The tool appears to delete the entire source folder not even to the recycle bin and says package.js not found even though it is in the folder. Also when it's not doing that it just runs for a moment then shuts itself down. Completely unusable right now.

Hello. Damyan!

Did you set the output folder to be the same as the source (or the parent folder of said source)?  It could result in deleting the source folder by mistake. As for the second issue, does this happen on the tool or the game?