How to reproduce:
1. install Drupal 6.16
2. enable the taxonomy module and create a vocabulary
3. disable the taxonomy module
4. upgrade to Drupal 7
Fatal error: Call to undefined function taxonomy_get_vocabularies() in /Applications/MAMP/htdocs/d7git/modules/taxonomy/taxonomy.install on line 263
(similar problem with the contact module)
If we want to upgrade all the modules in one go (including the disabled modules) we need to include their files during the upgrade process.