I'm pretty sure there have been some slight changes to Sigil's prettify (and some whitespace preservation changes in mend) since the last push to the User Guide repo. That might explain some of the changes. Or maybe we've not followed our own instructions for running mend & prettify for quite a while when pushing changes. I'll let Kevin speak to what the Folder In/Folder Out process may have contributed.
For small focused changes, I just tend to make direct edits to files in the git repo rather than using Sigil. That way I can use git --difftool --dir-diff to see what changed before committing them. But that involves installing/configuring a difftool for git. I use the cross-platform Meld program on Linux and Windows.
Can you share your github repo so we can see the changes before an Pull Request gets made? That way we might be able to determine whether it's a lot of changes due to pretty-print/mend changes? If so, they will probably make it into the official repo at some point anyway.
TL;DR: I don't think you did anything wrong.
