I was just monitoring some additions being made to our project, and spotted 

 create mode 100644 sites/all/modules/contrib/lightbox2/js/prototype.js
 create mode 100644 sites/all/modules/contrib/lightbox2/js/scriptaculous.js

which made me sad. I'm paranoid about library conflicts.

The project page says that a migration to jquery happened ages ago. Which made me happy again.
Scanning the code shows that these two libraries are not even called from code. lightbox2_add_files() has them commented out

Are they just source-control left-overs? Can they be safely removed from the project?