Mess up your modules, Mess up your registry...

and mess up your Drupal site "permanently". Not Really.

I screwed up my Drupal project one day by copying my modules directory and forgetting to move it out of it's parent directory. Details are unimportant.

The point is, I cleared my cache and did a few other things and Drupal started looking for modules in a location that was unavailable. Needless to say (I hope needless anyway), the system and registry tables were out of sync with some of the modules.
Fixing (or so I thought) the registry table manually was unsuccessful.

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