My own plugin (ecSTATic) has an option to use functions in supplemental files (Maxmind's geolocation routines) that aren't included in the basic plugin download. After upgrading ecSTATic to handle the WordPress 3.3 jQuery 1.7 change, I found that the four Maxmind files were gone from the plugin folder. It's possible other files were deleted as well. During plugin development I tend to stash test files in with the working ones.
Not sure if this is a bug or a feature.