diff --git a/Makefile.am b/Makefile.am
index e2fd9a338..c87e80b61 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,4 +1,4 @@
-include $(top_srcdir)/doxygen/aminclude.am
+include $(top_srcdir)/doc/doxygen/aminclude.am
 
 # Build in these directories:
 SUBDIRS  = ext src test_problems
diff --git a/configure.ac b/configure.ac
index 1b1f5d2d4..62fd7aba4 100644
--- a/configure.ac
+++ b/configure.ac
@@ -146,8 +146,8 @@ AC_OUTPUT(Makefile                                                         \
                    test_problems/cathermo/VPissp/Makefile                  \
                    test_problems/cathermo/wtWater/Makefile                 \
                    test_problems/PecosTransport/Makefile                   \
-		   docs/Makefile                                           \
-		   docs/doxygen/Makefile                                   \
+		   doc/Makefile                                            \
+		   doc/doxygen/Makefile                                    \
 		   src/Makefile                                            \
                    src/fortran/Makefile                                    \
                    src/base/Makefile                                       \
diff --git a/ext/f2c_math/Makefile.am b/ext/f2c_math/Makefile.am
index fbafff1ba..b8fdf8dab 100644
--- a/ext/f2c_math/Makefile.am
+++ b/ext/f2c_math/Makefile.am
@@ -50,3 +50,5 @@ all:
 	@echo copying headers $<
 	cp -p ../f2c_libs/sysdep1.h0 ../f2c_libs/sysdep1.h
 	cp -p ../f2c_libs/signal1.h0 ../f2c_libs/signal1.h
+	@echo installing config.h 
+	cp -p ../../config.h ../../include/cantera/base/