Waiting for the answers for battlestarcoind, as it runs on a debian "Xless" and headless server...
I spoke with the dev and the coin control functionality only exists within the qt wallet, which is what I suspected.
Another way to consolidate, if you can't select the inputs, is to try sending a transaction back to yourself for the largest coin amount it will successfully process.
I imagine the most efficient method is if you start by doing a send for half of your balance and, if it fails, reducing it by half again until a transaction does get processed. Although it occurs to me that if you then follow that with another send for the same amount it will simply use the same single input that just arrived from the first transaction. So I think you'll need to increase each subsequent send by slightly less than the sum of (the previous successful transaction)+(the amount that first one was for)
E.G.
If you can send a maximum of 1000BATL in that first transaction you send to yourself, then the second transaction should be for slightly less than 2000BATL and the third one for slightly less than 3000BATL etc. etc.
Let us know how you get on.