I haven't used autotools in mingw/msys environment but
I think you can specify those paths with autotools also.
Makefile.am is for those purpose in my case.
bin_PROGRAMS = logging_client
logging_client_CPPFLAGS = \
-I$(ACE_ROOT)\
-I$(HLM_ROOT)/include\
-D_GNU_SOURCE\
-D__ACE_INLINE__\
-DACE_NTRACE=0\
-DACE_HAS_WCHAR=1
logging_client_SOURCES = \
Logging_Client.cpp
logging_client_LDFLAGS = \
-L$(ACE_ROOT)/lib\
-L$(HLM_ROOT)/lib
logging_client_LDADD = \
-lACE\
-lHLM
This is one sample I use in Linux not in msys though.
You can specify whatever you need this way.
I don't know if this works same in msys though..
Journeyer