Answer: It's best for the roots not to add more than a few inches of soil over them. The feeder roots can suffocate if you add more than about 3" of soil. Can you arrange the stones around the tree and then add just enough soil behind the stones to accommodate your annuals and perennials without spreading the new soil all the way to the trunk of the tree? If you do this now and then next spring add an inch or two of soil, repeating over a period of a few years, it might be easier on the tree's roots.
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