I used configure --prefix=/usr/local/stow/xfce to build Xfce 4.5.90. The make install in libxfcegui4-4.5.90 failed because it tries to install to /usr/lib/libglade/2.0/libxfce4.so. make[3]: Entering directory `/home/scorpion/src/xfce-4.6-alpha1/libxfcegui4-4.5.90/glade' make[3]: Nothing to be done for `install-exec-am'. test -z "" || /bin/mkdir -p "" test -z "" || /bin/mkdir -p "" test -z "/usr/lib/libglade/2.0" || /bin/mkdir -p "/usr/lib/libglade/2.0" /bin/sh ../libtool --mode=install /usr/bin/install -c 'libxfce4.la' '/usr/lib/libglade/2.0/libxfce4.la' libtool: install: warning: relinking `libxfce4.la' libtool: install: (cd /home/scorpion/src/xfce-4.6-alpha1/libxfcegui4-4.5.90/glade; /bin/sh /home/scorpion/src/xfce-4.6-alpha1/libxfcegui4-4.5.90/libtool --tag CC --mode=relink gcc -I.. -I/usr/local/stow/xfce-4.6//include/xfce4 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/include/libxml2 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/pixman-1 -g -O2 -export-dynamic -avoid-version -module -Wl,-O1 -o libxfce4.la -rpath /usr/lib/libglade/2.0 libxfce4_la-libglade-xfce4.lo -lglade-2.0 -lgtk-x11-2.0 -lxml2 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lm -lpangocairo-1.0 -lpango-1.0 -lcairo -lgobject-2.0 -lgmodule-2.0 -ldl -lglib-2.0 ../libxfcegui4/libxfcegui4.la ) libtool: relink: gcc -shared .libs/libxfce4_la-libglade-xfce4.o -Wl,-rpath -Wl,/usr/local/stow/xfce-4.6/lib -Wl,-rpath -Wl,/usr/local/stow/xfce-4.6//lib -L/usr/lib -lglade-2.0 -lxml2 -L/usr/local/stow/xfce-4.6/lib -lxfcegui4 -L/usr/local/stow/xfce-4.6//lib -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lpango-1.0 -lcairo -lfreetype -lz -lfontconfig -lpng12 -lxcb-render-util -lxcb-render -lxcb -lXrender -lpixman-1 -lm -lgmodule-2.0 -ldl -lSM -lICE -lX11 -lxfce4util -lgobject-2.0 -lglib-2.0 -Wl,-O1 -Wl,-soname -Wl,libxfce4.so -o .libs/libxfce4.so libtool: install: /usr/bin/install -c .libs/libxfce4.soT /usr/lib/libglade/2.0/libxfce4.so /usr/bin/install: cannot create regular file `/usr/lib/libglade/2.0/libxfce4.so': Permission denied make[3]: *** [install-libglademoduleLTLIBRARIES] Error 1 make[3]: Leaving directory `/home/scorpion/src/xfce-4.6-alpha1/libxfcegui4-4.5.90/glade'
This is not a bug. xfce4.so needs to be installed in the libglade-module-path. the configure-script determines this based on the pkg-config file of libglade. you can override it with --libglade-module-path=SOME_PATH, but this will break the glade-stuff used by xfce. (since libglade doesn't care about xfce-prefixes, just about libglade prefixes) Anyways... not a bug.
Actually, I believe you can also set GLADE_MODULES and/or LIBGLADE_MODULES to your custom install path. Google around if that isn't working. Or look at the source; that's where I found it myself.