A couple days ago I made mention of a bug that I found in functions-formatting.php regarding how bare urls are filtered. Ryan B verified it exists this morning.
I've supplied a working fix to trac, and since it is minor for the devs but a major issue for those of us that like valid sites, I thought I would point out the code change.
It's available here:
I actually tried to make a simple plugin that disabled the standard make_clickable and instead used this new function. No luck.
If anyone wants to try, feel free, but for now, here is the code for anyone comfortable with doing some simple editing.