The .install file of a Drupal module contains many update functions. What these update functions do ? The names of these functions follow the format <module_name>_update_N. The details on this format can be found here hook_update_N.
Theme registry is built and cached by the drupal core as part of booting process. The function "_theme_build_registry" (theme.inc) builds the theme registry. Each and every implemented theming hook will have a corresponding entry inside the theme registry. Basically each entry indicates the process that takes place on invoking the theming hook to which the entry belongs. For the default bartik theme an entry inside theme registry for the theme hook "menu_link" looks like some thing as shown bellow.