Right now if you don't set a target-dir attribute on a source-file or header-file element, it will put everything flat in to the Plugins folder. For installing multiple plugins, this would look like a mess.
I worked around this by explicitly specifying the target-dir, but as you can see in this plugin.xml below, there is a lot of redundant information:
https://github.com/shazron/ZipUtil/blob/a0fd1b26964bbf55e061fa664f82598fae57a0ea/plugin.xml which may be prone to errors.
For a default, my suggestion is for plugman to install a plugin into a folder (specified by the plugin-name or id, then use the same child hierarchy specified in the src attribute of a source-file or header-file element.
If my suggestion was implemented – the removal of the target-dir attribute from the source-file and header-file elements of the plugin.xml specified above would have the same result as if I didn't remove them.