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I have used MXdirectory for some time now and been through a couple of upgrades. Never have I had to touch any of the files as mentioned. In fact I just double checked and the code in the index.php file is still in tact and MXdirectory is functioning fine.
I am using XOOPS 2.0.16 and have MXdirectory 3.01 RC installed. I have even went so far as to rename the directory. My recommendation is that you don't touch the code in the index.php.
You could try to contact Zyspec or Tripmon to verify this if you want. But mine works fine.
I would take a look at the install instructions again. Maybe uninstall the module and then re-install it paying close attention to the install instructions. If that doesn't work uninstall it, delete it, get rid of it, and go grab another copy of the module then reinstall it again. Just in case your copy is corrupted some how.
HTHs
Quest