GitHub is great for hosting / organizing large projects and helps with version control. I'm working with a team of four developing a Web App, and GitHub is basically a requirement for staying organized.
I challenge you to compare game development to other creative processes.
For example, writing a book.
The Lord of the Rings probably took stacks of thousands of extra papers, concepts, drafts and resources eventually getting edited down into the trilogy we see today.
On the other hand a comic book like Charlie Brown
may or
may not have take a great deal of organization, but is still great. Compare children's books to online puzzle games.
So I think it depends what the game is.. and that depends on what you enjoy playing.
How does game development compare to organizing film / animation projects?
When I make music I tend to focus more on sound design and effects first, then chords and melodies second. But that's just one of my tendencies.
My favorite paintings I've made are usually improvised based off a few initial random strokes on the canvas. However sometimes I imagine a detailed scene in my head and try to stick with it.
Every good game starts in a different place and takes a different path.
I don't think great projects are always going to let you fully wrap your head around them before they're done.
The most important part to me is enjoying what I'm doing, and giving myself a few small goals each day.
I think that's why I like programmers so much, we have the ability to transition between the big picture, and focusing in on little corner for a day.
If your getting bogged down by the big picture right now, try focusing on the fun parts of the project for a while and see where it takes you.