diff --git a/SWIG/Makefile.in b/SWIG/Makefile.in
new file mode 100644
index 000000000..b25b13b14
--- /dev/null
+++ b/SWIG/Makefile.in
@@ -0,0 +1,52 @@
+#######################################################################
+# $Header$
+# Simplified Wrapper and Interface Generator (SWIG)
+# 
+#######################################################################
+
+TARGET     = swig
+SHELL  = /bin/sh
+CC     = @CC@
+CXX    = @CXX@
+LIBS   =
+
+#
+#
+#
+
+SWIGOBJS   = SWIG1.1/*.o Modules1.1/*.o DOH/Doh/*.o Core/*.o Preprocessor/*.o
+
+swig: objs
+	$(CXX) $(SWIGOBJS) $(LIBS) -o $(TARGET)
+
+objs:		
+	@ORIG_DIR=`pwd`; \
+	for i in `ls Source/`; \
+	do \
+	  if [ -d Source/$$i -a -f Source/$$i/Makefile ]; then \
+            (cd Source/$$i && $(MAKE)) || exit 1; \
+            cd $$ORIG_DIR ;\
+          fi \
+        done;
+
+clean:
+	@ORIG_DIR=`pwd`; \
+	for i in `ls Source/`; \
+	do \
+	  if [ -d Source/$$i -a -f Source/$$i/Makefile ]; then \
+            (cd Source/$$i && $(MAKE) clean) || exit 1; \
+            cd $$ORIG_DIR ;\
+          fi \
+        done;
+	rm -f swig
+
+nuke:
+	@ORIG_DIR=`pwd`; \
+	for i in `ls Source/`; \
+	do \
+	  if [ -d Source/$$i -a -f Source/$$i/Makefile ]; then \
+            (cd Source/$$i && $(MAKE) nuke) || exit 1; \
+            cd $$ORIG_DIR ;\
+          fi \
+        done;
+	rm -f Makefile Makefile.template config.*
diff --git a/SWIG/Source/README b/SWIG/README
similarity index 100%
rename from SWIG/Source/README
rename to SWIG/README
diff --git a/SWIG/Source/.cvsignore b/SWIG/Source/.cvsignore
new file mode 100644
index 000000000..e69de29bb
diff --git a/SWIG/Source/DOH/.cvsignore b/SWIG/Source/DOH/.cvsignore
new file mode 100644
index 000000000..2ee5b3e29
--- /dev/null
+++ b/SWIG/Source/DOH/.cvsignore
@@ -0,0 +1,2 @@
+Makefile
+y.tab.*
diff --git a/SWIG/Source/DOH/Doh/Makefile b/SWIG/Source/DOH/Doh/Makefile
deleted file mode 100644
index 644b300e4..000000000
--- a/SWIG/Source/DOH/Doh/Makefile
+++ /dev/null
@@ -1,50 +0,0 @@
-# Generated automatically from Makefile.in by configure.
-#######################################################################
-# $Header$
-# DOH 
-#######################################################################
-
-#.KEEP_STATE:
-
-# Set your C++ compiler here.   g++ works on most machines,
-# but you might have to change it depending on your installation.
-#
-CC      = cc
-prefix     = /usr/local
-
-# Comment out the following line if you're on an SGI or don't have ranlib!
-RANLIB  = ranlib
-AR      = ar
-
-########################################################################
-# Normally, you shouldn't have to change anything below this point     #
-########################################################################
-
-LIBOBJS = callable.o void.o fio.o memory.o base.o file.o list.o hash.o string.o 
-
-LIBSRCS = callable.c void.c fio.c memory.c base.c file.c list.c hash.c string.c
-
-LIBHEADERS = ../Include/doh.h
-LIB      = ../libdoh.a
-INCLUDE  = -I../Include
-CFLAGS   = 
-SHELL  = /bin/sh
-
-#
-# Rules for creation of a .o file from .cxx
-.SUFFIXES: .c
-.c.o: 
-	$(CC) $(INCLUDE) $(CFLAGS) -c -o $*.o $<
-
-all: $(LIB)
-
-$(LIB): $(LIBOBJS) 
-	@echo "Building library"
-	$(AR) cr $(LIB) $(LIBOBJS)
-	$(RANLIB) $(LIB)
-
-clean::
-	rm -f *.o ../libdoh.a
-nuke::
-	rm -f Makefile *~ #* core a.out
-
diff --git a/SWIG/Source/Makefile.in b/SWIG/Source/Makefile.in
deleted file mode 100644
index ecfb2c084..000000000
--- a/SWIG/Source/Makefile.in
+++ /dev/null
@@ -1,46 +0,0 @@
-#######################################################################
-# $Header$
-# Simplified Wrapper and Interface Generator (SWIG)
-# 
-#######################################################################
-
-TARGET     = swig
-SHELL  = /bin/sh
-CC     = @CC@
-CXX    = @CXX@
-LIBS   =
-
-#
-#
-#
-
-DIRS       = DOH Core Preprocessor SWIG1.1 Modules1.1
-SWIGOBJS   = SWIG1.1/*.o Modules1.1/*.o DOH/Doh/*.o Core/*.o Preprocessor/*.o
-
-swig: objs
-	$(CXX) $(SWIGOBJS) $(LIBS) -o $(TARGET)
-
-objs:		
-	@for i in $(DIRS); \
-	do \
-          cd $$i; $(MAKE); cd .. ;\
-        done;
-
-clean:
-	@for i in $(DIRS); \
-	do \
-          cd $$i; $(MAKE) clean; cd ..; \
-        done;
-	rm -f swig
-
-nuke: 	clean
-	@cd SWIG; $(MAKE) nuke
-	@cd Modules; $(MAKE) nuke
-	@cd Examples; $(MAKE) nuke
-	@cd Tests; $(MAKE) clean
-	@cd Runtime; $(MAKE) clean
-	rm -f Makefile Makefile.template config.*
-
-
-
-
diff --git a/SWIG/Source/Modules1.1/.cvsignore b/SWIG/Source/Modules1.1/.cvsignore
new file mode 100644
index 000000000..2ee5b3e29
--- /dev/null
+++ b/SWIG/Source/Modules1.1/.cvsignore
@@ -0,0 +1,2 @@
+Makefile
+y.tab.*
diff --git a/SWIG/Source/Preprocessor/.cvsignore b/SWIG/Source/Preprocessor/.cvsignore
new file mode 100644
index 000000000..2ee5b3e29
--- /dev/null
+++ b/SWIG/Source/Preprocessor/.cvsignore
@@ -0,0 +1,2 @@
+Makefile
+y.tab.*
diff --git a/SWIG/Source/SWIG1.1/.cvsignore b/SWIG/Source/SWIG1.1/.cvsignore
new file mode 100644
index 000000000..c2e4380a3
--- /dev/null
+++ b/SWIG/Source/SWIG1.1/.cvsignore
@@ -0,0 +1,5 @@
+Makefile
+y.tab.*
+parser.h
+parser.cxx
+
diff --git a/SWIG/Source/Swig/.cvsignore b/SWIG/Source/Swig/.cvsignore
new file mode 100644
index 000000000..2ee5b3e29
--- /dev/null
+++ b/SWIG/Source/Swig/.cvsignore
@@ -0,0 +1,2 @@
+Makefile
+y.tab.*
diff --git a/SWIG/Source/configure.in b/SWIG/configure.in
similarity index 93%
rename from SWIG/Source/configure.in
rename to SWIG/configure.in
index c389be24f..382a1a266 100644
--- a/SWIG/Source/configure.in
+++ b/SWIG/configure.in
@@ -1,5 +1,5 @@
 dnl Process this file with autoconf to produce a configure script.
-AC_INIT(Core/swigcore.h)
+AC_INIT(Source/Core/swigcore.h)
 AC_PREREQ(2.0)
 
 # Set name for machine-dependent library files
@@ -168,5 +168,8 @@ fi
 AC_MSG_RESULT($RPATH)
 AC_SUBST(RPATH)
 
-
-AC_OUTPUT(Makefile Core/Makefile DOH/Doh/Makefile DOH/Makefile Preprocessor/Makefile SWIG1.1/Makefile Modules1.1/Makefile)
+# Note we write DOH's Makefiles for it -- if it has any special configure
+# stuff, we're going to skip it!
+AC_OUTPUT(Makefile Source/Core/Makefile Source/DOH/Doh/Makefile 
+    Source/DOH/Makefile Source/Preprocessor/Makefile Source/SWIG1.1/Makefile
+    Source/Modules1.1/Makefile)