I recently upgraded my WordPress installation (it was way way way out of date) and I thought it was weird that my old plugins weren’t showing up after the upgrade. It turns out that when I tell Transmit, the most convenient mac ftp application that I’ve found to date, to replace a folder, it deletes the old one and replaces all of it’s contents with the folder I’m uploading. This makes perfect sense in terms of the english language, but it’s not at all how I expect things to work based on years of ftp experience. In Transmit, if I want leave subfolders and files that aren’t on my local copy, I have to choose merge. Lesson: be careful with “apply to all” check boxes when playing with new software.