Perform a schema check before merge

It also may be possible to put columns in the correct order when using AWK.

Lowering priority due to new method of handling CCK fields. From the documentation:

Prevent CCK fields from unnecessarily changing the content type's table schema by forcing all fields to use their own table. Create a dummy content type (perhaps called field_holder) that will be used for no other purpose, and set permissions on that content type so no one can create any nodes of that type. Then, add every field to that content type as an 'existing field'.

Whenever you add a new field, also add that field to this dummy content type. This will force all fields to store their data in their own table, and allow you to create and delete fields during development and merge those changes with production much easier.
The fields in core for Drupal 7 will be storing their data in individual tables.