"Under that system, things like polishing and refactoring my code (which can be a valuable use of your time, but I would frequently use them to procrastinate),

"Under that system, things like polishing and refactoring my code (which can be a valuable use of your time, but I would frequently use them to procrastinate), counted equally towards my goals for the day, even if I wasn’t actually making any real progress." ...so set the goal before you start your Pomodo task. That's what I do. I choose something I can get done in say and hour and start the task for an hour and try and get it done during this time. This also gamifies my time, and I have to keep redirecting my focus on the goal. I get shitloads done during this. During my 10 minute break in between, i'll reflect on the task, decide next goal, etc. And repeat.