A preliminary action of the prepareGhPages task consists in deleting all files in the target directory (that is, the directory configured using into).
However, this doesn't work as expected: the current implementation creates a list containing the names of the files found in the target directory and then removes the corresponding files found in the root of the gh-pages branch of the repositiory.
Moreover, files in subdirectories of the target directory are ignored.

I will send a PR that fixes this issue.