1. Scrivener
You know this. Just go and buy it already.
Lots of writers feel this way about it. If you do a web search on “scrivener is the best”, you get a lot of responses, all of which you can investigate on your own free time.
The short version: Word (or even Pages) is a word processor, most often used as a WYSIWYG layout tool — not as powerful as a dedicated layout application, but what you see on screen affects what comes out when you print. Scrivener is an application for writing: how you lay the text out on screen as you write has nothing to do with what comes out the other end. I just concentrate on the writing. I can have one file for my entire book. Or, I can have each chapter in a separate text file. Or, I can have folders represent each chapter, and multiple text files in each chapter folder. And I can easily navigate the entire book through the binder, which is the main window.
Index cards! Folders for all my research! Click-and-drag to rearrange entire chapters! FULL SCREEN! (Ulysses had this feature first, but Scrivener really did a boss job with it.)
When it comes to publishing books, Scrivener is even more awesome: with a little bit of work on your part, Scrivener can easily (and I do mean easily) generate .epub, .mobi, .pdf — whatever files you need. You don’t need to follow any tricky “nuclear option” formatting solutions. You don’t need to fight with Word’s problems with Kindle, which has led to some books having seriously messed up formatting. Scrivener puts it together for you. Don’t fight the power. Let the power work for you.
2. Scapple
Well, okay, I’ll be honest: I haven’t used this much. Mindmapping isn’t a thing I’ve managed to make work for me yet. But I’m a total Scrivener fangirl and if it’s software from Scrivener’s developer, that’s good enough for me: shut up and take my money!
Holy crap, I am finding this so useful. Aeon Timeline allows you to make a timeline (duh) using our known calendar or a custom calendar format that you set up (like, for a fantasy world).
How am I using this? Well, I have one document named “Drusilla.” I have the General timeline, that has all of the events of her life, many of which I make up on the spot but then need to keep referring back to. I have the YKWIA timeline, which is a subset of the General timeline and has all of the events of that book written into it. I have the timeline for the new book: what happens when?
Aeon Timeline figures out how old Drusilla and Stevie are for each of these events. It can calculate how long it’s been between events. I can keep track of locations, names, and length of time. Which characters were where at which time of their lives.
Until such time as I can hire an assistant to do nothing but comb my stuff for continuity, this will have to do.
4. WriteRoom
Distraction-free writing for iOS and Mac. Which means: no bells and whistles. Minimal styles. If I’m on the go somewhere, I can write in there and then use DropBox to transfer to my Mac, where I can pop the text into Scrivener easily. Other writers like iA Writer, Writing Kit, or Daedalus (from the guys who brought you Ulysses).
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I have but don’t use Index Card for iOS, mostly because Scrivener has its own index card system.
Any other software I ought to know about?