fix(alembic): make tool_instances.clone_mode nullable

The workspace-first cleanup removed clone_mode from the creation flow,
so the API now inserts NULL. Align the database with the model by
making clone_mode nullable.

Apply with: cd apps/api && alembic upgrade head

apps/api/alembic/versions/2026_06_13_make_clone_mode_nullable.py

@@ -0,0 +1,35 @@
+"""make clone_mode nullable
+
+Revision ID: 2026_06_13_make_clone_mode_nullable
+Revises: 86cec91fdb00
+Create Date: 2026-06-13 10:00:00.000000
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision = "2026_06_13_make_clone_mode_nullable"
+down_revision = "86cec91fdb00"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # The workspace-first cleanup no longer writes clone_mode; existing rows
+    # keep their value, but new rows may be NULL.
+    op.alter_column(
+        "tool_instances",
+        "clone_mode",
+        existing_type=sa.String(20),
+        nullable=True,
+    )
+
+
+def downgrade() -> None:
+    op.alter_column(
+        "tool_instances",
+        "clone_mode",
+        existing_type=sa.String(20),
+        nullable=False,
+    )