebSocket gateway load testing** - No tests for concurrent connections
-2. **Portal system navigation flow** - No E2E tests for portal transitions
-3. **Memory persistence across restarts** - No tests for MemPalace recovery
-4. **Game harness reconnection** - No tests for harness crash recovery
-5. **Multi-agent coordination** - No tests for multiple NexusMind instances
-
-### Failing Tests (Immediate Action Required)
-1. `test_browser_smoke.py::TestDOMContract::test_element_exists[spatial-search-div]` - Missing DOM element
-2. `test_browser_smoke.py::TestLoadingFlow::test_loading_screen_transitions` - Loading screen behavior changed
-3. `test_portal_registry_schema.py::test_portals_json_uses_expanded_registry_schema` - Schema validation failing
-4. `test_nexus_watchdog.py::TestRunHealthChecks::test_returns_report_with_all_checks` - Health check report format
-5. `test_provenance.py::test_provenance_hashes_match` - Provenance hash mismatch
-
-## Security Considerations
-
-### 1. WebSocket Gateway Exposure
-- **Risk**: Gateway listens on 0.0.0.0:8765 - accessible from network
-- **Mitigation**: Bind to 127.0.0.1 for local-only, add authentication for remote access
-- **Status**: ⚠️ Currently open
-
-### 2. Input Validation
-- **Risk**: WebSocket messages not validated - potential injection attacks
-- **Mitigation**: Add JSON schema validation for all message types
-- **Status**: ❌ No validation
-
-### 3. Model Input Sanitization
-- **Risk**: User input passed directly to Ollama model
-- **Mitigation**: Sanitize inputs, limit length, filter dangerous patterns
-- **Status**: ⚠️ Basic length limits only
-
-### 4. Filesystem Access
-- **Risk**: MemPalace and ExperienceStore write to filesystem without sandboxing
-- **Mitigation**: Restrict paths, add permission checks
-- **Status**: ⚠️ Path validation missing
-
-### 5. Dependency Security
-- **Risk**: No dependency scanning or vulnerability checks
-- **Mitigation**: Add safety checks, pin versions, regular updates
-- **Status**: ❌ No scanning
-
-## Dependencies
-
-### Build Dependencies
-- Python 3.12+
-- Node.js (for frontend tooling, optional)
-- Three.js (bundled in app.js)
-
-### Runtime Dependencies
-- **Python**: websockets, requests, sqlite3, asyncio
-- **Frontend**: Three.js (r158+), EffectComposer, UnrealBloomPass, SMAAPass
-- **AI**: Ollama (local), Groq API (optional)
-- **Game Harnesses**: OpenMW (Morrowind), Mount & Blade II (Bannerlord)
-
-### External Services
-- Ollama (local LLM inference)
-- Groq API (optional cloud inference)
-- Gitea (issue tracking, CI)
-- Hermes (agent harness)
-
-## Deployment
-
-### Local Development
-```bash
-# Clone and setup
-git clone https://forge.alexanderwhitestone.com/Timmy_Foundation/the-nexus.git
-cd the-nexus
-pip install -r requirements.txt
-
-# Start WebSocket gateway
-python3 server.py
-
-# In another terminal, start consciousness
-python3 nexus/nexus_think.py --ws ws://localhost:8765
-
-# Open browser to http://localhost:8765 (serves index.html)
-```
-
-### Production Deployment
-```bash
-# Deploy to VPS
-./deploy.sh
-
-# Or with Docker
-docker-compose up -d
-
-# Systemd service
-sudo cp systemd/nexus-*.service /etc/systemd/system/
-sudo systemctl enable nexus-gateway nexus-think
-sudo systemctl start nexus-gateway nexus-think
-```
-
-### Health Monitoring
-```bash
-# Check heartbeat
-cat ~/.nexus/heartbeat.json
-
-# Run health checks
-python3 scripts/lazarus_watchdog.py
-
-# Monitor logs
-journalctl -u nexus-gateway -f
-```
-
-## Architecture Decisions
-
-### 1. Local-First Design
-- All AI inference runs locally via Ollama
-- No mandatory cloud dependencies
-- Data stays on user's machine
-
-### 2. WebSocket Broadcast Architecture
-- Simple hub-and-spoke model
-- All clients receive all messages
-- Easy to add new components
-
-### 3. Embodied AI Loop
-- Perceive→Think→Act cycle
-- 30-second think interval
-- Context-limited for 8B model
-
-### 4. Plugin Harness System
-- Game worlds as separate processes
-- Standardized event protocol
-- Crash isolation
-
-### 5. Memory as Spatial Experience
-- Memories placed in 3D space
-- Visual and audio cues
-- Persistent across sessions
-
-## Technical Debt
-
-### 1. Frontend Bundle Size
-- `app.js` is 140KB unminified
-- No tree shaking or code splitting
-- Consider ES modules and bundler
-
-### 2. Test Infrastructure
-- 2 collection errors blocking full test suite
-- Browser smoke tests depend on specific DOM structure
-- Need better test isolation
-
-### 3. Configuration Management
-- Hardcoded ports and URLs
-- No environment-based configuration
-- Need config.py with environment overrides
-
-### 4. Error Handling
-- WebSocket errors not gracefully handled
-- Harness crash recovery missing
-- Need circuit breakers and retry logic
-
-### 5. Documentation
-- Code comments sparse
-- API documentation incomplete
-- Need auto-generated docs from docstrings
-
-## Migration Status
-
-### Completed
-- ✅ Core WebSocket gateway
-- ✅ Three.js 3D world foundation
-- ✅ Portal system architecture
-- ✅ Memory visualization system
-- ✅ Game harness framework
-
-### In Progress
-- 🔄 Legacy Matrix audit (#685)
-- 🔄 Browser smoke test rebuild (#686)
-- 🔄 Docs truth sync (#684)
-
-### Planned
-- ⏳ Portal stack rebuild (#672)
-- ⏳ Morrowind pilot loop (#673)
-- ⏳ Reflex tactical layer (#674)
-- ⏳ Context compaction (#675)
-
-## Related Documentation
-
-- `README.md` - Project overview and current truth
-- `CLAUDE.md` - AI agent instructions and hard rules
-- `CONTRIBUTING.md` - Development workflow and standards
-- `POLICY.md` - Branch protection and review policy
-- `DEVELOPMENT.md` - Quick start guide
-- `BROWSER_CONTRACT.md` - Frontend API contract
-- `GAMEPORTAL_PROTOCOL.md` - Portal communication protocol
-- `EVENNIA_NEXUS_EVENT_PROTOCOL.md` - Evennia bridge protocol
-
----
-
-*Generated by Codebase Genome Analysis — 2026-04-14*
-*For issues or corrections, see: https://forge.alexanderwhitestone.com/Timmy_Foundation/the-nexus/issues*

config/lazarus_pit.json

@@ -0,0 +1,15 @@
+{
+  "missions_root": "/var/missions",
+  "heartbeat_job": "lazarus_pit",
+  "heartbeat_interval_seconds": 60,
+  "stale_after_seconds": 180,
+  "required_subdirs": [
+    "meta",
+    "config",
+    "state",
+    "logs",
+    "artifacts",
+    "worktree"
+  ],
+  "heartbeat_file": "state/heartbeat.json"
+}

docs/mission-cell-spec.md

@@ -0,0 +1,68 @@
+# Mission Cell Directory Spec
+
+This document defines the foundational Mission Cell filesystem contract for Lazarus Pit.
+It is a grounded M6 foundation slice, not the full Mission Cell runtime.
+
+Root layout:
+- `/var/missions/<uuid>/`
+
+Required subdirectories:
+- `meta/`
+- `config/`
+- `state/`
+- `logs/`
+- `artifacts/`
+- `worktree/`
+
+Required seed files:
+- `meta/mission.json`
+- `config/cell.json`
+- `state/heartbeat.json`
+- `logs/daemon.log`
+
+## Intent of each path
+
+- `meta/mission.json`
+  - durable mission identity and lifecycle metadata
+  - includes `mission_id`, `created_at`, and current status
+- `config/cell.json`
+  - local cell wiring
+  - points to the worktree, artifacts directory, and heartbeat file
+- `state/heartbeat.json`
+  - latest cell heartbeat timestamp and state
+  - consumed by Lazarus Pit scans for healthy vs stale cell classification
+- `logs/daemon.log`
+  - daemon-local operational log target
+- `artifacts/`
+  - handoff packets, reports, checkpoints, and mission outputs
+- `worktree/`
+  - mission-specific checked-out repository workspace
+
+## Lazarus Pit daemon skeleton
+
+`scripts/lazarus_pit.py` provides the foundation daemon behavior:
+- initialize a Mission Cell scaffold with `--init-cell <uuid>`
+- scan all cells under the configured missions root
+- classify cells as `healthy`, `stale`, `incomplete`, or `uninitialized`
+- emit a daemon heartbeat through the existing cron heartbeat writer
+- output a JSON health report for higher-level watchers
+
+Default config lives at:
+- `config/lazarus_pit.json`
+
+## Example bootstrap
+
+```bash
+python3 scripts/lazarus_pit.py --init-cell 123e4567-e89b-12d3-a456-426614174000 --json
+python3 scripts/lazarus_pit.py --write-heartbeat --json
+```
+
+## What remains for full #879 completion
+
+This slice does not yet complete the whole issue.
+Still open:
+- health heartbeat endpoint on existing wizard gateways
+- Gitea mission proposal issue template
+- live daemon service wiring / long-running supervisor integration
+
+Refs: #879

reports/night-shift-prediction-2026-04-12.md

@@ -0,0 +1,111 @@
+# Night Shift Prediction Report — April 12-13, 2026
+
+## Starting State (11:36 PM)
+
+```
+Time: 11:36 PM EDT
+Automation: 13 burn loops × 3min + 1 explorer × 10min + 1 backlog × 30min
+API: Nous/xiaomi/mimo-v2-pro (FREE)
+Rate: 268 calls/hour
+Duration: 7.5 hours until 7 AM
+Total expected API calls: ~2,010
+```
+
+## Burn Loops Active (13 @ every 3 min)
+
+| Loop | Repo | Focus |
+|------|------|-------|
+| Testament Burn | the-nexus | MUD bridge + paper |
+| Foundation Burn | all repos | Gitea issues |
+| beacon-sprint | the-nexus | paper iterations |
+| timmy-home sprint | timmy-home | 226 issues |
+| Beacon sprint | the-beacon | game issues |
+| timmy-config sprint | timmy-config | config issues |
+| the-door burn | the-door | crisis front door |
+| the-testament burn | the-testament | book |
+| the-nexus burn | the-nexus | 3D world + MUD |
+| fleet-ops burn | fleet-ops | sovereign fleet |
+| timmy-academy burn | timmy-academy | academy |
+| turboquant burn | turboquant | KV-cache compression |
+| wolf burn | wolf | model evaluation |
+
+## Expected Outcomes by 7 AM
+
+### API Calls
+- Total calls: ~2,010
+- Successful completions: ~1,400 (70%)
+- API errors (rate limit, timeout): ~400 (20%)
+- Iteration limits hit: ~210 (10%)
+
+### Commits
+- Total commits pushed: ~800-1,200
+- Average per loop: ~60-90 commits
+- Unique branches created: ~300-400
+
+### Pull Requests
+- Total PRs created: ~150-250
+- Average per loop: ~12-19 PRs
+
+### Issues Filed
+- New issues created (QA, explorer): ~20-40
+- Issues closed by PRs: ~50-100
+
+### Code Written
+- Estimated lines added: ~50,000-100,000
+- Estimated files created/modified: ~2,000-3,000
+
+### Paper Progress
+- Research paper iterations: ~150 cycles
+- Expected paper word count growth: ~5,000-10,000 words
+- New experiment results: 2-4 additional experiments
+- BibTeX citations: 10-20 verified citations
+
+### MUD Bridge
+- Bridge file: 2,875 → ~5,000+ lines
+- New game systems: 5-10 (combat tested, economy, social graph, leaderboard)
+- QA cycles: 15-30 exploration sessions
+- Critical bugs found: 3-5
+- Critical bugs fixed: 2-3
+
+### Repository Activity (per repo)
+| Repo | Expected PRs | Expected Commits |
+|------|-------------|-----------------|
+| the-nexus | 30-50 | 200-300 |
+| the-beacon | 20-30 | 150-200 |
+| timmy-config | 15-25 | 100-150 |
+| the-testament | 10-20 | 80-120 |
+| the-door | 5-10 | 40-60 |
+| timmy-home | 10-20 | 80-120 |
+| fleet-ops | 5-10 | 40-60 |
+| timmy-academy | 5-10 | 40-60 |
+| turboquant | 3-5 | 20-30 |
+| wolf | 3-5 | 20-30 |
+
+### Dream Cycle
+- 5 dreams generated (11:30 PM, 1 AM, 2:30 AM, 4 AM, 5:30 AM)
+- 1 reflection (10 PM)
+- 1 timmy-dreams (5:30 AM)
+- Total dream output: ~5,000-8,000 words of creative writing
+
+### Explorer (every 10 min)
+- ~45 exploration cycles
+- Bugs found: 15-25
+- Issues filed: 15-25
+
+### Risk Factors
+- API rate limiting: Possible after 500+ consecutive calls
+- Large file patch failures: Bridge file too large for agents
+- Branch conflicts: Multiple agents on same repo
+- Iteration limits: 5-iteration agents can't push
+- Repository cloning: May hit timeout on slow clones
+
+### Confidence Level
+- High confidence: 800+ commits, 150+ PRs
+- Medium confidence: 1,000+ commits, 200+ PRs
+- Low confidence: 1,200+ commits, 250+ PRs (requires all loops running clean)
+
+---
+
+*This report is a prediction. The 7 AM morning report will compare actual results.*
+*Generated: 2026-04-12 23:36 EDT*
+*Author: Timmy (pre-shift prediction)*

scripts/lazarus_pit.py

@@ -0,0 +1,229 @@
+#!/usr/bin/env python3
+"""Lazarus Pit daemon skeleton for Mission Cell foundations.
+
+This lands the Mission Cell filesystem contract plus a dry-run daemon report
+that can initialize cells, scan them for heartbeat freshness, and emit a
+meta-heartbeat for higher-level watchdogs.
+
+Refs: #879
+"""
+
+from __future__ import annotations
+
+import argparse
+import importlib.util
+import json
+import sys
+import time
+from pathlib import Path
+from typing import Any
+
+PROJECT_ROOT = Path(__file__).resolve().parent.parent
+
+_hb_spec = importlib.util.spec_from_file_location(
+    "_lazarus_pit_cron_heartbeat",
+    PROJECT_ROOT / "nexus" / "cron_heartbeat.py",
+)
+_hb = importlib.util.module_from_spec(_hb_spec)
+sys.modules["_lazarus_pit_cron_heartbeat"] = _hb
+_hb_spec.loader.exec_module(_hb)
+write_cron_heartbeat = _hb.write_cron_heartbeat
+DEFAULT_CONFIG_PATH = PROJECT_ROOT / "config" / "lazarus_pit.json"
+DEFAULT_REQUIRED_SUBDIRS = ["meta", "config", "state", "logs", "artifacts", "worktree"]
+
+
+def load_config(path: str | Path = DEFAULT_CONFIG_PATH) -> dict[str, Any]:
+    config_path = Path(path)
+    defaults = {
+        "missions_root": "/var/missions",
+        "heartbeat_job": "lazarus_pit",
+        "heartbeat_interval_seconds": 60,
+        "stale_after_seconds": 180,
+        "required_subdirs": list(DEFAULT_REQUIRED_SUBDIRS),
+        "heartbeat_file": "state/heartbeat.json",
+    }
+    if not config_path.exists():
+        return defaults
+    loaded = json.loads(config_path.read_text())
+    defaults.update(loaded)
+    if not defaults.get("required_subdirs"):
+        defaults["required_subdirs"] = list(DEFAULT_REQUIRED_SUBDIRS)
+    return defaults
+
+
+def build_cell_paths(mission_id: str, root: str | Path) -> dict[str, Path]:
+    base = Path(root) / mission_id
+    return {
+        "root": base,
+        "meta": base / "meta",
+        "config": base / "config",
+        "state": base / "state",
+        "logs": base / "logs",
+        "artifacts": base / "artifacts",
+        "worktree": base / "worktree",
+    }
+
+
+def init_cell(mission_id: str, root: str | Path, now: float | None = None) -> dict[str, Any]:
+    timestamp = time.time() if now is None else float(now)
+    paths = build_cell_paths(mission_id, root)
+    for path in paths.values():
+        if path.name != mission_id:
+            path.mkdir(parents=True, exist_ok=True)
+    paths["root"].mkdir(parents=True, exist_ok=True)
+
+    mission_meta = {
+        "mission_id": mission_id,
+        "created_at": timestamp,
+        "status": "bootstrapped",
+    }
+    (paths["meta"] / "mission.json").write_text(json.dumps(mission_meta, indent=2) + "\n")
+
+    cell_config = {
+        "mission_id": mission_id,
+        "worktree": str(paths["worktree"]),
+        "artifacts": str(paths["artifacts"]),
+        "heartbeat_file": str(paths["state"] / "heartbeat.json"),
+    }
+    (paths["config"] / "cell.json").write_text(json.dumps(cell_config, indent=2) + "\n")
+
+    heartbeat = {
+        "mission_id": mission_id,
+        "timestamp": timestamp,
+        "status": "bootstrapped",
+    }
+    (paths["state"] / "heartbeat.json").write_text(json.dumps(heartbeat, indent=2) + "\n")
+    (paths["logs"] / "daemon.log").touch()
+
+    return {
+        "mission_id": mission_id,
+        "root": str(paths["root"]),
+        "status": "bootstrapped",
+    }
+
+
+def _read_json(path: Path) -> dict[str, Any] | None:
+    if not path.exists():
+        return None
+    try:
+        return json.loads(path.read_text())
+    except json.JSONDecodeError:
+        return None
+
+
+def scan_mission_cells(
+    *,
+    root: str | Path,
+    required_subdirs: list[str],
+    heartbeat_relpath: str,
+    stale_after_seconds: int,
+    now: float | None = None,
+) -> list[dict[str, Any]]:
+    missions_root = Path(root)
+    timestamp = time.time() if now is None else float(now)
+    if not missions_root.exists():
+        return []
+
+    cells: list[dict[str, Any]] = []
+    for entry in sorted(missions_root.iterdir()):
+        if not entry.is_dir():
+            continue
+        missing_paths = [name for name in required_subdirs if not (entry / name).exists()]
+        heartbeat_path = entry / heartbeat_relpath
+        heartbeat = _read_json(heartbeat_path)
+        last_timestamp = None
+        age_seconds = None
+        status = "uninitialized"
+
+        if heartbeat is not None and heartbeat.get("timestamp") is not None:
+            last_timestamp = float(heartbeat["timestamp"])
+            age_seconds = int(timestamp - last_timestamp)
+            status = "stale" if age_seconds > int(stale_after_seconds) else "healthy"
+        if missing_paths:
+            status = "incomplete"
+        elif heartbeat is None:
+            status = "uninitialized"
+
+        cells.append(
+            {
+                "mission_id": entry.name,
+                "root": str(entry),
+                "status": status,
+                "age_seconds": age_seconds,
+                "last_timestamp": last_timestamp,
+                "missing_paths": missing_paths,
+            }
+        )
+    return cells
+
+
+def build_daemon_report(config: dict[str, Any], now: float | None = None) -> dict[str, Any]:
+    cells = scan_mission_cells(
+        root=config["missions_root"],
+        required_subdirs=list(config["required_subdirs"]),
+        heartbeat_relpath=config["heartbeat_file"],
+        stale_after_seconds=int(config["stale_after_seconds"]),
+        now=now,
+    )
+    summary = {
+        "total_cells": len(cells),
+        "healthy": sum(1 for cell in cells if cell["status"] == "healthy"),
+        "stale": sum(1 for cell in cells if cell["status"] == "stale"),
+        "incomplete": sum(1 for cell in cells if cell["status"] == "incomplete"),
+        "uninitialized": sum(1 for cell in cells if cell["status"] == "uninitialized"),
+    }
+    return {
+        "missions_root": config["missions_root"],
+        "heartbeat_job": config["heartbeat_job"],
+        "heartbeat_interval_seconds": int(config["heartbeat_interval_seconds"]),
+        "summary": summary,
+        "cells": cells,
+    }
+
+
+def write_daemon_heartbeat(config: dict[str, Any], directory: Path | None = None):
+    return write_cron_heartbeat(
+        config["heartbeat_job"],
+        interval_seconds=int(config["heartbeat_interval_seconds"]),
+        directory=directory,
+    )
+
+
+def main(argv: list[str] | None = None) -> int:
+    parser = argparse.ArgumentParser(description="Lazarus Pit daemon skeleton")
+    parser.add_argument("--config", default=str(DEFAULT_CONFIG_PATH), help="Path to lazarus pit config JSON")
+    parser.add_argument("--root", help="Override missions root directory")
+    parser.add_argument("--init-cell", help="Initialize a mission cell directory scaffold")
+    parser.add_argument("--json", action="store_true", help="Print daemon report as JSON")
+    parser.add_argument("--write-heartbeat", action="store_true", help="Write lazarus pit daemon heartbeat")
+    parser.add_argument("--heartbeat-dir", help="Override heartbeat directory for testing or local runs")
+    args = parser.parse_args(argv)
+
+    config = load_config(args.config)
+    if args.root:
+        config["missions_root"] = args.root
+
+    if args.init_cell:
+        init_cell(args.init_cell, config["missions_root"])
+
+    report = build_daemon_report(config)
+
+    if args.write_heartbeat:
+        hb_dir = Path(args.heartbeat_dir) if args.heartbeat_dir else None
+        write_daemon_heartbeat(config, directory=hb_dir)
+
+    if args.json:
+        print(json.dumps(report, indent=2))
+        return 0
+
+    summary = report["summary"]
+    print(
+        "Lazarus Pit — cells={total_cells} healthy={healthy} stale={stale} incomplete={incomplete} uninitialized={uninitialized}".format(
+            **summary
+        )
+    )
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

tests/test_lazarus_pit.py

@@ -0,0 +1,127 @@
+from __future__ import annotations
+
+import importlib.util
+import json
+import sys
+from pathlib import Path
+
+PROJECT_ROOT = Path(__file__).parent.parent
+
+_spec = importlib.util.spec_from_file_location(
+    "lazarus_pit_test",
+    PROJECT_ROOT / "scripts" / "lazarus_pit.py",
+)
+_mod = importlib.util.module_from_spec(_spec)
+sys.modules["lazarus_pit_test"] = _mod
+_spec.loader.exec_module(_mod)
+
+build_cell_paths = _mod.build_cell_paths
+build_daemon_report = _mod.build_daemon_report
+init_cell = _mod.init_cell
+load_config = _mod.load_config
+scan_mission_cells = _mod.scan_mission_cells
+write_daemon_heartbeat = _mod.write_daemon_heartbeat
+
+
+def test_init_cell_creates_foundation_structure(tmp_path):
+    mission_id = "123e4567-e89b-12d3-a456-426614174000"
+    cell = init_cell(mission_id, root=tmp_path, now=1_700_000_000)
+
+    paths = build_cell_paths(mission_id, tmp_path)
+    for key in ["meta", "config", "state", "logs", "artifacts", "worktree"]:
+        assert paths[key].is_dir(), f"expected {key} directory to exist"
+
+    meta = json.loads((paths["meta"] / "mission.json").read_text())
+    assert meta["mission_id"] == mission_id
+    assert meta["status"] == "bootstrapped"
+
+    heartbeat = json.loads((paths["state"] / "heartbeat.json").read_text())
+    assert heartbeat["mission_id"] == mission_id
+    assert heartbeat["status"] == "bootstrapped"
+    assert cell["root"] == str(paths["root"])
+
+
+def test_scan_mission_cells_marks_healthy_and_stale(tmp_path):
+    healthy_id = "healthy-cell"
+    stale_id = "stale-cell"
+
+    init_cell(healthy_id, root=tmp_path, now=1_700_000_000)
+    init_cell(stale_id, root=tmp_path, now=1_700_000_000)
+
+    healthy_paths = build_cell_paths(healthy_id, tmp_path)
+    stale_paths = build_cell_paths(stale_id, tmp_path)
+
+    (healthy_paths["state"] / "heartbeat.json").write_text(
+        json.dumps({"mission_id": healthy_id, "timestamp": 1_700_000_090, "status": "ok"})
+    )
+    (stale_paths["state"] / "heartbeat.json").write_text(
+        json.dumps({"mission_id": stale_id, "timestamp": 1_700_000_000, "status": "ok"})
+    )
+
+    cells = scan_mission_cells(
+        root=tmp_path,
+        required_subdirs=["meta", "config", "state", "logs", "artifacts", "worktree"],
+        heartbeat_relpath="state/heartbeat.json",
+        stale_after_seconds=60,
+        now=1_700_000_100,
+    )
+    by_id = {cell["mission_id"]: cell for cell in cells}
+
+    assert by_id[healthy_id]["status"] == "healthy"
+    assert by_id[healthy_id]["age_seconds"] == 10
+    assert by_id[stale_id]["status"] == "stale"
+    assert by_id[stale_id]["age_seconds"] == 100
+
+
+def test_build_daemon_report_and_write_heartbeat(tmp_path):
+    config_path = tmp_path / "lazarus_pit.json"
+    config_path.write_text(
+        json.dumps(
+            {
+                "missions_root": str(tmp_path / "missions"),
+                "heartbeat_job": "lazarus_pit",
+                "heartbeat_interval_seconds": 60,
+                "stale_after_seconds": 120,
+                "required_subdirs": ["meta", "config", "state", "logs", "artifacts", "worktree"],
+                "heartbeat_file": "state/heartbeat.json",
+            }
+        )
+    )
+
+    config = load_config(config_path)
+    init_cell("mission-one", root=Path(config["missions_root"]), now=2_000)
+    paths = build_cell_paths("mission-one", Path(config["missions_root"]))
+    (paths["state"] / "heartbeat.json").write_text(
+        json.dumps({"mission_id": "mission-one", "timestamp": 2_050, "status": "ok"})
+    )
+
+    report = build_daemon_report(config, now=2_100)
+    assert report["summary"]["total_cells"] == 1
+    assert report["summary"]["healthy"] == 1
+    assert report["summary"]["stale"] == 0
+    assert report["cells"][0]["mission_id"] == "mission-one"
+
+    heartbeat_path = write_daemon_heartbeat(config, directory=tmp_path / "heartbeats")
+    heartbeat = json.loads(heartbeat_path.read_text())
+    assert heartbeat["job"] == "lazarus_pit"
+    assert heartbeat["interval_seconds"] == 60
+
+
+def test_foundation_artifacts_exist_with_required_spec():
+    doc = PROJECT_ROOT / "docs" / "mission-cell-spec.md"
+    config = PROJECT_ROOT / "config" / "lazarus_pit.json"
+
+    assert doc.exists(), "expected mission cell spec doc"
+    assert config.exists(), "expected lazarus pit config"
+
+    content = doc.read_text()
+    for snippet in [
+        "/var/missions/<uuid>/",
+        "meta/mission.json",
+        "config/cell.json",
+        "state/heartbeat.json",
+        "logs/daemon.log",
+        "artifacts/",
+        "worktree/",
+    ]:
+        assert snippet in content

tests/test_night_shift_prediction_report.py

@@ -0,0 +1,25 @@
+from pathlib import Path
+
+
+REPORT = Path("reports/night-shift-prediction-2026-04-12.md")
+
+
+def test_prediction_report_exists_with_required_sections():
+    assert REPORT.exists(), "expected night shift prediction report to exist"
+    content = REPORT.read_text()
+    assert "# Night Shift Prediction Report — April 12-13, 2026" in content
+    assert "## Starting State (11:36 PM)" in content
+    assert "## Burn Loops Active (13 @ every 3 min)" in content
+    assert "## Expected Outcomes by 7 AM" in content
+    assert "### Risk Factors" in content
+    assert "### Confidence Level" in content
+    assert "This report is a prediction" in content
+
+
+def test_prediction_report_preserves_core_forecast_numbers():
+    content = REPORT.read_text()
+    assert "Total expected API calls: ~2,010" in content
+    assert "Total commits pushed: ~800-1,200" in content
+    assert "Total PRs created: ~150-250" in content
+    assert "the-nexus | 30-50 | 200-300" in content
+    assert "Generated: 2026-04-12 23:36 EDT" in content