docs: add Mission Cell foundation spec (#879)

config/lazarus_pit.json

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+{
+  "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

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+# 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

scripts/lazarus_pit.py

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+#!/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

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+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