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I think it was a lot of things, all at once.What is your guess on partial rot??
The stems were thicker than usual, as the plants were bigger and heartier. So there was more moisture. The outer leaves dried, but I think that helped to seal in the moisture, and the humidity surely didn't help.
I think I have some insect pest as well. They eat their way in, and the mush they leave starts to rot too. The bugs I've seen are tiny little wormy things, pale reddish brown, about a 1/32" in diameter, and about 1/8" long.
I wish I'd checked them a week ago. I trimmed all but about 4" of the stem, and peeled the wrapping leaves off. I have them hanging between the bars of a shelving unit.
Some of the stems seemed ... ickier ... and those I broke the cloves off to check them more closely. A few I will peel and use asap. The clove is good, but the wrapper leaves show signs of going bad soon.