I got duplicated modules after updating an installation. How to remove them? I have a site built using the Commerce Kickstart profile. Then there are enabled modules provided by the distribution at:


  profiles/commerce_kickstart/modules/contrit


and also there are modules which I added at:


  sites/all/modules


The distribution added some modules: colorbox, entity, etc. in its last version.

The problem is that I already had these modules at sites/all/modules.

The I got those modules duplicated at:


  profiles/commerce_kickstart/modules/contrit/colorbox


and


  site/all/modules/colorbox


I guess this is wrong. My question is which folder do I have to delete?
Here are the steps I would perform to address this question, in the specified order:


Download and unpack a fresh copy of the new Commerce Kickstart release.
Create a list of all your modules in your sites/all/modules folder, and identify all modules in there with the same name (module namespace) as in the new Kickstart release. The result should be a list of the duplicate modules that need to be resolved.
Use the Hacked! module to identify any hacks, patches, customizations, etc that might have been applied to any of these duplicate modules in the sites/all/modules folder.
Disable and uninstall the duplicate modules.
Backup and then delete the entire folder of each of the duplicate modules in the sites/all/modules (or move them to a folder outside your Drupal root directory).
Enable the fresh copy of the new Kickstart release. That inherently will also re-enable the vanilla version of the duplicate modules, as contained in the new Kickstart release.
Reply any hacks, patches, customizations, etc that are appropriate to be  re-applied (e.g. because upgrading to the new Kickstart release does not make them obsolete).
Should you run into weird problems because of some of the duplicate modules being moved to another directory, then download and enable the Registry Rebuild module (and/or related Drush RR command). That will probably resolve those problems.