TODO lists for which I use org mode, but you could use practically anything. I like a text editor for this rather than an app, per se, just because it keeps me in the flow. All you need is a place to jot down what you are planning to do next and to be able to arrange the order.
Usually I'll start with pretty high level ideas. If I have a story I'm working on, I'll put the description of the story in my TODO list. Then I'll think for about 5 minutes about what general things need to get done. I'll order these by some priority (doesn't really matter usually, to be honest). Then I'll start working on the first one.
Normally I need to poke into the code to really see what I have to do. I'll often add a sub-task to my first one that says, "Figure out what to do" or something like that. Then I'll do some exploratory coding for a few minutes. As I discover what needs to get done, I write it down in my TODO.
It's hard at first to stop yourself from just writing code, but pulling yourself back for the 20 seconds or so it takes to write down what you are just about to do can be surprisingly valuable. Don't censor yourself either. It's fine to guess what you need to do and then delete stuff that you realise is unnecessary later. As you are coding, any time you think, "Oh, I'm going to need X", add it to the TODO (again, difficult to train yourself to do it consistently!)
Once you get good at this, in my experience you will be quite interruptible. Any time I get distracted, or unfocussed or lack motivation, I just look at the top think on the TODO and say, "I'm just going to do that top thing". It always pulls me in.
I don't always code like this, but every time I do I'm dramatically more productive. I should always code like this, but... sometimes you want a relaxed day ;-)