I suggest getting consensus with your colleagues that the application needs changing and that the new organization is a better one and will be easier to work with and save time for everyone, not just for you. That should be combined with assurance that there will be a last version of each deleted module that just says "this module's functions moved to ... in a July 2006 re-org of the pieces.", and a comment on new modules saying "taken from a re-write of ... for clarity and a cleaner organization". This is what Grandfather suggested in the first response, and it should establish that a history of the old structure will be kept intact, with pointer to the knew structure where people can find it.

The buy-in from others is important, since they have to fix or find things in the app when you are on vacation, and your manager is supposed to be thinking about this. It should allay any concerns about ending up with code that may be clear and well organized, but which only one person can find their way around easily.

If that doesn't convince your manager, then it may be a "Do we delay now for a better future?", type of resource allocation question, as Tanktalus suggests, or he's just too short-sighted and narrow-minded as you suspect. (For purposes of discussion, we assume that you're the one that's wiser and better informed, since you're the monk and you're the one we're talking to.)

Good Luck