WGET does not move base html files into subfolders. Using archive as an example, both /archive and /archive/2018 are valid links, and WGET will save them as /archive.html and /archive/2018.html. However, going to /achive will open up /archive/ rather than /archive.html.
After the WGET is run from the generate_website script, there should be additional scripts that will iterate over directories and if it finds an html file with the same name as that directory, it should move that file into the directory and rename it to index.html.
WGET does not move base html files into subfolders. Using archive as an example, both /archive and /archive/2018 are valid links, and WGET will save them as /archive.html and /archive/2018.html. However, going to /achive will open up /archive/ rather than /archive.html.
After the WGET is run from the generate_website script, there should be additional scripts that will iterate over directories and if it finds an html file with the same name as that directory, it should move that file into the directory and rename it to index.html.