Simplify code documentation, remove organism terminology

- Remove biological metaphors from docstrings (organism, sensory, genetic, nutrient, etc.)
- Simplify documentation to be minimal and structured for fast model parsing
- Complete SQLite to JSON storage migration (project_manager.py, json_store.py)
- Add Integrations and IntegrationHealth classes to json_store.py
- Add kill_port() function to server.py for port conflict handling
- All 33 tests pass

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

tools/storage/json_store.py

@@ -960,6 +960,164 @@ class TokenDrift:
         return None
 
 
+# === Integrations ===
+
+class Integrations:
+    """Project integration configuration storage."""
+
+    @staticmethod
+    def _integrations_path(project_id: str) -> Path:
+        return PROJECTS_DIR / project_id / "integrations.json"
+
+    @staticmethod
+    def list(project_id: str, user_id: int = None) -> List[Dict]:
+        """List integrations for a project."""
+        data = read_json(Integrations._integrations_path(project_id), {"integrations": []})
+        integrations = data.get("integrations", [])
+
+        if user_id is not None:
+            integrations = [i for i in integrations if i.get("user_id") == user_id]
+
+        return integrations
+
+    @staticmethod
+    def get(project_id: str, user_id: int, integration_type: str) -> Optional[Dict]:
+        """Get specific integration."""
+        integrations = Integrations.list(project_id, user_id)
+        for i in integrations:
+            if i.get("integration_type") == integration_type:
+                return i
+        return None
+
+    @staticmethod
+    def upsert(project_id: str, user_id: int, integration_type: str,
+               config: str, enabled: bool = True) -> Dict:
+        """Create or update integration."""
+        path = Integrations._integrations_path(project_id)
+        data = read_json(path, {"integrations": []})
+        now = datetime.utcnow().isoformat()
+
+        # Find existing
+        for i in data["integrations"]:
+            if i.get("user_id") == user_id and i.get("integration_type") == integration_type:
+                i["config"] = config
+                i["enabled"] = enabled
+                i["updated_at"] = now
+                write_json(path, data)
+                return i
+
+        # Create new
+        new_integration = {
+            "id": str(uuid.uuid4())[:8],
+            "project_id": project_id,
+            "user_id": user_id,
+            "integration_type": integration_type,
+            "config": config,
+            "enabled": enabled,
+            "created_at": now,
+            "updated_at": now,
+            "last_used_at": None
+        }
+
+        data["integrations"].append(new_integration)
+        write_json(path, data)
+        return new_integration
+
+    @staticmethod
+    def update(project_id: str, user_id: int, integration_type: str,
+               config: str = None, enabled: bool = None) -> Optional[Dict]:
+        """Update integration fields."""
+        path = Integrations._integrations_path(project_id)
+        data = read_json(path, {"integrations": []})
+
+        for i in data["integrations"]:
+            if i.get("user_id") == user_id and i.get("integration_type") == integration_type:
+                if config is not None:
+                    i["config"] = config
+                if enabled is not None:
+                    i["enabled"] = enabled
+                i["updated_at"] = datetime.utcnow().isoformat()
+                write_json(path, data)
+                return i
+
+        return None
+
+    @staticmethod
+    def delete(project_id: str, user_id: int, integration_type: str) -> bool:
+        """Delete integration."""
+        path = Integrations._integrations_path(project_id)
+        data = read_json(path, {"integrations": []})
+
+        original_len = len(data["integrations"])
+        data["integrations"] = [
+            i for i in data["integrations"]
+            if not (i.get("user_id") == user_id and i.get("integration_type") == integration_type)
+        ]
+
+        if len(data["integrations"]) < original_len:
+            write_json(path, data)
+            return True
+        return False
+
+
+class IntegrationHealth:
+    """Integration health tracking."""
+
+    @staticmethod
+    def _health_path() -> Path:
+        return SYSTEM_DIR / "integration_health.json"
+
+    @staticmethod
+    def list_all() -> List[Dict]:
+        """List all integration health status."""
+        data = read_json(IntegrationHealth._health_path(), {"health": {}})
+        return [
+            {"integration_type": k, **v}
+            for k, v in data.get("health", {}).items()
+        ]
+
+    @staticmethod
+    def get(integration_type: str) -> Optional[Dict]:
+        """Get health for specific integration."""
+        data = read_json(IntegrationHealth._health_path(), {"health": {}})
+        if integration_type in data.get("health", {}):
+            return {"integration_type": integration_type, **data["health"][integration_type]}
+        return None
+
+    @staticmethod
+    def update(integration_type: str, is_healthy: bool = True,
+               failure_count: int = None, circuit_open_until: str = None) -> Dict:
+        """Update integration health."""
+        path = IntegrationHealth._health_path()
+        data = read_json(path, {"health": {}})
+
+        if integration_type not in data["health"]:
+            data["health"][integration_type] = {
+                "is_healthy": True,
+                "failure_count": 0,
+                "last_failure_at": None,
+                "last_success_at": None,
+                "circuit_open_until": None
+            }
+
+        now = datetime.utcnow().isoformat()
+        data["health"][integration_type]["is_healthy"] = is_healthy
+
+        if is_healthy:
+            data["health"][integration_type]["last_success_at"] = now
+        else:
+            data["health"][integration_type]["last_failure_at"] = now
+
+        if failure_count is not None:
+            data["health"][integration_type]["failure_count"] = failure_count
+
+        if circuit_open_until is not None:
+            data["health"][integration_type]["circuit_open_until"] = circuit_open_until
+
+        write_json(path, data)
+        return {"integration_type": integration_type, **data["health"][integration_type]}
+
+
 # === Stats ===
 
 def get_stats() -> Dict: