Index: /issm/trunk-jpl/externalpackages/autotools/patches/libtool.m4.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/autotools/patches/libtool.m4.patch	(revision 19374)
+++ /issm/trunk-jpl/externalpackages/autotools/patches/libtool.m4.patch	(revision 19375)
@@ -1,4 +1,13 @@
---- m4/libtool.m4	2013-06-19 22:19:27.313488900 -0700
-+++ m4/libtool.m4.bak	2013-06-18 18:45:55.766285300 -0700
+--- ./externalpackages/autotools/install/share/aclocal/libtool.m4	2015-05-22 18:31:17.780392900 -0700
++++ ./m4/libtool.m4	2015-05-22 18:35:16.669058700 -0700
+@@ -3142,7 +3142,7 @@
+ case $host_os in
+   cygwin* | mingw* | pw32* | cegcc*)
+     if test "$GCC" != yes; then
+-      reload_cmds=false
++      reload_cmds='lib /OUT:$output$reload_objs'
+     fi
+     ;;
+   darwin*)
 @@ -4752,7 +4752,7 @@
        _LT_TAGVAR(exclude_expsyms, $1)=['[_]+GLOBAL_OFFSET_TABLE_|[_]+GLOBAL__[FID]_.*|[_]+head_[A-Za-z0-9_]+_dll|[A-Za-z0-9_]+_dll_iname']
@@ -6,5 +15,5 @@
        if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
 -        _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
-+        _LT_TAGVAR(archive_cmds, $1)='$CC /LD $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib '
++        _LT_TAGVAR(archive_cmds, $1)='$CC /LD $libobjs $deplibs $compiler_flags -o $output_objdir/$soname '
  	# If the export-symbols file already is a .def file (1st line
  	# is EXPORTS), use it as is; otherwise, prepend...
@@ -15,5 +24,5 @@
  	fi~
 -	$CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
-+	$CC /LD $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib '
++	$CC /LD $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname '
        else
  	_LT_TAGVAR(ld_shlibs, $1)=no
@@ -24,5 +33,5 @@
  	  if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
 -	    _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
-+	    _LT_TAGVAR(archive_cmds, $1)='$CC /LD -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib '
++	    _LT_TAGVAR(archive_cmds, $1)='$CC /LD -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname '
  	    # If the export-symbols file already is a .def file (1st line
  	    # is EXPORTS), use it as is; otherwise, prepend...
@@ -33,5 +42,5 @@
  	    fi~
 -	    $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
-+	    $CC /LD -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib '
++	    $CC /LD -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname '
  	  else
  	    _LT_TAGVAR(ld_shlibs, $1)=no
Index: /issm/trunk-jpl/src/c/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/c/Makefile.am	(revision 19374)
+++ /issm/trunk-jpl/src/c/Makefile.am	(revision 19375)
@@ -6,8 +6,14 @@
 
 #Library declaration {{{
-
+if !WINDOWS
 lib_LTLIBRARIES = libISSMCore.la libISSMOverload.la 
 if WRAPPERS
 lib_LTLIBRARIES += libISSMModules.la
+endif
+else
+noinst_LTLIBRARIES = libISSMCore.la libISSMOverload.la 
+if WRAPPERS
+noinst_LTLIBRARIES += libISSMModules.la
+endif
 endif
 #}}}
@@ -558,5 +564,7 @@
 libISSMCore_la_FFLAGS = $(AM_FFLAGS)
 
+if !WINDOWS
 libISSMCore_la_LIBADD = $(PETSCLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB)   $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB)
+endif
 
 if WRAPPERS
@@ -570,8 +578,10 @@
 endif
 libISSMModules_la_CXXFLAGS = $(ALLCXXFLAGS)
+if !WINDOWS
 if STANDALONE_LIBRARIES
 libISSMModules_la_LIBADD = ./libISSMCore.la
 else
 libISSMModules_la_LIBADD = ./libISSMCore.la $(TRIANGLELIB)
+endif
 endif
 endif
@@ -592,5 +602,10 @@
 if WRAPPERS
 libISSMModules_la_LDFLAGS = -static
-endif
+else
+libISSMModules_la_LDFLAGS = 
+endif
+else
+libISSMCore_la_LDFLAGS = 
+libISSMOverload_la_LDFLAGS =
 endif
 
@@ -637,5 +652,9 @@
 #Automatic differentiation (must be done at the end) {{{
 if ADIC2 
+if !WINDOWS
 lib_LTLIBRARIES += libAD.la libISSMRose.la
+else
+noinst_LTLIBRARIES += libAD.la libISSMRose.la
+endif
 
 #ADIC2 library, for automatic differentiation 
Index: /issm/trunk-jpl/src/wrappers/matlab/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 19374)
+++ /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 19375)
@@ -8,5 +8,10 @@
 
 #matlab io{{{
+if !WINDOWS
 lib_LTLIBRARIES = libISSMMatlab.la
+else
+noinst_LTLIBRARIES = libISSMMatlab.la
+lib_LTLIBRARIES = 
+endif
 
 io_sources= ./io/CheckNumMatlabArguments.cpp\
@@ -20,5 +25,9 @@
 #}}}
 #api io{{{
+if !WINDOWS
 lib_LTLIBRARIES += libISSMApi.la
+else
+noinst_LTLIBRARIES += libISSMApi.la
+endif
 
 api_sources= ./io/ApiPrintf.cpp
@@ -92,12 +101,8 @@
 AM_CXXFLAGS +=  -D_HAVE_MATLAB_MODULES_ -fPIC
 
-# This is a temporary fix to an issue with Libtool regarding linking against 
-# static libraries for Windows. Ideally, we would build all libraries as DLLs
-# and and avoid this workaround which removes the dependency of ISSM libraries
-# from the perspective of our build system.
+deps += ./libISSMMatlab.la ../../c/libISSMModules.la ../../c/libISSMCore.la ./libISSMApi.la
+
 if WINDOWS
-AM_LDFLAGS += $(METISLIB) -Wl,./.libs/libISSMMatlab.lib -Wl,./../../c/.libs/libISSMModules.lib -Wl,./../../c/.libs/libISSMCore.lib -Wl,././.libs/libISSMApi.lib
-else
-deps += ./libISSMMatlab.la ../../c/libISSMModules.la ../../c/libISSMCore.la ./libISSMApi.la
+deps += $(METISLIB)
 endif
 
@@ -117,5 +122,7 @@
 #}}}
 # Module sources and dependencies {{{
+if !WINDOWS
 libISSMMatlab_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB) $(MATHLIB) $(MEXLIB) 
+endif
 
 if STANDALONE_LIBRARIES