Table of Contents issue

My current project has the following file hierarchy.

Level 1 Folders: Part names
Level 1 docs: Title page, about the author, etc.
Level 2 Folders: Chapter names
Level 3 docs: individual scenes

This was to make it easier to move scenes around and reorganize chapters. However, when I compile to epub or mobi, it creates the Table of Contents with individual entries for each scene.

That’s a lot of entries, and not terribly useful to the reader.

Is there a way to leave the level three doc titles out of the generated ToC, or will I have to manually recombine them into single Chapter-length docs before I compile?

The key thing here is “page breaks” as defined in the Separators pane. These are what determine whether something becomes a visible section in the ToC. So for your layout, I would recommend making sure adjoining text files do not generate a page break universally. For those files that need it, like the title page, you can manually click the checkbox in the Inspector.