By default, IkiWiki will leave any existing files in the destination directory alone.

In some circumstances (a force push being one), files that IkiWiki did once generate can be left behind in the destination directory if it no longer does.

Since IkiWiki generates a list of all destination file paths that it is responsible for, a plugin (armed with that knowledge) could identify the files it isn't responsible for, too, and clean them up. This would be useful if the user wishes to keep a 1:1 correspondence between source and destination directories. —Jon, 2021-02-07