Say my account is an app, I would publish a not that looks like this…

*****
Version 1.0

File 1 @nevent000001…
File 2 @nevent000002…
File 3 @nevent000003…

[…]
*****

Then say I modify the code base (I only change file 2), I publish a new note that looks like this…

*****
Version 1.1

File 1 @nevent000001…
File 2 @nevent000017…
File 3 @nevent000003…

[…]
*****

I have modified file 2 and so I just publish a version 1.1 note from the account with the modified code note included as a link.

For users to update their software they just lookup the nostr account, find the latest published version note and retrieve each of the file notes.