Clearer Build pane
In the help page "Build Pane" page, perhaps a bit more explanation of the relationship between the markdown and HTML files.
After experimenting, I think this is how it works (of course you know for sure!):
"Generate Markdown" creates the .txt file. "Edit Markdown" edits the .txt file. "View HTML" creates a .htm file from the .txt file. "Create e-book" creates the e-book from the .txt file, via a re-created .htm file.
Thus, and this is the important part, any manual edits to the HTML file will not only be ignored, they will be over-written and lost.
Perhaps a note about that in the "A few things to know" section.