To modify the Siebel application, you would need to edit the object definitions that make up the repository file.

Option A is incorrect because application engines are used to process data and perform complex business logic. They are not used to modify the Siebel application.

Option B is incorrect because stored procedures are used to encapsulate SQL statements for reuse and improve performance. They are not used to modify the Siebel application.

Option C is incorrect because SQL statements are used to query and manipulate data in a database. They are not used to modify the Siebel application.

Option D is correct because the Siebel repository file is made up of object definitions and these object definitions are edited to modify the Siebel application.

Therefore, the answer is: D. Edit object definitions that make up the repository file.