Drupal Update: Watch out when copying the files!

I just did my first update of my drupal website, modules, drupal and all.

I ran into problems, propably I had copied some files the wrong way into my directory structure. The modules were in modules/modules instead of modules before I ran the update script. That is what I guess now that happend. After the update I noticed the wrong location and cleaned up. The result were tons of fatal errors: the horror of every software developper. The website was down for hours and I did not know what went wrong.

Finally found something useful while googling: "Check the systems table!" It had gotten all the wrong entries. Same with menu_router. It was now searching the programms in a modules/modules directory that no longer existed after the clean up. I corrected about 100 database records in the two tables and the website went up again.