So far, I have not been able to recreate what @philja is experiencing. I've tried to duplicate as close as possible the steps they took and the changes they made. I'm using the latest version of Sigil (on Linux) and the latest versions of the FolderIn/FolderOut plugins
- I have an up to date clone of the sigil-user-guide repository
- I use the FolderIn plugin to load the guide's source into a new epub in Sigil
- I make the same modification @philja did to the tutorial_find_replace.xhtml file (using Sigil's Code View)
- I run Mend and Prettify on that one file
- I delete the saved-searches-find-replace-context-menu.png file and add a different image with the same name (using Sigil's Delete and Add Existing tools from BookBrowser)
- I make the same two modifications @philja did to the tutorial_regex_reference.xhtml file (using Sigil's Code View)
- I run Mend and Prettify on that one file
- I use the FolderOut plugin to write the the epub's src back to the sigil-user-guide repository
Using the git command line in the sigil-user-guide repository, git status shows me 4 files have been modified:
- the saved-searches-find-replace-context-menu.png file (binary diffs not shown)
- the content.opf file
- the tutorial_find_replace.xhtml file
- the tutorial_regex_reference.xhtml file
git diff shows me the very minimal changes to those two xhtml files and the content.opf file that I would expect.
My first question would be which platform (Windows, Linux, macOS) are you using to do this?
My second would be how exactly are you making theses edits? Are you manually editing in Sigil's Code View, or are you using external editing tools? Are you making the simple edits your diffs show, or are you copy/pasting larger swathes of code (or possibly whole file contents)? Are you copy/pasting anything into the sigil-user-guide repository at a file system level, or is everything being done from within Sigil?
P.S. I did a Mend & Prettify on the entire epub just as a test and the results were no different.