Function merge 

pub fn merge(
    current_etc_fd: &Dir,
    current_etc_dirtree: &Directory<CustomMetadata>,
    new_etc_fd: &Dir,
    new_etc_dirtree: &Directory<CustomMetadata>,
    diff: &Diff,
) -> Result<()>

Goes through the added, modified, removed files and apply those changes to the new_etc This will overwrite, remove, modify files in new_etc Paths in diff are relative to etc