Stone associated with strata according to plan (3)

I believe the answer is:

gem

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'stone' is the definition.
(gemstone)

I can't explain the rest of the clue.

(Other definitions for gem that I've seen before include "A jewel or precious stone" , "perfect specimen" , "Pleasant and cheerful (from German)" , "36 Across or any other jewel" , "Treasured person" .)

I've seen this clue in the Evening Standard.

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