VaultingFrog:

Harvest wasnt completely glass as already mentioned. The only reason why (that I can think of) that the Covenant didnt glass the entire planet is because of the Tiara. Under the guidence of the Rouge AI "Mack" the JOTUNs buried the strands from the Tiara after they had fallen from orbit. The Tiara itself is gone (most of it anyways) and what little of it remained fell to Harvest with the strands.

Since its looks were similar to that of a Halo ring the Covenant probably thought it was a holy relic from the Forerunners (yes its mentioned in the book but the continuation of that belief isnt in there) and were not inclined to destroy it. Therefore they probably didnt glass the entire planet in an attempt to preserve the Tiara or what was left of it. The actual glassing happend to "purify" the planet for reclemation of the Tiara. 

mistake there it wasnt completely glassed if you read contact harvest there was only one ship to glass it. when cole's fleet got there there was only one fleet to attack they lost 2 out of the 3 that they had. but if you read the ending of contact harvest it says that mack was still on harvest(for you who dont remember mack he was the AO-AI or agriculteral operations AI.) he hid. and it says he was trying to hide from the covies but they would find him soon enough. it was in the very back of the book.

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