not2easy - 7:30 pm on Sep 17, 2012 (gmt 0)
http://www.example.com/subdirectory/index.html would give you a 404 since I replaced it with index.php
http://www.example.com/subdirectory/index.php would let you see a page with nothing on it but a nofollowed link to the right page. It has not been indexed, anyone coming to that page is playing with the URL.
Index.php to the subdirectory URL and both pages are/were noindexed.
If I were to rename the what-is-here.html pages I would need to rewrite all the navigation for the site and every link on the site would use a redirect.
Subdirectory pages only have links to the home page and the what-is-here.html page for that subdirectory but I prefer not to have every link require a redirect. Ideally I would have thought much more prior to making these changes, but I had 4 days notice that all links had been changed and would cease to function when I rebuilt the site. All I wanted to do was to remove the subdirectory URLs from the sitemap, they were not indexed anyway, I imagine because #G found nothing to index at that URL. I do realize that your recommendation is Best Practice, I can redo the site a section at a time and do it without redirects now that I have taken care of inviting the unused URLs to be crawled.