If you have a copy of, for example, JBDS 2.0.0 installed to /opt/jbds and then try to install 2.1.0 to that location it gives you the "Are you sure you want to overwrite that folder" warning, the same as for any existing directory.

It would be good if it detected that there was an older copy of JBDS installed to that location, and gave you a stronger "You can't upgrade by installing over the top" warning. Installing 2.1.0 over the top of 2.0.0 leaves you with a mixed up installation, with some versions of plugins from the old version and some from the new version.