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I've seen plenty of guides saying why it's a good thing to organise modules in different folders... (and I'd agree) e.g.:

...and how to move the modules to the new place(s) after installation

... but these haven't worked for me, perhaps I need to try again. My site broke, even after trying the registry rebuild and clear cache many times.

So my question is this: How can I run the installation of Drupal to set up the modules to be installed in different folders (e.g. like in examples http://befused.com/drupal/module-directory-structure )?

There doesn't seem to be anything out there if you want your module paths (sub-folders) structured in a certain way, right from the beginning. NOT after the fact.

I want the folders to be set up in the first place, right from the beginning. So example, whenever I use drush to download a contrib module, the module is placed in the contrib sub-folder: sites/all/modules/contrib for example.

Some other references:

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Actually it seems like all you need to do is just create a folder called contrib in /sites/all/modules

when I issued drush dl views (at the docroot/install top level root of my site), drush put the views module in the contrib folder

as for features - you specify where you want the module to go when you (re)create the Feature (in the Feature section of the Drupal config)

as for custom - I'm hoping that Drupal will discover custom modules here - but is discovering, rather than a setting determining the path, a good thing?

Thought I'd still ask the question even after I'd found an answer, didn't want to waste the effort in making the question - hope someone else finds it useful.

Please provide your own answer or comment to enhance what I found.

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    Did you try to rebuild the registry using drupal.org/project/registry_rebuild? I usually build a site inside a custom installation profile and by using make files specify which folders different modules and themes should go into. I usually place custom modules under /profiles/MYPROFILE/modules/custom and contrib modules goes in /profiles/MYPROFILE/modules/contrib – Pontus Nilsson Jun 19 '14 at 7:47
  • +1 Great tips thanks Pontus Nilsson - I did try registry rebuild - I think I'd moved my modules into certain folders, it didn't work out (errors) then moved them back to the original place (still errors) and then tried registry_rebuild to sort it all out, but it wouldn't install. So now when I remember more of what happened, I think what would have worked would be to have installed registry_rebuild before attempting to move any modules to other folders. – therobyouknow Jun 19 '14 at 11:06
  • That said I prefer the idea of having everything in the certain folders (contrib, custom etc) in the first place so your input on install profiles is something I'd want to explore. – therobyouknow Jun 19 '14 at 11:07
  • Be aware that registry_rebuild isn't a module. It's a php script, see the documentation for more info. – Pontus Nilsson Jun 19 '14 at 12:37

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