Added soft deletes to all deletion functions and added deleted_at filters as required

gatehouse_app/services/auth_service.py

@@ -36,9 +36,9 @@ class AuthService:
         Raises:
             EmailAlreadyExistsError: If email is already registered
         """
-        # Check if email already exists
-        existing_user = User.query.filter_by(email=email.lower()).first()
-        if existing_user and existing_user.deleted_at is None:
+# Check if email already exists
+        existing_user = User.query.filter_by(email=email.lower(), deleted_at=None).first()
+        if existing_user:
             raise EmailAlreadyExistsError()
 
         # Create user
@@ -280,12 +280,11 @@ class AuthService:
             raise ConflictError("TOTP is already enabled for this account")
 
         # Clean up any existing unverified TOTP enrollment attempts
-        # Use hard delete for unverified methods since they're incomplete enrollment attempts
+        # Soft delete for unverified methods since they're incomplete enrollment attempts
         existing_totp_method = user.get_totp_method()
         if existing_totp_method and not existing_totp_method.verified:
             logger.debug(f"Removing existing unverified TOTP method for user {user.id}")
-            db.session.delete(existing_totp_method)  # Hard delete - unverified methods are temporary
-            db.session.commit()  # Commit to ensure deletion before creating new record
+            existing_totp_method.delete(soft=True)  # Soft delete - unverified methods are temporary
 
         # Generate TOTP secret
         secret = TOTPService.generate_secret()