I think IDEs are missing some project management tools that would make it easier to keep track of stuff. At least the community version of Visual Studio and also Code::Blocks, although I'm using mainly VS to code. I'm so desperate that I'm probably just going to list the files and put them into a spreadsheet, so I can mark them with different colors depending on what state it is. That way you could fix files from least to most important, at least that's the plan.
When I get back to this project I'm always astonished by it, because it should not be that difficult to handle, really. But for some reason it is. It must be just the amount of files and places that need fixing, there is always something to fix, mostly a result of bad planning. Then again, you can't create good plans if you don't know how to plan something that works.
I see this problem in other roguelike source codes I'm working on, like Legend of Saladir. You can just see how the developer got deeper into problems of everything falling apart and then gave up. I believe firm project management would help, but the tools that we have for that are surprisingly primitive. Or maybe I have missed some great, possibly free, project management software. Most likely.