no problem. then you will have to go through the classic way. save the documentation for your hacks and every time you upgrade, you must check every file manually. is time consuming but have the same results.

jelsoft upgrades it's software almost every month. if you spend 2hours/month to upgrade your board for 20$/hour (average php tech-troubleshooting charge), that's about 400$/year you save.
i must add that firefly uses this piece of software also and he thinks (i quote) "is a life saver".