"changing search order for system directory" warnings building libgcc

["Billinghurst, David (CRTS)" <David dot Billinghurst at riotinto dot com>]

On irix6.5 and cygwin I get lots of warnings "changing search order for
system directory"  while building libgcc.  Recompiling with --verbose I see
that "-isystem ./include" appears twice, but I can't work out why.

An example is:

./xgcc -B./ -B/exd4/billingd/tmp/gcc-mainline/mips-sgi-irix6.5/bin/ -isystem
/exd4/billingd/tmp/gcc-mainline/mips-sgi-irix6.5/include -O2   -DIN_GCC
-W -Wall -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -isystem
./include   -g1  -DIN_LIBGCC2 -D__GCC_FLOAT_NOT_NEEDED  -I. -I.
-I/exd4/billingd/src/gcc-mainline/gcc
-I/exd4/billingd/src/gcc-mainline/gcc/.
-I/exd4/billingd/src/gcc-mainline/gcc/config
-I/exd4/billingd/src/gcc-mainline/gcc/../include  -DL_muldi3 -c
/exd4/billingd/src/gcc-mainline/gcc/libgcc2.c -o libgcc/./_muldi3.o

which produces warnings 

cc1: warning: changing search order for system directory "include"
cc1: warning:   as it has already been specified as a system directory

Adding --verbose to the command line shows that  "-isystem ./include"
appears twice. 

Reading specs from ./specs
Configured with: /exd4/billingd/src/gcc-mainline/configure --enable-shared
--enable-haifa --enable-threads=single
--prefix=/exd4/billingd/tmp/gcc-mainline
Thread model: single
gcc version 3.1 20010711 (experimental)
 ./cc1 -lang-c -v -I. -I. -I/exd4/billingd/src/gcc-mainline/gcc
-I/exd4/billingd/src/gcc-mainline/gcc/.
-I/exd4/billingd/src/gcc-mainline/gcc/config
-I/exd4/billingd/src/gcc-mainline/gcc/../include -iprefix
./../lib/gcc-lib/mips-sgi-irix6.5/3.1/ -isystem ./include -isystem
/exd4/billingd/tmp/gcc-mainline/mips-sgi-irix6.5/bin/include -D__GNUC__=3
-D__GNUC_MINOR__=1 -D__GNUC_PATCHLEVEL__=0 -Dunix -Dmips -Dsgi -Dhost_mips
-DMIPSEB -D_MIPSEB -DSYSTYPE_SVR4 -D_LONGLONG -D_SVR4_SOURCE -D_MODERN_C
-D__DSO__ -D__unix__ -D__mips__ -D__sgi__ -D__host_mips__ -D__MIPSEB__
-D_MIPSEB -D__SYSTYPE_SVR4__ -D_LONGLONG -D_SVR4_SOURCE -D_MODERN_C
-D__DSO__ -D__unix -D__mips -D__sgi -D__host_mips -D__MIPSEB
-D__SYSTYPE_SVR4 -Asystem=unix -Asystem=svr4 -Acpu=mips -Amachine=sgi
-D__CHAR_UNSIGNED__ -D__OPTIMIZE__ -D__STDC_HOSTED__=1 -W -Wall
-Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -D__LANGUAGE_C
-D_LANGUAGE_C -DLANGUAGE_C -D__SIZE_TYPE__=unsigned int
-D__PTRDIFF_TYPE__=int -D__WCHAR_TYPE__=long int -D__WINT_TYPE__=long int
-D__EXTENSIONS__ -D_SGI_SOURCE -D_MIPS_FPSET=32 -D_MIPS_ISA=_MIPS_ISA_MIPS3
-D_ABIN32=2 -D_MIPS_SIM=_ABIN32 -D_MIPS_SZINT=32 -D_MIPS_SZLONG=32
-D_MIPS_SZPTR=32 -D_COMPILER_VERSION=601 -U__mips -D__mips=3 -D__mips64
-DIN_GCC -DIN_LIBGCC2 -D__GCC_FLOAT_NOT_NEEDED -DL_muldi3 -isystem
/exd4/billingd/tmp/gcc-mainline/mips-sgi-irix6.5/include -isystem ./include
/exd4/billingd/src/gcc-mainline/gcc/libgcc2.c -quiet -dumpbase libgcc2.c -g1
-O2 -W -Wall -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-version -o /var/tmp//ccj6OQKd.s
ignoring nonexistent directory
"/exd4/billingd/tmp/gcc-mainline/mips-sgi-irix6.5/bin/include"
ignoring nonexistent directory
"/exd4/billingd/tmp/gcc-mainline/mips-sgi-irix6.5/include"
GNU CPP version 3.1 20010711 (experimental) (cpplib) [AL 1.1, MM 40] SGI
running IRIX 6.x
GNU C version 3.1 20010711 (experimental) (mips-sgi-irix6.5)
        compiled by GNU C version 3.1 20010711 (experimental).
ignoring nonexistent directory "../lib/gcc-lib/mips-sgi-irix6.5/3.1/include"
ignoring nonexistent directory
"../lib/gcc-lib/mips-sgi-irix6.5/3.1/../../../../mips-sgi-irix6.5/include"
ignoring nonexistent directory
"/exd4/billingd/tmp/gcc-mainline/lib/gcc-lib/mips-sgi-irix6.5/3.1/include"
ignoring nonexistent directory
"/exd4/billingd/tmp/gcc-mainline/lib/gcc-lib/mips-sgi-irix6.5/3.1/../../../.
./mips-sgi-irix6.5/include"
ignoring duplicate directory "."
ignoring duplicate directory "/exd4/billingd/src/gcc-mainline/gcc"
cc1: warning: changing search order for system directory "include"
cc1: warning:   as it has already been specified as a system directory
ignoring duplicate directory "include"
#include "..." search starts here:
#include <...> search starts here:
 .
 /exd4/billingd/src/gcc-mainline/gcc
 /exd4/billingd/src/gcc-mainline/gcc/config
 /exd4/billingd/src/gcc-mainline/include
 include
 /usr/local/include
 /usr/include
End of search list.