Answer: I would leave the garden plot as is; the rye may yet emerge. Did you test your soil, and determine that it needs lime? If so, then you don't want to neutralize its effect--which is good because I can't think of an easy way to do so. If it's only been a week or 10 days since you planted, I would just be patient. If it's been longer, try reseeding and covering the area with a thin layer of straw or perhaps some floating row cover. I'm wondering whether by chance birds have been eating the seed and plucking up the new shoots.
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