Scrivener
I don’t have much experience with Scrivener thus far, but I’ve met people who take a lot of the things I’ve been talking about and include them in the Scrivener files for their stories. I’ve done this some. I can take the maps, location sheets, character sheets, pictures, and timelines and include them all in one convenient place.
Honestly, I think it confuses me more than helps me because I can’t keep everything separate, but for some people, it works great.