Can I move deployment scripts?

Yeah, revert to the change before it, then edit sqitch.plan and move the file where you want it. So if you wanted to move deploy/widgets.sql into deploy/tables/widgets.sql, you'd first revert (assuming your'e doing dev, not production):

sqitch revert --to widgets^

Move the file and change the name in the sqitch.plan file from widgets to tables/widgets (always a slash, regardless of your OS or file system). Then you can sqitch deploy and be back in business.

from issue #76.