Currently there is the option in Geany to clean up whitespace characters at the end of lines. However, many people and projects prefer to leave empty lines with the correct indent. Unfortunately this means that clean spaces can't be used as it removes all of these spaces. It would be nice to be able to prevent the cleaning of empty lines, or if the proper indent could be put there. I think the first option is quite sufficient as the second has a large chance for error.
Okay, I have updated the pull request with the docs. I didn't regenerate the manual because it seems like you guys just do that every once and a while.