The problem is coming from this line in configure:

echo "running ${CONFIG_SHELL-/bin/sh} $ac_sub_configure
$ac_sub_configure_args --cache-file=$ac_sub_cache_file
--srcdir=$ac_sub_srcdir"

For some reason $ac_sub_configure is being set to
./build/autoconf/configure instead of /MOZILLA/nsprpub/configure a few
lines early by these blocks:

    case "$srcdir" in
    .) # No --srcdir option.  We are building in place.
      ac_sub_srcdir=$srcdir ;;
    /* | [A-Za-z]:*) # Absolute path.
      ac_sub_srcdir=$srcdir/$ac_config_dir ;;
    *) # Relative path.
      ac_sub_srcdir=$ac_dots$srcdir/$ac_config_dir ;;
    esac

    # Check for guested configure; otherwise get Cygnus style configure.
    if test -f $ac_sub_srcdir/configure; then
      ac_sub_configure=$ac_sub_srcdir/configure
    elif test -f $ac_sub_srcdir/configure.in; then
      ac_sub_configure=$ac_configure
    else
      echo "configure: warning: no configuration information is in
$ac_config_dir" 1>&2
      ac_sub_configure=
    fi

It looks like you're falling into the ac_sub_configure=$ac_configure
block because near the top of configure you'll find:

ac_configure=$ac_aux_dir/configure # This should be Cygnus configure.

$ac_aux_dir is build/autoconf.

A few things you might try:
- setting MOZ_OBJDIR to the subdirectory in which you're building
(assuming you're building in an objdir; if not, try creating a
subdirectory off mozilla, cd into it and run ../configure [options] from
there);
- setting SHELL=gbash;
- making sure the first pwd in your path is the one whose output
includes the driveletter.

autoconf'd nsprpub builds are new territory for emx so problems are to
be expected.

The confdefs.h failure appears to be the result of your having
os2\sort.exe first in your path.

h~

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