Both SpecialAllpages.php and SpecialAllmessages.php have been changed to proper CamelCase in include/AutoLoader.php but haven't been renamed in the filesystem.
rMW2dc420dd2ae7c47984a15d84c06a57a684a7dd54 and rMWa161ea79a261ff80b4cfb79fe920bece5863cc79 are the commits which caused this.