I am having this issue as as well. As there is no way to create a correctly functional link from the file manager (that I can see), I have been in the habit of clicking on my domain, which formerly opened a list of folders and files for me to link from. My domain is now 403 Forbidden, and the /edit hta access file (mentioned above) that I made in Public html merely opened my own personal desktop. I do have an .index file in each of the subfolders I use, one index for each topic; I do not have a main 'home' page, but that has not been an issue previously.
On a side note, I see that 99% of the folders in the file manager are ones that I can't or won't be using. Public is right near the bottom, and getting into the particular folder I want to be in is a bit like opening a bunch of nesting dolls. Could some of these folders be given the option to be invisible or at least rearranged so I can put the ones I actually use in a more convenient position?
Thank you, ~SW