autotools new (with readline+history and icu) 2.9.13 (proposed version)
cmake (with readline+history and icu) 2.9.13 (current in tree)
autotools old (without readline+history and icu) 2.9.12 (previous version)

Notes:
autotools sets includedir in cflags and xml2Conf to -I/usr/include (???)
First section in xml2Conf.sh doesn't expand do anything using autotools (?)
Patch: https://cgit.freebsd.org/ports/tree/textproc/libxml2/files/patch-xml2Conf.sh.in?id=4c0c936fe9f8e602e56b1b0862e2cfa538cea219

Source data:

work/stage/usr/local/bin/xml2-config	--prefix=DIR          change libxml prefix [default /usr/local]			(autotools new)
/usr/local/bin/xml2-config		--prefix=DIR          change libxml prefix [default /usr/local]			(cmake)
/usr/local/bin/xml2-config		--prefix=DIR          change libxml prefix [default /usr/local]			(autotools old)
work/stage/usr/local/bin/xml2-config  	--exec-prefix=DIR     change libxml exec prefix [default /usr/local]		(autotools new)
/usr/local/bin/xml2-config		--exec-prefix=DIR     change libxml exec prefix [default /usr/local]		(cmake)
/usr/local/bin/xml2-config		--exec-prefix=DIR     change libxml exec prefix [default /usr/local]		(autotools old)

work/stage/usr/local/bin/xml2-config --libs	-L/usr/local/lib -lxml2 -lz -L/usr/lib -llzma -L/usr/lib -licui18n -L/usr/local/lib -licuuc -licudata -lm -L/usr/local/lib	(autotools new)
/usr/local/bin/xml2-config --libs		-L/usr/local/lib -lxml2 -lz -llzma -pthread -licudata -licui18n -licuuc -lm -ldl						(cmake)
/usr/local/bin/xml2-config --libs		-L/usr/local/lib -lxml2 -lz -L/usr/lib -llzma -L/usr/lib -lm									(autotools old)
work/stage/usr/local/bin/xml2-config --cflags	-I/usr/local/include/libxml2 -I/usr/include											(autotools new)
/usr/local/bin/xml2-config --cflags		-I/usr/local/include/libxml2 -I/usr/local/include										(cmake)
/usr/local/bin/xml2-config --cflags		-I/usr/local/include/libxml2 -I/usr/include											(autotools old)
work/stage/usr/local/bin/xml2-config --modules	1																(autotools new)
/usr/local/bin/xml2-config --modules		1																(cmake)
/usr/local/bin/xml2-config --modules		1																(autotools old)
work/stage/usr/local/bin/xml2-config --version	2.9.13																(autotools new)
/usr/local/bin/xml2-config --version		2.9.13																(cmake)
/usr/local/bin/xml2-config --version		2.9.12																(autotools old)



cat work/stage/usr/local/libdata/pkgconfig/libxml-2.0.pc
prefix=/usr/local																(autotools new)
prefix=/usr/local																(cmake)
prefix=/usr/local																(autotools old)
exec_prefix=${prefix}																(autotools new)
exec_prefix=${prefix}																(cmake)
exec_prefix=${prefix}																(autotools old)
libdir=${exec_prefix}/lib															(autotools new)
libdir=${prefix}/lib																(cmake)
libdir=${exec_prefix}/lib															(autotools old)
includedir=${prefix}/include															(autotools new)
includedir=${prefix}/include															(cmake)
includedir=${prefix}/include															(autotools old)
modules=1																	(autotools new)
modules=1																	(cmake)
modules=1																	(autotools old)

Name: libXML																	(autotools new)
Name: libXML																	(cmake)
Name: libXML																	(autotools old)
Version: 2.9.13																	(autotools new)
Version: 2.9.13																	(cmake)
Version: 2.9.12																	(autotools old)
Description: libXML library version2.														(autotools new)
Description: libXML library version2.														(cmake)
Description: libXML library version2.														(autotools old)
Requires:																	(autotools new)
Requires:																	(cmake)
Requires:																	(autotools old)
Libs: -L${libdir} -lxml2															(autotools new)
Libs: -L${libdir} -lxml2															(cmake)
Libs: -L${libdir} -lxml2															(autotools old)
Libs.private: -lz  -L/usr/lib -llzma  -L/usr/lib -licui18n -L/usr/local/lib -licuuc -licudata  -lm -L/usr/local/lib  -L/usr/local/lib		(autotools new)
Libs.private: -lz -llzma -pthread  -licudata -licui18n -licuuc -lm										(cmake)
Libs.private:  -lz  -L/usr/lib -llzma -L/usr/lib -lm												(autotools old)
Cflags: -I${includedir}/libxml2 -I/usr/include													(autotools new)
Cflags: -I${includedir}/libxml2 -I${includedir}													(cmake)
Cflags: -I${includedir}/libxml2 -I/usr/include													(autotools old)

cat work/stage/usr/local/lib/xml2Conf.sh
prefix=@prefix@															(autotools new)
prefix=@prefix@															(autotools old)
exec_prefix=@exec_prefix@													(autotools new)
exec_prefix=@exec_prefix@													(autotools old)
includedir=@includedir@														(autotools new)
includedir=@includedir@														(autotools old)
libdir=@libdir@															(autotools new)
libdir=@libdir@															(autotools old)

XML2_LIBDIR="-L/usr/local/lib"													(autotools new)
XML2_LIBDIR="-L/usr/local/lib"													(cmake)
XML2_LIBDIR="-L/usr/local/lib"													(autotools old)
XML2_LIBS="-lxml2 -lz  -L/usr/lib -llzma  -L/usr/lib -licui18n -L/usr/local/lib -licuuc -licudata  -lm -L/usr/local/lib"	(autotools new)
XML2_LIBS="-lxml2 -lz -llzma -pthread  -licudata -licui18n -licuuc -lm"								(cmake)
XML2_LIBS="-lxml2 -lz  -L/usr/lib -llzma  -L/usr/lib  -lm"									(autotools old)
XML2_INCLUDEDIR="-I/usr/local/include/libxml2 -I/usr/include"									(autotools new)
XML2_INCLUDEDIR="-I/usr/local/include/libxml2"											(cmake)
XML2_INCLUDEDIR="-I/usr/local/include/libxml2 -I/usr/include"									(autotools old)
MODULE_VERSION="xml2-2.9.13"													(autotools new)
MODULE_VERSION="xml2-2.9.13"													(cmake)
MODULE_VERSION="xml2-2.9.12"													(autotools old