My initial reaction to these questions was that they are off topic (possibly because of how I first came to them, but that's another discussion), but now I'm not sure. My current feeling (it's been flopping around) is that the first feels more off topic because it focuses on the arXiv. It feels like the most reasonable answer is, "ask someone at the arXiv to do something about it." But the second question is explicitly a clarification of the first one, saying that a client side solution is desired. I think you could get a good answer to the question at Stack Overflow or Super User, but is there a good reason not to have it on MO? If yes, what are the important differences between it an these other questions?
Tools for Organizing Papers?
http://mathoverflow.net/questions/1785/how-do-you-keep-your-research-notes-organized

By the way, once the other thread about these questions cools off and the comment threads are no longer relevant, is there any reason not to merge these two questions?