I'm seeing a lot of comments here along the lines of "this is just a problem Java newbies would have and this Tim Bray guy, whoever he is, doesn't want to take the time to learn the tools."
Well. True, to a degree, I suppose, but whoever this Tim Bray guy is adds some pretty important context. He co-authored the XML spec and was director of web technologies at Sun. You know, the people who made Java and promoted it as a web technology. Going out on a limb here, but it doesn't seem to me that the man is a Java newbie.
The point of Bray's rant, I'd suggest, is that these tools largely haven't gotten any easier since 2004. It frequently seems to be controversial in these parts to assert that it's worthwhile to make developer tools easy to use ("what you're complaining about is obviously easily addressed by whipping together something with bash, awk and sed and therefore isn't a pain point at all, you whiner"), which has always vaguely irritated me. A toolchain which requires you to wrangle it into place for every project is a toolchain which could benefit from usability improvements.