diff --git a/Makefile.am b/Makefile.am
index 718871cdb..e2fd9a338 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -2,7 +2,7 @@ include $(top_srcdir)/doxygen/aminclude.am
 
 # Build in these directories:
 SUBDIRS  = ext src test_problems
-SUBDIRS += doxygen
+SUBDIRS += doc
 
 # Distribute these directories:
 DISTDIRS = src
diff --git a/configure.ac b/configure.ac
index 9f5ccc94e..1b1f5d2d4 100644
--- a/configure.ac
+++ b/configure.ac
@@ -90,7 +90,7 @@ DX_RTF_FEATURE(OFF)
 DX_XML_FEATURE(OFF)
 DX_PDF_FEATURE(ON)
 DX_PS_FEATURE(OFF)
-DX_INIT_DOXYGEN(cantera, doxygen/cantera.dox, docs) 
+DX_INIT_DOXYGEN(cantera, doc/doxygen/cantera.dox, docs) 
 
 # Generate Output Files
 AC_OUTPUT(Makefile                                                         \
@@ -146,7 +146,8 @@ AC_OUTPUT(Makefile                                                         \
                    test_problems/cathermo/VPissp/Makefile                  \
                    test_problems/cathermo/wtWater/Makefile                 \
                    test_problems/PecosTransport/Makefile                   \
-		   doxygen/Makefile                                        \
+		   docs/Makefile                                           \
+		   docs/doxygen/Makefile                                   \
 		   src/Makefile                                            \
                    src/fortran/Makefile                                    \
                    src/base/Makefile                                       \
diff --git a/doc/doxygen/aminclude.am b/doc/doxygen/aminclude.am
index 5e2adb2a1..c035d2422 100644
--- a/doc/doxygen/aminclude.am
+++ b/doc/doxygen/aminclude.am
@@ -5,6 +5,7 @@
 
 PECOS_extra_dependencies = doxygen/cantera.page \
 			   doxygen/txt_common/about.page \
+			   doxygen/txt_common/gpl.page \
 			   doxygen/txt_common/acknowledgment.page
 
 ## --------------------------------- ##
diff --git a/ext/cvode/Makefile.am b/ext/cvode/Makefile.am
index a51aa8d34..e5abaf427 100644
--- a/ext/cvode/Makefile.am
+++ b/ext/cvode/Makefile.am
@@ -1 +1 @@
-SUBDIRS=source
\ No newline at end of file
+SUBDIRS=source