When wanting to upgrade from 1.2 to 1.2.1 I had the problem that I'd made lots of modifications to various files which would be lost if I did the upgrade. The instructions say not to overwrite files you've modified: but then you don't get the updates do you?
So I've thrown together a diff between the two versions which will allow you to update only the files which have actually changed between the two versions without (in most cases) losing any modifications you've made.
I should point out that this is for Linux/UNIX users who know how to use the patch command.
This worked fine for updating my installation, but that doesn't mean it won't trash yours. Use it entirely at your own risk and backup your files first!