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For the arrangement of the actual files, I put the index page and the seven level-2-pages into the same folder, the level-3-pages are in one of seven subfolders that have keyword-names.
Now I wondered whether I shouldn't have put all files in the same folder or whether it doesn't matter at all or whether it even helped (keywords in the URL). The names of the html files themselves contain relevant keywords, but do directory names make an impact, too?
However that only served to make things more messy for me as the images folder got full of junk, so now I keep each html page + graphics in their own folder if they are unique types of pages as well.
So I have
index.html -- top
--folders of topic names -- 2nd
-- sub folders of page names + images for that page.
eg: site.com/games/online_games/kill_the_pengiun.html (few graphics for this page)
or site.com/all_jokes/fake_moon_landings/fake_moon_landings.html (heaps of graphics for this page)
stuff like that (examples only)
Keeping pages and images together made it easiy to update the pages and then just upload the folder. If the page is deleted then the images go too and keep the site ordered.
Just my system.