Drupal - How to move installed modules from /sites/all/modules/* to /sites/all/contrib/modules/*

You only need to move your modules to the your new location and rebuild the regisry. When the registry rebuilds the path to the modules will be updated. Check registry_rebuild().

Rescans all code in modules or includes directories, storing the location of each interface or class in the database.

Although, I would recommend you to backup you database before testing this.

If you are using drush you could also rebuild the registry using the following command:

drush cc registry

You can also install the registry_rebuild command for drush:

// install registry_rebuild
drush dl registry_rebuild
// rebuild the registry
drush rr

Try the cool tool from Mark Sonnabaum: Drush Rebuild Project Paths. It automates the process; worked great for me. Uses Drush, of course.

I will second the suggestion that you try this on a copy of your site database, though.

I restored a backup from production locally and tried to just move things and hit admin/modules or to run registry_rebuild() but it didn't stop fatal errors from being thrown. This makes sense to me since some modules may use includes or whatever in their hook_init(), or you may have a menu router path set that depends on a module or include that Drupal can't find on bootstrap. Ultimately, this is what I did (your paths may be different):

Step 1: Replace sites/all/modules with sites/all/modules/contrib

UPDATE system SET filename = REPLACE(filename, 'sites/all/modules', 'sites/all/modules/contrib');
UPDATE registry SET filename = REPLACE(filename, 'sites/all/modules', 'sites/all/modules/contrib');
UPDATE registry_file SET filename = REPLACE(filename, 'sites/all/modules', 'sites/all/modules/contrib');

Step 2: Replace sites/all/modules/contrib with sites/all/modules/custom for custom namespaced modules

UPDATE system SET filename = REPLACE(filename, 'sites/all/modules/contrib', 'sites/all/modules/custom') WHERE name LIKE 'my_custom_namespace_%';
UPDATE registry SET filename = REPLACE(filename, 'sites/all/modules/contrib', 'sites/all/modules/custom') WHERE name LIKE 'my_custom_namespace_%';
UPDATE registry_file SET filename = REPLACE(filename, 'sites/all/modules/contrib', 'sites/all/modules/custom') WHERE filename LIKE '%my_custom_namespace_%';

Step 3: Move dev modules into sites/all/modules/dev

UPDATE system SET filename = REPLACE(filename, 'sites/all/modules/contrib', 'sites/all/modules/dev') WHERE name LIKE 'devel%';
UPDATE registry SET filename = REPLACE(filename, 'sites/all/modules/contrib', 'sites/all/modules/dev') WHERE name LIKE 'devel%';
UPDATE registry_file SET filename = REPLACE(filename, 'sites/all/modules/contrib', 'sites/all/modules/dev') WHERE filename LIKE '%devel%';

Step 4: Clear caches so that things will bootstrap properly

TRUNCATE TABLE cache
TRUNCATE TABLE cache_bootstrap
TRUNCATE TABLE cache_menu
TRUNCATE TABLE cache_page
TRUNCATE TABLE cache_path

Note: If you use a custom module or a contrib like LoginToboggan to handle 403 (access denied) and you've gotten logged out during this process, you may need to update the include_file column in the menu_roter table to use the new path for the include file. This is probably a rare occurrence.

UPDATE menu_router SET include_file = 'sites/all/modules/custom/my_custom_namespace/includes/foo.inc' WHERE path = 'access-denied'

Once these queries have run – which will only take a split second – hit up admin/config/development/performance and clear the cache so that menu paths rebuild.