There is definitely something wrong at the moment.  In
_AC_OUTPUT_FILES, amongst other things, $ac_dots is always
"../" (at least for separate builddir configure runs with
relative path to configure), which screws up everything.
Here is some debug output from a configure run...

Haven't detected what introduced the bug yet, though...

$ ../../src/SoXt-HEAD/configure --prefix=$HOME
[...]
checking Linux Joystick device handle... (cached) /dev/js0
creating ./config.status
srcdir:      ../../../src/SoXt-HEAD/
top_srcdir:  ../../../src/SoXt-HEAD
ac_dots:     ../
creating Makefile
srcdir:      ../../../src/SoXt-HEAD/
top_srcdir:  ../../../src/SoXt-HEAD
ac_dots:     ../
creating soxt-config
srcdir:      ../../../src/SoXt-HEAD/src
top_srcdir:  ../../../src/SoXt-HEAD
ac_dots:     ../
creating src/Makefile
srcdir:      ../../../src/SoXt-HEAD/Inventor
top_srcdir:  ../../../src/SoXt-HEAD
ac_dots:     ../
creating src/Inventor/Makefile
srcdir:      ../../../src/SoXt-HEAD/Xt
top_srcdir:  ../../../src/SoXt-HEAD
ac_dots:     ../
creating src/Inventor/Xt/Makefile
srcdir:      ../../../src/SoXt-HEAD/devices
top_srcdir:  ../../../src/SoXt-HEAD
ac_dots:     ../
creating src/Inventor/Xt/devices/Makefile
srcdir:      ../../../src/SoXt-HEAD/widgets
top_srcdir:  ../../../src/SoXt-HEAD
ac_dots:     ../
creating src/Inventor/Xt/widgets/Makefile
srcdir:      ../../../src/SoXt-HEAD/viewers
top_srcdir:  ../../../src/SoXt-HEAD
ac_dots:     ../
creating src/Inventor/Xt/viewers/Makefile
srcdir:      ../../../src/SoXt-HEAD/build
top_srcdir:  ../../../src/SoXt-HEAD
ac_dots:     ../
creating build/soxt.spec
srcdir:      ../../../src/SoXt-HEAD/build
top_srcdir:  ../../../src/SoXt-HEAD
ac_dots:     ../
creating build/soxt.doxygen

  Lars J

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