I don’t understand why WordPress upgrades are only provided as a zip/tgz of the entire thing. Upgrades could be made significantly smaller and easier if incremental patches were provided, especially for security releases. You could have upgrade.php run the patch for those without shell access.
Those with a heavily modified installation would first need to take a diff -ur of their files against the stock WordPress of their current version, reverse apply it (or just reinstall the stock), then apply the upgrade patch, then reapply their modification patch. It shouldn’t be rocket science to do most of that automatically too, even down to fetching the full tgz of the current version as required. The system as it stands is needlessly painful.
As a start, I’ve made some patches for the latest upgrade and the one before. If you have shell access (and it’s a unix box) you can apply them by copying the patch file to your wordpress root, cd there, and type patch -p1 <wordpress-xxx-to-xxx.patch
Both patches applied cleanly on my system, but your mileage may vary and no warranty, so I strongly advise you take backups before doing this.
