Switch "forum" taxonomy to a post type.  WordPress has grown over the years, but it's still not ready for a forum taxonomy.  Taxonomies still lack many of the things that would make them suitable for this job.  It was a tough decision, but I'd rather make it and move on to actually finishing up version 1.0 than worrying about it.
Rename handler functions.
Rename functions-type included files by prefixing them with "functions-".
Move query functions to their respective template files.  Cleanup.  Inline docs.
Introduce functions files for forums, topics, and replies plus getter functions for returning post type names.
Use mb_get_topic_post_type() instead of 'forum_topic'.
Use mb_get_forum_post_type() instead of 'forum'.
Fix where wrong post object was being pulled for single forums.
Use mb_get_reply_post_type() instead of 'forum_reply'.
Add the 'forum-link' class.
Correct front page.  Properly handle the forum archive query.
Add the mb_is_subforum() function.
Change version number to "1.0.0-pre-alpha" so that it's clear that this isn't even an alpha version yet.
Check if viewing the forum post type archive rather than the forum front page.
Clean up template hierarchy.