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/project.py

@@ -0,0 +1,31 @@
+import uuid
+from typing import TYPE_CHECKING
+
+from sqlalchemy import ForeignKey, String, Text
+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 import GitRepository
+    from src.models import SSHKey
+    from src.models.user import User
+
+
+class Project(UUIDPrimaryKeyMixin, TimestampMixin, Base):
+    __tablename__ = "projects"
+
+    name: Mapped[str] = mapped_column(String(255))
+    description: Mapped[str | None] = mapped_column(Text, nullable=True)
+    owner_id: Mapped[uuid.UUID] = mapped_column(UUID(), ForeignKey("users.id"), nullable=False)
+    default_ssh_key_id: Mapped[uuid.UUID | None] = mapped_column(
+        UUID(),
+        ForeignKey("ssh_keys.id"),
+        nullable=True,
+    )
+
+    owner: Mapped["User"] = relationship(back_populates="projects")
+    repositories: Mapped[list["GitRepository"]] = relationship(back_populates="project")
+    default_ssh_key: Mapped["SSHKey | None"] = relationship(foreign_keys=[default_ssh_key_id])
+    ssh_keys: Mapped[list["SSHKey"]] = relationship(back_populates="project", foreign_keys="SSHKey.project_id")