Add clean target to Makefile
These invocations of rm -rf $@ for each target in the Makefile should be put in a separate clean target. That way it doesn't remove everything each time the user re-runs make.
This would be especially helpful for all of the large files that are downloaded during the build process.
A good example would be this: https://github.com/rgl/windows-vagrant/issues/20
Not sure what you mean. What do you think it's being deleted, why and when?
One example is this line: https://github.com/rgl/windows-vagrant/blob/master/Makefile#L205
Deleting that directory also deletes the ISO that gets downloaded, which is over 1GB.