template_preprocess_HOOK functions have been deprecated. They are defined as initial preprocess callbacks: see template_preprocess_HOOK are defined as callbacks in the theme hook.
The file and includes keys on hook_theme have also been deprecated.
These allowed conditionally loading some files which contained relevant functions for the given definition. The only remaining reason to use them was template_preprocess callbacks. Since these have been moved to initial preprocess callbacks these keys are no longer necessary.
hook_theme() definitions that still rely on these keys should remove them when converting their template_preprocess functions to initial preprocess and move the code to a class, which will be automatically loaded. See the linked change record for more information.
