I have a common .htaccess file that I use for a number of wiki directories scattered around my server. I keep it along with the wiki software in git. This makes it easy when I fix/change things in the wiki software etc. as I can copy the whole lot out to all the wikis when I do an upgrade.
I want to prevent access to some sub-directories of the wiki (specifically the data, conf, bin and inc directories) and I can't see any easy way to do this. OK, I *could* put a .htaccess file in each of data, conf, bin and inc but that seems a lot of unnecessary junk. If I could dream up a directive to put in the top level (wiki top level that is) .htaccess to deny access it would be much simpler to maintain.
I'm only using .htaccess anyway because it simplifies maintenance, I could of course put all the contents of the .htaccess files in <Directory> sections of the main apache.conf file, it would be more efficient but I'd have to have a <Directory> section for every wiki and, if I moved a wiki, I'd have to change the apache.conf file. It's much easier to maintain if I put the wiki specific stuff in the .htaccess file.