As an ontologist, I probably should have known better and got this right in the first place. I have changed Ontogenesis to use semantic-free identifiers. From initial testing, it appears that WordPress is doing-the-right-thing. The old permalinks redirect to the right place, and internal links have been automatically updated. So, it should work from inside and outside, but please let me know if it is broken anywhere.
The motivation for this came from two sources. First, some one suggested that I change the name of my article; the suggestion was a good suggestion, but I started to worry that it would make my permalink out-of-date. Second, Duncan Hull decided to shorten the permalink for his article. Perfectly sensible but, again, this caused some consternation as it broke the implied semantics.
Bottom line, here, is that semantics free identifiers seemed like a sensible way to go. The flip side is, of course, that they are a little harder to remember, and there is more chance of error when inserting them in text, because you can’t tell whether it’s the right link or not. However, this is also true if articles change during review so that the implicit semantics in the link are wrong.
There isn’t really a way to square this circle. Comments welcome.