I’ve been noticing that Sublime Text has a folder in my %appdata%/Sublime Text 2/ folder called backups. For some reason I can’t seem to find out how to disable this backup system and it keeps filling up with more and more folders full of ST2’s plugins. Also every time I close the program it seems to think it needs to reapply the installation of the sublime-vagrant plugin which crashes ST2 as soon as I run the command palette, I’ve deleted the plugin’s folder multiple times and it keeps coming back so I assume this is the backups reapplying the plugin folder.

I don’t know about the backup stuff, but I don’t think ST does anything to manage packages (though I could be wrong). Did you install sublime-vagrant with package control? If so, did you remove it from the package control list of installed packages?