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/project/git_repository.py

@@ -0,0 +1,33 @@
+import uuid
+from datetime import datetime
+from typing import TYPE_CHECKING
+
+from sqlalchemy import Boolean, DateTime, ForeignKey, String
+from sqlalchemy import Uuid as UUID
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
+from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
+
+if TYPE_CHECKING:
+    from src.models.project import Project
+    from src.models import SSHKey
+    from src.models.user import User
+
+
+class GitRepository(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "git_repositories"
+
+    name: Mapped[str] = mapped_column(String(255))
+    path: Mapped[str] = mapped_column(String(1024))
+    project_id: Mapped[uuid.UUID | None] = mapped_column(UUID(), ForeignKey("projects.id"), nullable=True)
+    owner_id: Mapped[uuid.UUID] = mapped_column(UUID(), ForeignKey("users.id"), nullable=False)
+    is_mirror: Mapped[bool] = mapped_column(Boolean, default=False, nullable=False)
+    remote_url: Mapped[str | None] = mapped_column(String(1024), nullable=True)
+    last_push: Mapped[datetime | None] = mapped_column(DateTime(timezone=True), nullable=True)
+    ssh_key_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(), ForeignKey("ssh_keys.id"), nullable=True
+    )
+
+    project: Mapped["Project"] = relationship(back_populates="repositories")
+    owner: Mapped["User"] = relationship()
+    ssh_key: Mapped["SSHKey | None"] = relationship()