diff --git a/doc/Makefile b/doc/Makefile
index 7f4c35cd..78c2785c 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -3,9 +3,9 @@ TARGET = IPhreeqc.chm
 DOXYGEN = doxygen
 
 HEADERS = \
-	../include/IPhreeqc.h \
-	../include/Var.h \
-	../include/IPhreeqc.hpp
+	../src/IPhreeqc.h \
+	../src/Var.h \
+	../src/IPhreeqc.hpp
 
 EXAMPLES = \
 	examples/AccumulateLine.c \
@@ -19,10 +19,10 @@ EXAMPLES = \
 	examples/F90CreateIPhreeqc.f90 \
 	examples/F90DestroyIPhreeqc.f90 \
 	examples/F90GetComponent.f90 \
+	examples/F90GetDumpStringLine.f90 \
 	examples/F90GetLogStringLine.f90 \
 	examples/F90GetOutputStringLine.f90 \
-	examples/F90GetSelectedOutputValue.f90 \
-	examples/F90GetDumpStringLine.f90
+	examples/F90GetSelectedOutputValue.f90
 
 
 all: $(TARGET)
diff --git a/doc/examples/Makefile b/doc/examples/Makefile
index 07ad0c53..527a425b 100644
--- a/doc/examples/Makefile
+++ b/doc/examples/Makefile
@@ -1,11 +1,11 @@
 CC = gcc
-CPPFLAGS = -I../../include 
+CPPFLAGS = -I../../src -I../../src/phreeqcpp
 CXX = g++
 DEFS = -DNDEBUG=1 -DFC_FUNC\(name,NAME\)=name\ \#\#\ _ -DFC_FUNC_\(name,NAME\)=name\ \#\#\ _ -DFC_MAIN=MAIN__ 
 F77 = gfortran
 FC = gfortran
 CFLAGS = -g -O2 -Wall
-FFLAGS = -I../../include -g -O2 -Wall
+FFLAGS = -I../../src -g -O2 -Wall
 FCLIBS =  -L/usr/lib/gcc/i586-manbo-linux-gnu/4.4.1 -L/usr/lib/gcc/i586-manbo-linux-gnu/4.4.1/../../.. -lgfortranbegin -lgfortran -lm
 LIBTOOL = /bin/sh ../../_build/libtool
 LDFLAGS = 
diff --git a/include/IPhreeqc.f.inc b/src/IPhreeqc.f.inc
similarity index 100%
rename from include/IPhreeqc.f.inc
rename to src/IPhreeqc.f.inc
diff --git a/include/IPhreeqc.f90.inc b/src/IPhreeqc.f90.inc
similarity index 100%
rename from include/IPhreeqc.f90.inc
rename to src/IPhreeqc.f90.inc
diff --git a/include/IPhreeqc.h b/src/IPhreeqc.h
similarity index 100%
rename from include/IPhreeqc.h
rename to src/IPhreeqc.h
diff --git a/include/IPhreeqc.hpp b/src/IPhreeqc.hpp
similarity index 100%
rename from include/IPhreeqc.hpp
rename to src/IPhreeqc.hpp
diff --git a/include/IPhreeqcCallbacks.h b/src/IPhreeqcCallbacks.h
similarity index 100%
rename from include/IPhreeqcCallbacks.h
rename to src/IPhreeqcCallbacks.h
diff --git a/src/Makefile.am b/src/Makefile.am
index 8b11517d..a03c80f6 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,6 +1,6 @@
 EXTRA_DIST = fwrap2.cpp fwrap3.cpp
 
-AM_CPPFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/src/phreeqcpp -I$(top_srcdir)/src/phreeqcpp/phreeqc
+AM_CPPFLAGS=-I$(top_srcdir)/src -I$(top_srcdir)/src/phreeqcpp -I$(top_srcdir)/src/phreeqcpp/phreeqc
 
 # libtool libraries to build
 lib_LTLIBRARIES=libiphreeqc.la
@@ -141,10 +141,12 @@ libiphreeqc_la_SOURCES=\
 	phreeqcpp/phreeqc/utilities.cpp
 
 include_HEADERS=\
-	$(top_srcdir)/include/IPhreeqc.h\
-	$(top_srcdir)/include/IPhreeqc.hpp\
-	$(top_srcdir)/include/IPhreeqcCallbacks.h\
-	$(top_srcdir)/include/Var.h
+	$(top_srcdir)/src/IPhreeqc.h\
+	$(top_srcdir)/src/IPhreeqc.hpp\
+	$(top_srcdir)/src/IPhreeqcCallbacks.h\
+	$(top_srcdir)/src/Var.h\
+	$(top_srcdir)/src/phreeqcpp/PHRQ_io.h\
+	$(top_srcdir)/src/phreeqcpp/Keywords.h
 
 
 if BUILD_FORTRAN
@@ -155,8 +157,8 @@ libiphreeqc_la_SOURCES+=\
 	IPhreeqcF.f
 
 include_HEADERS+=\
-	$(top_srcdir)/include/IPhreeqc.f90.inc\
-	$(top_srcdir)/include/IPhreeqc.f.inc
+	$(top_srcdir)/src/IPhreeqc.f90.inc\
+	$(top_srcdir)/src/IPhreeqc.f.inc
 
 endif
 
diff --git a/include/Var.h b/src/Var.h
similarity index 100%
rename from include/Var.h
rename to src/Var.h
diff --git a/tests/Makefile.am b/tests/Makefile.am
index 21c9650b..f6a0717b 100644
--- a/tests/Makefile.am
+++ b/tests/Makefile.am
@@ -1,8 +1,8 @@
 EXTRA_DIST = test_c.vcproj test_cxx.vcproj test_f90.vfproj test_f.vfproj main77.f main.f90
 
-AM_CPPFLAGS = -I$(top_srcdir)/include
-AM_FCFLAGS = -I$(top_srcdir)/include
-AM_FFLAGS = -I$(top_srcdir)/include
+AM_CPPFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/src/phreeqcpp
+AM_FCFLAGS = -I$(top_srcdir)/src
+AM_FFLAGS = -I$(top_srcdir)/src
 
 TESTS = test_c test_cxx
 check_PROGRAMS = test_c test_cxx