This is a age old problem, I try to address it in my platform, this was inspited by the way Flamerobin, does the DDL extract, create procedures / then later alters them with actual content, to avoid inter dependencies.

The main pain point is, referral integrity, is not catered for yet, it would make it a lot more complex.

It does things like optionally reordering columns to match, adding or removing defaults...

Don't run on production databases without backups and careful testing.

https://github.com/quale-quest/sql-mvc/blob/master/server/database/db_fb_sql_updater.js