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Hey Khatti,
I'm just across the water from you in Seattle
Glad to see another local user!
First, the .htaccess file is a common file that provides some permissions in linux. It's typically not used within XOOPS for permission purposes though, which is why you don't see other references to it elsewhere. (I have seen a couple of modules that require it, though.)
Are you on a shared server or your own server? If you're on a shared/hosted server, you will not have access to the php.ini file to make any changes, and it's unlikely that your host will make any changes to it even if you request it.
My first suggestion is to recopy (FTP) the entire system module back onto your server. Replace any files when requested. (This is not affecting your database, so no worries.) Once that is complete, update the System module in the Modules directory (the disk icon in the far right).
Once that is done, check to see if you have access to the missing areas again. I suspect that there may have been errors in the installation that prevented these files from all being copied over properly.
