skill-system-pgysiology

⚠️ ARCHIVED — Typo Compatibility Only

skill-system-pgysiology is a historical typo path. The canonical skill is skill-system-physiology.

• Do not add new features here.
• Do not fix bugs here — fix them in skill-system-physiology.
• This directory is retained only for backward compatibility with references that used the typo name.
• Ratification: .tkt/decisions/sk-physiology-classification-ratified-2026-04-14.md

Original Description (superseded)

skill-system-pgysiology was the operational biology layer for agent systems.

Organ Map

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

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

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

Commands

python3 scripts/pgysiology.py init --project-root /tmp/new-project
python3 scripts/pgysiology.py scan --project-root /tmp/new-project --repair
python3 scripts/pgysiology.py pain-log --project-root /tmp/new-project --type amnesia --summary "missing context"
python3 scripts/pgysiology.py myelinize --project-root /tmp/new-project --command "tmux send-keys -t pane hi" --command "tmux send-keys -t pane hi"
python3 scripts/pgysiology.py boot-profile --project-root /tmp/new-project
python3 scripts/pgysiology.py export --project-root /tmp/new-project --output /tmp/portable-pgysiology

{
  "schema_version": "2.0",
  "id": "skill-system-pgysiology",
  "version": "0.1.0",
  "capabilities": ["pgysiology-init", "pgysiology-scan", "pgysiology-pain-log", "pgysiology-myelinize", "pgysiology-boot-profile", "pgysiology-export"],
  "effects": ["fs.read", "fs.write"],
  "operations": {
    "init": {
      "description": "Bootstrap a portable pgysiology 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/pgysiology.py", "init"], "windows": ["python", "scripts/pgysiology.py", "init"]}
    },
    "scan": {
      "description": "Scan a project root for pgysiology 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/pgysiology.py", "scan"], "windows": ["python", "scripts/pgysiology.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/pgysiology.py", "pain-log"], "windows": ["python", "scripts/pgysiology.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/pgysiology.py", "myelinize"], "windows": ["python", "scripts/pgysiology.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/pgysiology.py", "boot-profile"], "windows": ["python", "scripts/pgysiology.py", "boot-profile"]}
    },
    "export": {
      "description": "Export the portable pgysiology 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/pgysiology.py", "export"], "windows": ["python", "scripts/pgysiology.py", "export"]}
    }
  },
  "stdout_contract": {
    "last_line_json": true
  }
}