refactor: reorganize models into subpackages

Move models into domain subpackages (max 4 files each):
- models/tool/ — tool_type, tool_instance, tool_definition_manifest
- models/config/ — config_profile
- models/user/ — user, user_config, ssh_key
- models/project/ — project, git_repository, workspace
- models/system/ — health_check, notification, instance_event, terminal_session

models/__init__.py continues to re-export all symbols, so consumers
using 'from src.models import X' are unaffected. Updated direct file
imports across the backend to use the new paths.

Quality gates: py_compile passed, ruff passed.

apps/api/src/models/system/notification.py

@@ -0,0 +1,43 @@
+"""Notification SQLAlchemy model."""
+
+from datetime import datetime
+from typing import Any
+import uuid
+
+from sqlalchemy import DateTime, ForeignKey, JSON, String, Text
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column
+from sqlalchemy.sql import func
+
+from src.models.base import Base, UUIDPrimaryKeyMixin
+
+
+class Notification(UUIDPrimaryKeyMixin, Base):
+    __tablename__ = "notifications"
+
+    user_id: Mapped[uuid.UUID] = mapped_column(
+        UUID(as_uuid=True),
+        ForeignKey("users.id", ondelete="CASCADE"),
+        nullable=False,
+        index=True,
+    )
+    category: Mapped[str] = mapped_column(String(32), nullable=False)
+    severity: Mapped[str] = mapped_column(String(16), nullable=False)
+    title: Mapped[str] = mapped_column(String(255), nullable=False)
+    message: Mapped[str | None] = mapped_column(Text, nullable=True)
+    source_type: Mapped[str | None] = mapped_column(String(64), nullable=True)
+    source_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(as_uuid=True), nullable=True
+    )
+    notification_metadata: Mapped[dict[str, Any]] = mapped_column(
+        "metadata", JSON, nullable=False, default=dict
+    )
+    read_at: Mapped[datetime | None] = mapped_column(
+        DateTime(timezone=True), nullable=True, index=True
+    )
+    dismissed_at: Mapped[datetime | None] = mapped_column(
+        DateTime(timezone=True), nullable=True
+    )
+    created_at: Mapped[datetime] = mapped_column(
+        DateTime(timezone=True), server_default=func.now(), nullable=False, index=True
+    )