I got duplicated modules after updating an installation. How to remove them?

Question

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?

You should delete from your sites/all/modules. I don't understand the need of your to put it at first place. Did it come at update itself ? — RajeevK, Commented Aug 8, 2013 at 7:16
I'm almost sure that these modules weren't in previous version of the distribution. Then I added them in site/all/modules. And I added them just because I needed. — chefnelone, Commented Aug 8, 2013 at 7:20
As per my understanding with distribution, module needed for it need to be inside it as it's mentioned in there, so you will need to delete from your sites/all/modules. But I will recommend you to ask this question at drupalcommerce.org before you go to take any action regarding this.. — RajeevK, Commented Aug 8, 2013 at 7:28
What @RajeevK said - you need to get rid of the ones in sites/all/modules. Download a fresh copy of Kickstart, and any modules under profiles/kickstart/modules/contrib that are also under sites/all/modules in the offending site...delete from sites/all/modules. Make sure you take a backup first, of course — Clive, Commented Aug 8, 2013 at 11:23

Pierre.Vriens · Accepted Answer · 2015-12-26 10:08:45Z

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.

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