Note to self: don't delete the ibdata in /var/lib/mysql. They do stuff. Thank god for hourly backups.
Let me tell you why that is the worst choice ever. They call it 'InnoDB' so I would assume anything that involves 'InnoDB' would have AT LEAST 'idb' in the name. NOT JUST IB!!!! It's like if I called a SQL dump, .sl. Does that make any sense to you?!In this case, "ib" in "ibdata" stands for "InnoDB"... Thought, I might point that out before anyone gets confused. #cough
Ah alright, well the more you know, I guess xDWell, honestly I think they didn't think at all. One developer just thought that the technology needs a file to store stuff in and dropped it in ibdata. And if you ask him, he asks you back who would ever want to delete files from that directory.
Perhaps this is from before it was called InnoDB, maybe the codename was "Innovative and Brilliant", so this would make sense then.
Edit: According to Wikipedia, the company that invented InnoDB is Innobase, so this would be where "ib" comes from. They have been acquired by Oracle, though.