I actually use concrete 5, a nice and simple CMS but took me some time to figure out it's "hooks".

I found the site.php config file and identified that it needed the install folder defined.

Removing it and relying on my .htaccess file to redirect to the folder took the site down.

I then use DW to search the site for all PHP calls for DIR_REL which seems to be hard coded everywhere for the links. something like:

which I believe is putting the install folder in all the links. These links are everywhere. I can use DW find/replace of course, but...If I modify the code, future upgrades of my CMS will have to manually edited again.

I did get this resolved but only after pressuring my host support. I basically had them change my primary domain to something non-existant like myfakeprimarydomain.com and then re-added my real domain as an add-on domain into it's own folder.

Then removed the install folder line in my CMS config file, removed the custom .htaccess file in public_html and fixed all my subdomains that had changed due to changing the primary domain via my host company.

My site and some sub-sites were down for about a half hour until I could make the fixes but this ultimately fixed the problem.

In retrospect, it seems like *nix hosts all have this idea of the primary domain being in public_html and add-on/sub domains being in folders, which is fine, but shouldn't it be simpler to have a clean public_html folder if the owner chooses?

And finally, I do admit that this was all my doing because I didn't want my main site files strewn about the public_html folder. I like a tidy place where each site can exist in it's own tidy folder space.

If there is a better way, I'd love to hear about it.