skill-system-physiology

Skill System Physiology

skill-system-physiology is the operational biology layer for agent systems.

Canonical owner: skill-system-physiology. skill-system-pgysiology is historical typo compatibility only and is not the canonical owner.

Organ Map

Canonical body-map document: body-map.md

Organ	Owner
CNS	active reasoning agent
Soul	skill-system-soul identity/profile calibration
Hippocampus	skill-system-memory continuity + recall
ANS	skill-system-ans cron/hooks/reflexes
Myelin	scripts / skills / CLI wrappers / MCP tools
Limbs	skill-system-tkt worker-task lifecycle
Immune system	guards / safety checks
Endocrine system	quota / urgency / priority signals

Important local mapping:

• meeting / reviewer-comms = corpus callosum / 胼胝體, the circulation tract for same-level CNS region communication and ratification.
• live tmux board = useful callosal surface, not durable memory.
• durable decisions still require .tkt/meetings, .tkt/decisions, and memory when behavior changes.

Pain Taxonomy

• amnesia
• sensory loss
• motor fallback
• limb silence
• config drift
• metabolic overload
• infection

Clinical repair protocol:

1. lesion
2. containment
3. repair
4. prevention
5. durable memory/artifact

Myelination Lifecycle

1. Explore with raw shell when a maneuver is new.
2. Log friction/pattern.
3. After repeated success, wrap as script/CLI/SK.
4. Register as myelin metadata.
5. Recommend the whole-muscle command.
6. Retire repeated muscle-cell commands.

Boundaries

• Physiology does not replace soul, memory, ANS, or TKT.
• Physiology bootstraps organism scaffolds and clinical protocols so those subsystems can compose coherently in a fresh environment.
• Finch/Wren are optional examples, not portable defaults.

Skill Anatomy Classification

Anatomy classification turns labels into clinical gates.

Tissue class	Meaning	Required gate
reflex	hot-path trigger/response loop	latency budget + no_hot_path_embeddings
organ	stateful subsystem	owner + status_command_or_doctor
circulation	task/message/artifact flow	queue backpressure or staleness gate
skeleton	schema/index/routing connective tissue	schema or index validation
hybrid	mixed tissue role	primary_class + secondary_classes + owner split

Rules:

• endocrine is modulation, not a tissue_class.
• v1 source of truth is sidecar-first: .sk/physiology/skill-anatomy.yaml.
• projection deadline: 2026-04-21 or before v1 close.
• hybrid ratio >30% emits WARN.
• invalid hybrid entries block health.
• no Dream/vector embeddings in hot paths.
• generated anatomy artifacts must not contain /share/nas165/arthur0824hao, dino4ur, Finch, Wren, or nv960.

Minimum doctor output fields:

• tissue_class
• organ_system
• status
• severity
• owner
• age
• next_safe_probe
• checks

Commands

python3 scripts/physiology.py init --project-root /tmp/new-project
python3 scripts/physiology.py scan --project-root /tmp/new-project --repair
python3 scripts/physiology.py pain-log --project-root /tmp/new-project --type amnesia --summary "missing context"
python3 scripts/physiology.py myelinize --project-root /tmp/new-project --command "tmux send-keys -t pane hi" --command "tmux send-keys -t pane hi"
python3 scripts/physiology.py boot-profile --project-root /tmp/new-project
python3 scripts/physiology.py export --project-root /tmp/new-project --output /tmp/portable-physiology
python3 scripts/physiology.py anatomy init --project-root /tmp/new-project
python3 scripts/physiology.py anatomy scan --project-root /tmp/new-project
python3 scripts/physiology.py anatomy classify --project-root /tmp/new-project
python3 scripts/physiology.py anatomy doctor --project-root /tmp/new-project --json
python3 scripts/physiology.py anatomy project --project-root /tmp/new-project [--skills-root /path/to/skills]
python3 scripts/physiology.py anatomy drift-check --project-root /tmp/new-project [--skills-root /path/to/skills]

anatomy project reads the sidecar and writes per-skill SKILL.meta.yaml files containing a physiology section. After projection, the sidecar serves as a drift sensor: drift-check compares sidecar entries against projected manifests and reports divergences.

Fallback public entry until sk physiology anatomy ... routing is wired:

python3 Project/skills/skills/skill-system-physiology/scripts/physiology.py anatomy doctor --project-root /share/nas165/arthur0824hao/Work --json

{
  "schema_version": "2.0",
  "id": "skill-system-physiology",
  "version": "0.2.0",
  "capabilities": [
    "physiology-init",
    "physiology-scan",
    "physiology-pain-log",
    "physiology-myelinize",
    "physiology-boot-profile",
    "physiology-export",
    "physiology-anatomy"
  ],
  "effects": ["fs.read", "fs.write"],
  "operations": {
    "init": {
      "description": "Bootstrap a portable physiology scaffold in an arbitrary project root.",
      "input": {
        "project_root": {"type": "string", "required": false},
        "dry_run": {"type": "boolean", "required": false, "default": false}
      },
      "output": {"description": "Created or planned files", "fields": {"status": "ok | error", "files": "array"}},
      "entrypoints": {"unix": ["python3", "scripts/physiology.py", "init"], "windows": ["python", "scripts/physiology.py", "init"]}
    },
    "scan": {
      "description": "Scan a project root for physiology scaffold health and optionally repair missing files.",
      "input": {
        "project_root": {"type": "string", "required": false},
        "dry_run": {"type": "boolean", "required": false, "default": false},
        "repair": {"type": "boolean", "required": false, "default": false}
      },
      "output": {"description": "Missing-file report", "fields": {"status": "ok | error", "missing_files": "array", "healthy": "boolean"}},
      "entrypoints": {"unix": ["python3", "scripts/physiology.py", "scan"], "windows": ["python", "scripts/physiology.py", "scan"]}
    },
    "pain-log": {
      "description": "Record operational pain events for clinical repair loops.",
      "input": {
        "project_root": {"type": "string", "required": false},
        "type": {"type": "string", "required": true},
        "summary": {"type": "string", "required": true},
        "details": {"type": "string", "required": false},
        "dry_run": {"type": "boolean", "required": false, "default": false}
      },
      "output": {"description": "Pain-log result", "fields": {"status": "ok | error", "path": "string"}},
      "entrypoints": {"unix": ["python3", "scripts/physiology.py", "pain-log"], "windows": ["python", "scripts/physiology.py", "pain-log"]}
    },
    "myelinize": {
      "description": "Record repeated raw-shell sequences as myelin candidates and suggest promotion.",
      "input": {
        "project_root": {"type": "string", "required": false},
        "command": {"type": "string", "required": true, "description": "Repeatable input; operation may be repeated"},
        "dry_run": {"type": "boolean", "required": false, "default": false}
      },
      "output": {"description": "Candidate result", "fields": {"status": "ok | error", "candidate": "object"}},
      "entrypoints": {"unix": ["python3", "scripts/physiology.py", "myelinize"], "windows": ["python", "scripts/physiology.py", "myelinize"]}
    },
    "boot-profile": {
      "description": "Render or refresh opencode-compatible portable boot/profile templates.",
      "input": {
        "project_root": {"type": "string", "required": false},
        "dry_run": {"type": "boolean", "required": false, "default": false}
      },
      "output": {"description": "Boot-profile result", "fields": {"status": "ok | error", "path": "string"}},
      "entrypoints": {"unix": ["python3", "scripts/physiology.py", "boot-profile"], "windows": ["python", "scripts/physiology.py", "boot-profile"]}
    },
    "export": {
      "description": "Export the portable physiology scaffold for reuse in another project.",
      "input": {
        "project_root": {"type": "string", "required": false},
        "output": {"type": "string", "required": true},
        "dry_run": {"type": "boolean", "required": false, "default": false}
      },
      "output": {"description": "Export result", "fields": {"status": "ok | error", "output": "string"}},
      "entrypoints": {"unix": ["python3", "scripts/physiology.py", "export"], "windows": ["python", "scripts/physiology.py", "export"]}
    },
    "anatomy": {
      "description": "Initialize, scan, classify, doctor, project, and drift-check anatomy sidecars with class-specific gates.",
      "input": {
        "action": {"type": "string", "required": true, "description": "init | scan | classify | doctor | project | drift-check"},
        "project_root": {"type": "string", "required": false},
        "skills_root": {"type": "string", "required": false, "description": "Path to skills directory; auto-detected if omitted"},
        "dry_run": {"type": "boolean", "required": false, "default": false},
        "json": {"type": "boolean", "required": false, "default": false}
      },
      "output": {
        "description": "Anatomy sidecar result, classification map, doctor report, projection result, or drift check.",
        "fields": {"status": "ok | error", "skills": "object", "warnings": "array", "latency_ms": "number", "written": "array", "diverged": "array", "drift_free": "boolean"}
      },
      "entrypoints": {"agent": "Run python3 scripts/physiology.py anatomy <action> [flags]"}
    }
  },
  "stdout_contract": {
    "last_line_json": true
  }
}