It's easiest to leave the file where it is so it is ready to use when it is needed. Taking out the file and the associated build task adds more complexity when it comes time to use. Much easier to tell them to edit this file then add this script reference rather than telling them where to create the file, how to name it, how to add the build tasks and then how to add the script references.

Another option could be to include the script reference but make it conditional so it is only loaded when a certain condition is met (e.g., set a variable to true in sir.json). That would be much cleaner and easier for users than the other two approaches.