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13 across: Leaf essence maybe cloves, in retrospect? (5)
15 across: Dr Watson's companion's a pain in the neck. (5)
16 across: Bomb over Shetland's interior cleared area to the cape. (7)
6 down: One opposes the Republican side in the Civil War. (8)

15a Crick ? - Nobel prize-winner with Watson

Many thanks Siamcat. I didn't know about the Nobel connection.

6d Royalist ?

Thanks Joker. If I am correct in what I have in already, it should be ?n?o????. Royalist would certainly appear to make more sense.

I think the answer here is UNIONIST,the civil war being the conflict in the "occupied" territory in the North of Ireland.
Do you smoke St Bruno in your pipe as I do?

Brilliant. Thanks, Joker. I have tried St Bruno, among many others, but I always seem to come back to Condor. Despite the exhortations of spouse and doctor, I have no intention of giving up my pipe. We seem to be a dying breed.

Thanks again.

With Unionist in place, the letters available for the remaining clues are:

Leaf essence maybe cloves, in retrospect? ?o?i?
Could this be folic?
Bomb over Shetland's interior cleared area to the cape. ?o?e?t?

MOZETTA is a cape but I haven't figured out the wordplay (if correct)

mozetta is correct. Bomb = atom (turn that over and insert zet)
old spelling for shetland is Zetland..get rid of the area (land) and you have Zet.