build in directory /home/sgm/cvs/pan-try
ran ./autogen.sh --prefix /home/devel/pan2
ran make; partitial output below

make  all-recursive
make[1]: Entering directory `/home/sgm/cvs/pan-try'
Making all in po
make[2]: Entering directory `/home/sgm/cvs/pan-try/po'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/sgm/cvs/pan-try/po'
Making all in gmime
make[2]: Entering directory `/home/sgm/cvs/pan-try/gmime'
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I..\gmime -D_REENTRANT -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include       -g -O2 -c gmime.c
make[2]: Leaving directory `/home/sgm/cvs/pan-try/gmime'
Making all in pan
make[2]: Entering directory `/home/sgm/cvs/pan-try/pan'
Making all in base
make[3]: Entering directory `/home/sgm/cvs/pan-try/pan/base'
gcc -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I/home/devel/pan2/include/pan -DGNOMELOCALEDIR=\""/home/devel/pan2/share/locale"\"  -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/pango-1.0 -I/usr/X11R6/include -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -D_REENTRANT -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -I/usr/include/libxml2        -g -O2 -c acache.c
/home/devel/pan2/include/pan: Permission denied
make[3]: *** [acache.o] Error 1
make[3]: Leaving directory `/home/sgm/cvs/pan-try/pan/base'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/sgm/cvs/pan-try/pan'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/sgm/cvs/pan-try'
make: *** [all-recursive-am] Error 2

The problem IMO is that the directory /home/devel/pan2/include/pan should not be XS'ed during the build phase.