All plugins should be placed inside<prefix>/lib/lives This is where "make install" will place them.
If the plugins are installed to a non-standard location then you still need to edit the config file by hand,
the config file is now in ~/.config/lives/settings
If this is an issue then please feel free to create a feature request either on github or on sourceforge, and it will be considered for the next release.
Regards,
Gabriel.