Abandon install profile

drushrc.php

// Site specific options
$options['destination'] = 'sites/all/modules/contrib';

old-drushrc.php

// Site specific options
$options['destination'] = 'profiles/my_profile/modules/contrib';

relocate.sh

# Run from the root of your site directory

export $PROFILE="my_profile"
mv "profiles/$PROFILE/modules/contrib/" sites/all/modules/contrib
mv "profiles/$PROFILE/modules/custom/" sites/all/modules/custom
mv "profiles/$PROFILE/themes/*" sites/all/themes/

relocate.sql

-- Update contrib modules location
UPDATE system SET filename = REPLACE(filename,'profiles/myprofile/modules/contrib','sites/all/modules/contrib');
UPDATE registry SET filename = REPLACE(filename,'profiles/myprofile/modules/contrib','sites/all/modules/contrib');
UPDATE registry_file SET filename = REPLACE(filename,'profiles/myprofile/modules/contrib','sites/all/modules/contrib');

-- Update custom modules location
UPDATE system SET filename = REPLACE(filename,'profiles/myprofile/modules/custom','sites/all/modules/custom');
UPDATE registry SET filename = REPLACE(filename,'profiles/myprofile/modules/custom','sites/all/modules/custom');
UPDATE registry_file SET filename = REPLACE(filename,'profiles/myprofile/modules/custom','sites/all/modules/custom');

-- Update themes location
UPDATE system SET filename = REPLACE(filename,'profiles/myprofile/themes','sites/all/themes');
UPDATE registry SET filename = REPLACE(filename,'profiles/myprofile/themes','sites/all/themes');
UPDATE registry_file SET filename = REPLACE(filename,'profiles/myprofile/themes','sites/all/themes');

-- Truncate cache
TRUNCATE cache;
TRUNCATE cache_bootstrap; -- Drupal 7 only
TRUNCATE cache_path; -- Drupal 7 only

-- NOTE: if you are using Drupal 6, change 'registry' and 
-- 'registry_file' to 'autoload_registry' and 
-- 'autoload_registry_file' and skip truncating 'cache_bootstrap' 
-- and 'cache_path'. The rest of the instructions should 
-- work unmodified.