One of my Tasks customers asked if I had any advice for tracking customizations he makes to Tasks in some organized fashion. I don’t actually customize my software (I use it as it ships), but I do customize WordPress, PunBB, etc. – here is what I do:

Let’s say I want to edit the themes/index.php file of PunBB. I create a folder called ‘punbb-customizations’ (or similar) and a folder inside it called ‘themes’, then I copy the original index.php file into ‘punbb-customizations/themes’ folder. Once I’m happy with my customizations, I then diff the original file and the file with my mods and save the output as index.php.diff in the ‘punbb-customizations/themes’ folder.

That gives me both the original file and the diff of my changes so I can refer back to them when the next version is released and re-apply the changes.