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I have successfully run the ./configure --prefix=C:/usr script but the compilation fails due to some shell syntax problem:

make[3]: Entering directory 'G:/Files/C++/repos/fontconfig-2.13.1/src'
gcc -DHAVE_CONFIG_H -I. -I..  -I.. -I../src -IC:/usr/include/freetype2 -IC:/usr/include/libpng16 -IC:/mingw64/mingw64/include   -IC:/mingw64/mingw64/include  -Wall -Wpointer-arith -Wstrict-prototypes     -Wmissing-prototypes -Wmissing-declarations     -Wnested-externs -fno-strict-aliasing -DFC_CACHEDIR='"LOCAL_APPDATA_FONTCONFIG_CACHE"' -DFONTCONFIG_PATH='"C:/usr/etc/fonts"' -DFC_TEMPLATEDIR='"C:/usr/share/fontconfig/conf.avail"'   -g -O2 -MT fcarch.o -MD -MP -MF .deps/fcarch.Tpo -c -o fcarch.o fcarch.c
mv -f .deps/fcarch.Tpo .deps/fcarch.Po
C:/Git/usr/bin/sh.exe ../libtool  --tag=CC   --mode=link gcc  -g -O2   -o fcarch.exe fcarch.o -lintl
libtool: link: gcc -g -O2 -o .libs/fcarch.exe fcarch.o  -lintl
C:/Git/usr/bin/sh.exe ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..  -I.. -I../src -IC:/usr/include/freetype2 -IC:/usr/include/libpng16 -IC:/mingw64/mingw64/include   -IC:/mingw64/mingw64/include  -Wall -Wpointer-arith -Wstrict-prototypes         -Wmissing-prototypes -Wmissing-declarations     -Wnested-externs -fno-strict-aliasing -DFC_CACHEDIR='"LOCAL_APPDATA_FONTCONFIG_CACHE"' -DFONTCONFIG_PATH='"C:/usr/etc/fonts"' -DFC_TEMPLATEDIR='"C:/usr/share/fontconfig/conf.avail"'   -g -O2 -MT fcatomic.lo -MD -MP -MF .deps/fcatomic.Tpo -c -o fcatomic.lo fcatomic.c
Xfcatomic.Tpo -c -o fcatomic.lo fcatomic.lo
libtool: warning: libobj name 'fcatomic.Tpo -c -o fcatomic.lo fcatomic.lo' may not contain shell special characters.

Looks like the call to libtool has an unwanted linebreak in its arguments

GNU bash, version 4.4.23(1)-release (x86_64-pc-msys)

GNU Make 4.2.1 Built for x86_64-w64-mingw32

Using the 2.13.1 release version of fontconfig, but the issue also reproduces on older ones.