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.:
http://befused.com/drupal/module-directory-structure (particularly like this guide, more folders and options to choose from)
...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:
Can Drupal be configured to find modules in other locations? - this suggests Drupal can just discover the location, I'm not so keen on this, I'd rather Drupal always know where the modules are rather than having to discover where they are.
Is it possible to change the path of modules/themes installed using an installation profile? - I just want to use the plain vanilla Drupal 7 core install. If I was going to use this option, what would be the minimum I would need to provide in a setup to have module sub-folders?