Hey Jide,

I took a break from my issue, but I've found the problem! Thanks again for all your hard work and responding quickly!

Although I'm not super cool enough to make a .patch file (sorry, I know it's way easier), here is the problem:

Line 557&558 of "scaffold.module" should be this:

'system' => $root . base_path() . $path,
'cache' => $root . base_path() .$scaffold_path,

NOT this:

'system' => $root . '/' . $path,
'cache' => $root . '/' .$scaffold_path,

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What's happened is that you've essentially hard-coded the base_path(), assuming that everyone is using the document_root as their base path. In my case, we have drupal in a subfolder of our document root, and so Scaffold was unable to process my files.

Cheers!
Brian