On some packages I use they provide insert points for additional code.

So they have a check for 'userfunctions.php' at the top of the main code

then at handy points an include with exist check for a named php file.

So that for example when you want to add extra fields you could simply write the code to a userfile for each master and it would be included automatically.

This means on new releases most changes will move up smoothly to the new release.