Personally, I think plugins in `$HOME` should override anything else. If you're developing a plugin and you have a conflicting one in `$HOME` you should sort that out. Some people might want to run Picard straight from a git clone since their OS/distro may not provide a good way to install/use a VCS package. (Or because they want to install the stable package from their package repository to check if behaviour in their VCS clone run Picard is a regression or not. Or something else entirely.)