Per the bukkit team's instructions, you should never use the word "bukkit' in your package namespace.

I had no clue, I was actually using it to help me tell if the project was a bukkit project. I will change ASAP

No worries - don't want things to break on you! The best thing to do is to make a source folder named bukkit, then place any packages that use Bukkit calls underneath that. Many mods that are compatible with more than one API sort their code like this; have a folder for "core" and then one for "bukkit", one for "canary", etc. if you are careful about your code, you can write the meat & potatoes of your plugin just once, and serve the whole thing up on whatever plate the user wants, if that makes any sense. WorldEdit/WorldGuard is a good example of this organization.

I already changed it and am working on improving the code to make all commands be handled in a method in the Utils class, I actually already have pushed these changes and now am just debugging.