I decided to try updating my autogen.sh to get rid of this nag:

***Warning*** PKG_NAME is deprecated, you may remove it from autogen.sh

The new instructions for crafting an autogen.sh (from the README) look like this:

#!/bin/sh
srcdir=`dirname $0`
[ -z "$srcdir" ] && srcdir=.

if [ ! -f "$srcdir/configure.ac" ]; then
 echo "$srcdir doesn't look like source directory for $PKG_NAME" >&2
 exit 1
fi

which gnome-autogen.sh || {
	echo "You need to install gnome-common from GNOME Git"
	exit 1
}

. gnome-autogen.sh "$@"

But $PKG_NAME is used before it's defined, so that's problem #1. Then gnome-autogen.sh computes $PKG_NAME with some autoconf trickery:

PKG_NAME=`autoconf --trace "AC_INIT:$1" "$srcdir/configure.ac"`

Which expands to the string "--prefix":

Epiphany was configured with the following options:

	Source code location	   : .
	Compiler		   : gcc
	Prefix			   : /home/mcatanzaro/jhbuild/install
	Extra debugging support	   : yes
	Build tests		   : yes
	Code coverage		   : no

	NSS support		   : yes

Now type `make' to compile --prefix

I think I will not update my autogen.sh quite yet. :)