Modules working but not visible from administer modules page!

This is a Drupal 5 site, and there was one piece of Ubercart functionality that wasn't showing up on the live site, as opposed to the test site, so we went to enable the module. And noticed not a single Ubercart module was listed at admin/build/modules even though Ubercart functionality was most certainly working on the site.

Yeah. Freakiest thing ever.

The deal was that these modules were in another multisite directory. That is, the site was running off sites/default and using modules from sites/all/modules except for these modules – the ones working and in use but not visible on the modules page – which were in sites/subdomain.example.com/modules

Looking at the system table showed them to be present at this path. So Drupal knew they were there, and was using them, but didn't show them on the administration page because the didn't actually belong to the site!

Moving them into the sites/all/modules directory and saving the modules page meant all was well.

A final missing module was a special case, the one we went looking for originally:

This Ubercart contrib module had been developed and released as a download but not on Drupal.org, and certainly not a part of Ubercart, so when

In case that's the case with any others, here are the modules available in the Ubercart directory before and after upgrading:

Original site ubercart directory:

-rw-r--r-- 1 1080 1080 1406 Nov 5 2007 CREDITS.txt
-rw-r--r-- 1 1080 1080 14940 Apr 23 2006 LICENSE.txt
-rw-r--r-- 1 1080 1080 1631 Nov 5 2007 README.txt
drwxr-xr-x 2 1080 1080 4096 Oct 24 06:34 contrib
drwxr-xr-x 2 1080 1080 4096 Oct 7 12:05 docs
drwxr-xr-x 4 root root 4096 Oct 24 06:34 nodewords
drwxr-xr-x 12 1080 1080 4096 Oct 24 06:34 payment
drwxr-xr-x 9 1080 1080 4096 Oct 24 06:34 shipping
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_attribute
drwxr-xr-x 4 1080 1080 4096 Oct 24 06:34 uc_cart
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_cart_links
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_catalog
drwxr-xr-x 3 root root 4096 Oct 24 06:34 uc_discounts
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_file
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_googleanalytics
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_importer
drwxr-xr-x 3 root root 4096 Oct 24 06:34 uc_inventory_api
drwxr-xr-x 3 root root 4096 Oct 24 06:34 uc_manufacturer
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_notify
drwxr-xr-x 5 1080 1080 4096 Oct 24 06:34 uc_order
drwxr-xr-x 2 root root 4096 Oct 24 06:34 uc_order_export
drwxr-xr-x 4 root root 4096 Oct 24 06:34 uc_payment
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_product
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_product_kit
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_repeater
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_reports
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_roles
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_stock
drwxr-xr-x 6 1080 1080 4096 Oct 24 06:34 uc_store
drwxr-xr-x 3 1080 1080 4096 Oct 24 06:34 uc_taxes

Fresh (upgraded) Ubercart ubercart directory:

drwxr-xr-x 3 scworkers scworkers 4096 2008-10-25 05:00 contrib
-rw-r--r-- 1 scworkers scworkers 1406 2007-11-05 15:31 CREDITS.txt
drwxr-xr-x 2 scworkers scworkers 4096 2008-10-25 05:00 CVS
drwxr-xr-x 3 scworkers scworkers 4096 2008-10-25 05:00 docs
drwxr-xr-x 11 scworkers scworkers 4096 2008-10-25 05:00 payment
-rw-r--r-- 1 scworkers scworkers 1631 2007-11-05 15:31 README.txt
drwxr-xr-x 10 scworkers scworkers 4096 2008-10-25 05:06 shipping
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-29 16:48 uc_attribute
drwxr-xr-x 5 scworkers scworkers 4096 2008-10-25 05:00 uc_cart
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-25 05:00 uc_cart_links
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-25 05:00 uc_catalog
drwxr-xr-x 3 scworkers scworkers 4096 2008-10-25 05:08 uc_discounts
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-25 05:00 uc_file
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-25 05:00 uc_googleanalytics
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-25 05:00 uc_importer
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-25 05:00 uc_notify
drwxr-xr-x 6 scworkers scworkers 4096 2008-10-25 05:00 uc_order
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-25 05:00 uc_product
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-25 05:00 uc_product_kit
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-25 05:00 uc_repeater
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-25 05:00 uc_reports
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-29 16:11 uc_roles
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-29 15:31 uc_stock
drwxr-xr-x 7 scworkers scworkers 4096 2008-10-25 05:00 uc_store
drwxr-xr-x 4 scworkers scworkers 4096 2008-10-25 05:00 uc_taxes

(Contrib, in both cases, was empty.)

Resolution