When you get hosting you have to have one domain placed in a wrapper of the shared domain host. Then you create wrappers around you, so logically they are in folders below your initial domain. That initial domain claims the set of wrappers you create. It is a hierarchy system just like directories.

I like the same neatness you addressed and for the main hosting domain name I use either a throwaway or put the programs in a folder below public_html.

Edit .htaccess to 301 or 302 all index.php or index.html calls go to the new folder (remove all those rewrites and put them in the folder if needed for the program). Once in that folder uses will use the program like normal - most CMS do not care where you put them and the line of text defining the directories shows that by picking up its variables.

Now you only have the .htaccess, the error shtmls, favicon.ico and a robots.txt in the root dir to pass muster with search engines.

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