I find this is time consuming. I have a project that’s a series of books. I did this to save all my character and location sheets and research in one spot, and also make it easier to check other books in the series for details that affect whatever I’m working on. I now have 3 novels, a novella, a short story, and various bits of marketing material in there.
I have chapter folders, with scenes underneath, anywhere from 1 to 6 scenes. Sometimes I only want to compile 3 chapters of a particular book for my critique group. Other times an entire book.
I may be doing this incorrectly, but is there some way to not have to deselect every file I don’t want, and select every file I do want, one at a time? When I’m in a particular book, when I select a folder with six items in it, all those items should be automatically selected. If I unselect the folder, everything in it should be deselected. As it stands, why do those folders even show up in the compile list,?
So, either I’m doing something wrong, or this is just a not terribly friendly interface, or it was designed for another need in mind. Is there some way to more easily select/deselect items for compilation?
The general idea most certainly was to have one project for one text (book, in your case).
That would make compiling much easier when you want to exclude or include only certain parts. And not only that, it would help getting the project so big it might become sluggish to handle (depending on the hardware). And if you’re using cloud backup there probably is a size limit per file too.
That said, from your point of writing a series it makes perfect sense to keep all the books and their research material (i. e. non-manuscript stuff of whatever kind) in one project.
You still might think about if it is feasible to keep a project for each. For a new book you could copy the whole project of its predecessor and only keep the research material. If the latter gets updated you could copy it back to the other projects to keep each one of them up to date. This could work, at least when the research contains only data and no linking between items.
But if not … there still is the Filter. Tiny icon, huge powers:
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You could set the status of every text chunk of every old book to, say, “Published”. And then you set the filter to exclude every item with the status “Published”.
Instead of that you could use a colour or collections to include or exclude. That will depend on how you are using this features already.
Finding the best possible solution for you might take some playing around. But once you have decided which approach fits your needs most it will be a one-time action and you will not have to tick boxes for every compile process.
To add to @suavito’s advice, I think if you set the following in the options:
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then by clicking on your Chapter folder, all its scene document children will automatically be included in the file list. That way you simply select the chapters you want and set the filter to “Current Selection” and you should be good to go.

Mark
Thank you for the suggestions. I’ll take a look.
I can‘t believe I forgot to mention the probably most simple solution: As Compile only affects the Drafts folder—just move your old books out of it! Into a sub-folder of the Research folder or a new one on the same level as Research and Drafts, call it “Archive”, “Previous Books” or whatever you like.