diff --git a/src/doc/.cvsignore b/src/doc/.cvsignore
index 282522db03..e009dad290 100644
--- a/src/doc/.cvsignore
+++ b/src/doc/.cvsignore
@@ -1,2 +1,5 @@
+doxygen.cfg
+doxygen.log
+html
 Makefile
 Makefile.in
diff --git a/src/doc/Makefile.am b/src/doc/Makefile.am
index 5d5be5745e..106c7f3374 100644
--- a/src/doc/Makefile.am
+++ b/src/doc/Makefile.am
@@ -11,7 +11,7 @@ EXTRA_DIST = \
   finutil.html \
   plugin.txt \
   tax.txt \
-  doxygen.cfg
+  doxygen.cfg.in
 
 docdir = ${GNC_DOC_INSTALL_DIR}
 
@@ -19,7 +19,7 @@ all:
 
 doc: doxygen.cfg
 	echo "doc: " && pwd && 	echo "distdir: " && echo $(distdir)
-	rm -rf html/ refman.pdf
+	rm -rf html refman.pdf
 	$(DOXYGEN) doxygen.cfg
 #	$(MAKE) -C latex/ 
 #	mv latex/refman.pdf ./refman.pdf
@@ -27,12 +27,11 @@ doc: doxygen.cfg
 dist-hook:
 	echo "dist-hook: " && pwd
 	cd $(srcdir) && pwd && rm -rf html refman.pdf && $(DOXYGEN) doxygen.cfg
-	cp -rp $(srcdir)/html ${distdir}
+	cp -rp html ${distdir}
 
 clean-local:
 	echo "clean-local: " && pwd
 	rm -rf latex/
-	rm -f *~
 	rm -f doxygen.log
 
 maintainer-clean-local: clean-local
@@ -41,9 +40,20 @@ maintainer-clean-local: clean-local
 
 install-data-hook:
 	$(mkinstalldirs) $(DESTDIR)$(docdir)/html
-#	mkdir -p $(srcdir)/html #Workaround to allow libofx-cvs user to install without doc.
+	mkdir -p html #Workaround to allow libofx-cvs user to install without doc.
 #	cp -rp $(srcdir)/html ${docdir}
-	cp -rp $(srcdir)/html $(DESTDIR)$(docdir)/html
+	cp -rp html $(DESTDIR)$(docdir)/html
 
 uninstall-hook:
 	rm -rf ${docdir}/html
+
+## We borrow guile's convention and use @-...-@ as the substitution
+## brackets here, instead of the usual @...@.  This prevents autoconf
+## from substituting the values directly into the left-hand sides of
+## the sed substitutions.
+doxygen.cfg: doxygen.cfg.in Makefile
+	rm -f $@.tmp
+	sed < $< > $@.tmp \
+            -e 's:@-top_srcdir-@:${top_srcdir}:g'
+	mv $@.tmp $@
+
diff --git a/src/doc/doxygen.cfg b/src/doc/doxygen.cfg.in
similarity index 99%
rename from src/doc/doxygen.cfg
rename to src/doc/doxygen.cfg.in
index 91d7f3af0b..189f14f064 100644
--- a/src/doc/doxygen.cfg
+++ b/src/doc/doxygen.cfg.in
@@ -56,7 +56,7 @@ WARN_LOGFILE           = doxygen.log
 #---------------------------------------------------------------------------
 # configuration options related to the input files
 #---------------------------------------------------------------------------
-INPUT                  = ../
+INPUT                  = @-top_srcdir-@/src
 FILE_PATTERNS          = 
 RECURSIVE              = YES
 EXCLUDE                =