diff --git a/ChangeLog b/ChangeLog
index 5dfaf1a9a0..cf0f05be9c 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,38 @@
+2006-02-17  Derek Atkins <derek@ihtfp.com>
+
+        * intl-scm/Makefile.am:
+        * lib/guile-www/Makefile.am:
+        * src/app-utils/Makefile.am:
+	* src/business/business-core/Makefile.am:
+        * src/business/business-gnome/Makefile.am:
+        * src/business/business-reports/Makefile.am:
+        * src/business/business-utils/Makefile.am:
+        * src/business/dialog-tax-table/Makefile.am:
+	* src/core-utils/Makefile.am:
+        * src/engine/Makefile.am:
+	* src/gnc-module/Makefile.am:
+	* src/gnome/Makefile.am:
+        * src/gnome-utils/Makefile.am:
+	* src/import-export/hbci/Makefile.am:
+        * src/import-export/Makefile.am:
+        * src/import-export/qif-import/Makefile.am:
+        * src/import-export/qif-io-core/Makefile.am:
+	* src/register/register-core/Makefile.am:
+	* src/report/locale-specific/us/Makefile.am:
+        * src/report/report-gnome/Makefile.am:
+        * src/report/report-system/Makefile.am:
+        * src/report/standard-reports/Makefile.am:
+        * src/report/stylesheets/Makefile.am:
+        * src/report/utility-reports/Makefile.am:
+        * src/scm/gnumeric/Makefile.am:
+        * src/scm/Makefile.am:
+        * src/scm/printing/Makefile.am:
+        * src/tax/us/Makefile.am:
+          Make the build work if the build directory is not the source
+          directory.  Also symlink .scm files into the build directory
+          so it's possible to run from it.
+	  Also fix "fin.scm installed twice", bug #168629.
+
 2006-02-15  Derek Atkins <derek@ihtfp.com>
 
 	* configure.in:  get --disable-gui to actually do what we want.
diff --git a/intl-scm/Makefile.am b/intl-scm/Makefile.am
index c803c838d6..76ed236016 100644
--- a/intl-scm/Makefile.am
+++ b/intl-scm/Makefile.am
@@ -1,3 +1,5 @@
+abs_top_srcdir=@abs_top_srcdir@
+
 EXTRA_DIST = \
   guile-strings.c \
   xgettext.scm
@@ -8,7 +10,7 @@ noinst_HEADERS = guile-strings.c
 
 BUILT_SOURCES = guile-strings.c
 
-SCMFILES = $(shell find ${top_srcdir}/src -name test -prune -o -name '*.scm' -print )
+SCMFILES = $(shell find ${abs_top_srcdir}/src -name test -prune -o -name '*.scm' -print )
 
 # This needs to be generated in srcdir
 guile-strings.c: $(SCMFILES)
diff --git a/lib/guile-www/Makefile.am b/lib/guile-www/Makefile.am
index 7d1f825dc9..f0b78ba1ae 100644
--- a/lib/guile-www/Makefile.am
+++ b/lib/guile-www/Makefile.am
@@ -10,13 +10,23 @@ gncscm_DATA = cgi.scm http.scm main.scm url.scm
 
 noinst_DATA = .scm-links
 
+if GNUCASH_SEPARATE_BUILDDIR
+SCM_FILE_LINKS = ${gncscm_DATA}
+endif
+
 .scm-links: 
 	rm -f www
 	ln -sf . www
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
 	touch .scm-links
+
 CLEANFILES = www .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}
 
 endif # GNC_HAVE_GUILE_WWW (else clause)
 
 EXTRA_DIST = README README.gnucash wwwcat cgi.scm http.scm main.scm url.scm
-
diff --git a/src/app-utils/Makefile.am b/src/app-utils/Makefile.am
index f5b2699b0e..3dce6bfd60 100644
--- a/src/app-utils/Makefile.am
+++ b/src/app-utils/Makefile.am
@@ -107,7 +107,9 @@ if GNUCASH_SEPARATE_BUILDDIR
 #For compiling
 SCM_FILE_LINKS = gw-app-utils-spec.scm
 #For executing test cases
-SCM_FILE_LINKS += app-utils.scm
+SCM_FILE_LINKS += \
+  ${gncmod_DATA} \
+  ${gncscm_DATA}
 endif
 
 .scm-links: 
diff --git a/src/business/business-core/Makefile.am b/src/business/business-core/Makefile.am
index d91e68a6da..5bafd4f368 100644
--- a/src/business/business-core/Makefile.am
+++ b/src/business/business-core/Makefile.am
@@ -85,7 +85,7 @@ if GNUCASH_SEPARATE_BUILDDIR
 #For compiling
 SCM_FILE_LINKS = gw-business-core-spec.scm
 #For executing test cases
-SCM_FILE_LINKS += business-core.scm
+SCM_FILE_LINKS += ${gncmod_DATA}
 endif
 
 .scm-links: 
diff --git a/src/business/business-gnome/Makefile.am b/src/business/business-gnome/Makefile.am
index 42a453de12..8c60b8467a 100644
--- a/src/business/business-gnome/Makefile.am
+++ b/src/business/business-gnome/Makefile.am
@@ -104,7 +104,10 @@ EXTRA_DIST = \
 
 if GNUCASH_SEPARATE_BUILDDIR
 #Only needed when srcdir and builddir are different
+#for compiling
 SCM_FILE_LINKS = gw-business-gnome-spec.scm
+#for running
+SCM_FILE_LINKS += ${gncmod_DATA}
 endif
 
 .scm-links: 
@@ -132,6 +135,5 @@ gw-business-gnome.scm gw-business-gnome.c gw-business-gnome.h: \
 	 (gw:generate-wrapset \"gw-business-gnome\")"
 
 BUILT_SOURCES = gw-business-gnome.scm gw-business-gnome.c gw-business-gnome.h
-DISTCLEANFILES = g-wrapped gnucash .scm-links ${SCM_FILE_LINKS} \
-                 gw-business-gnome.html
-
+CLEANFILES = g-wrapped gnucash .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS} gw-business-gnome.html
diff --git a/src/business/business-reports/Makefile.am b/src/business/business-reports/Makefile.am
index e63f99b711..e3872ce8b1 100644
--- a/src/business/business-reports/Makefile.am
+++ b/src/business/business-reports/Makefile.am
@@ -1,11 +1,3 @@
-.scm-links:
-	rm -f gnucash report
-	ln -sf . gnucash
-	ln -sf ${srcdir} report 
-	touch .scm-links
-
-noinst_DATA = .scm-links
-
 gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report
 gncscmmod_DATA = \
    business-reports.scm \
@@ -17,7 +9,25 @@ gncscmmod_DATA = \
    invoice.scm \
    owner-report.scm
 
+if GNUCASH_SEPARATE_BUILDDIR
+SCM_FILE_LINKS = ${gncscmmod_DATA}
+endif
+
+.scm-links:
+	rm -f gnucash report
+	ln -sf . gnucash
+	ln -sf ${srcdir} report 
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
+	touch .scm-links
+
+noinst_DATA = .scm-links
+
 EXTRA_DIST = \
   ${gncscmmod_DATA}
 
 CLEANFILES = gnucash report .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}
diff --git a/src/business/business-utils/Makefile.am b/src/business/business-utils/Makefile.am
index 3f49ef497c..5d89b5d573 100644
--- a/src/business/business-utils/Makefile.am
+++ b/src/business/business-utils/Makefile.am
@@ -41,9 +41,20 @@ EXTRA_DIST = \
 
 noinst_DATA = .scm-links
 
+if GNUCASH_SEPARATE_BUILDDIR
+SCM_FILE_LINKS = business-utils.scm \
+  ${gncscm_DATA}
+endif
+
 .scm-links: 
 	rm -f gnucash
 	ln -sf ${srcdir} gnucash 
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
 	touch .scm-links
 
-DISTCLEANFILES = gnucash .scm-links
+CLEANFILES = gnucash .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}
diff --git a/src/business/dialog-tax-table/Makefile.am b/src/business/dialog-tax-table/Makefile.am
index 5671999902..ae3f36dd94 100644
--- a/src/business/dialog-tax-table/Makefile.am
+++ b/src/business/dialog-tax-table/Makefile.am
@@ -61,7 +61,10 @@ EXTRA_DIST = \
 
 if GNUCASH_SEPARATE_BUILDDIR
 #Only needed when srcdir and builddir are different
+# for compline
 SCM_FILE_LINKS = gw-dialog-tax-table-spec.scm
+# for running
+SCM_FILE_LINKS += ${gncmod_DATA}
 endif
 
 .scm-links: 
@@ -89,5 +92,5 @@ gw-dialog-tax-table.scm gw-dialog-tax-table.c gw-dialog-tax-table.h: \
 
 BUILT_SOURCES = gw-dialog-tax-table.scm gw-dialog-tax-table.c \
 	gw-dialog-tax-table.h
-DISTCLEANFILES = g-wrapped gnucash .scm-links ${SCM_FILE_LINKS} \
-                 gw-dialog-tax-table.html
+CLEANFILES = g-wrapped gnucash .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS} gw-dialog-tax-table.html
diff --git a/src/core-utils/Makefile.am b/src/core-utils/Makefile.am
index f4482284b3..7ac831e010 100644
--- a/src/core-utils/Makefile.am
+++ b/src/core-utils/Makefile.am
@@ -67,5 +67,5 @@ gw-core-utils.scm gw-core-utils.h gw-core-utils.c gw-core-utils.html: \
            (gw:generate-wrapset \"gw-core-utils\")"
 
 BUILT_SOURCES = gw-core-utils.scm gw-core-utils.h gw-core-utils.c
-DISTCLEANFILES = g-wrapped gnucash .scm-links ${SCM_FILE_LINKS} \
-                 gw-core-utils.html
+CLEANFILES = g-wrapped gnucash .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS} gw-core-utils.html
diff --git a/src/engine/Makefile.am b/src/engine/Makefile.am
index 6a637b102c..093d9e8afc 100644
--- a/src/engine/Makefile.am
+++ b/src/engine/Makefile.am
@@ -151,7 +151,9 @@ if GNUCASH_SEPARATE_BUILDDIR
 #For compiling
 SCM_FILE_LINKS = gw-engine-spec.scm gw-kvp-spec.scm iso-4217-currencies.scm
 #For executing test cases
-SCM_FILE_LINKS += engine.scm
+SCM_FILE_LINKS += \
+  ${gncmod_DATA} \
+  ${gncscm_DATA}
 endif
 
 .scm-links: 
@@ -190,8 +192,8 @@ BUILT_SOURCES = \
   gw-engine.scm gw-engine.c gw-engine.h \
   gw-kvp.scm gw-kvp.c gw-kvp.h gncla-dir.h
 
-DISTCLEANFILES = gnucash g-wrapped .scm-links ${SCM_FILE_LINKS} \
-                 gw-engine.html gw-kvp.html gncla-dir.h
+CLEANFILES = gnucash g-wrapped .scm-links 
+DISTCLEANFILES = ${SCM_FILE_LINKS} gw-engine.html gw-kvp.html gncla-dir.h
 
 gncla-dir.h: gncla-dir.h.in
 	rm -f $@.tmp
diff --git a/src/gnc-module/Makefile.am b/src/gnc-module/Makefile.am
index 3ce11b9ac5..d9b0efd88b 100644
--- a/src/gnc-module/Makefile.am
+++ b/src/gnc-module/Makefile.am
@@ -49,7 +49,7 @@ if GNUCASH_SEPARATE_BUILDDIR
 #For compiling
 SCM_FILE_LINKS = gw-gnc-module-spec.scm
 #For executing test cases
-SCM_FILE_LINKS += gnc-module.scm
+SCM_FILE_LINKS += ${gncmod_DATA}
 endif
 
 .scm-links: 
@@ -71,7 +71,5 @@ gw-gnc-module.scm gw-gnc-module.c gw-gnc-module.h: \
 	  (gw:generate-wrapset \"gw-gnc-module\")"
 
 BUILT_SOURCES = gw-gnc-module.scm gw-gnc-module.h gw-gnc-module.c
-DISTCLEANFILES = .scm-links g-wrapped gnucash ${SCM_FILE_LINKS} \
-                 gw-gnc-module.html
-
-
+CLEANFILES = .scm-links g-wrapped gnucash
+DISTCLEANFILES = ${SCM_FILE_LINKS} gw-gnc-module.html
diff --git a/src/gnome-utils/Makefile.am b/src/gnome-utils/Makefile.am
index 3b07812eb2..36a6f4a974 100644
--- a/src/gnome-utils/Makefile.am
+++ b/src/gnome-utils/Makefile.am
@@ -280,7 +280,9 @@ if GNUCASH_SEPARATE_BUILDDIR
 #For compiling
 SCM_FILE_LINKS = gw-gnome-utils-spec.scm
 #For executing test cases
-SCM_FILE_LINKS += gnome-utils-spec.scm gnome-utils.scm
+SCM_FILE_LINKS += \
+  ${gncmod_DATA} \
+  ${gncscm_DATA}
 endif
 
 .scm-links: 
@@ -305,8 +307,8 @@ gw-gnome-utils.scm gw-gnome-utils.c gw-gnome-utils.h: \
 	  (gw:generate-wrapset \"gw-gnome-utils\")"
 
 BUILT_SOURCES += gw-gnome-utils.scm gw-gnome-utils.c gw-gnome-utils.h
-DISTCLEANFILES = gnucash g-wrapped .scm-links ${SCM_FILE_LINKS} \
-                 gw-gnome-utils.html gnc-svninfo.h
+CLEANFILES = gnucash g-wrapped .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS} gw-gnome-utils.html
 
 #
 # I hate inconsistent standards. Autotools puts help files into
diff --git a/src/gnome/Makefile.am b/src/gnome/Makefile.am
index 05a8b3c145..5d2072fb3e 100644
--- a/src/gnome/Makefile.am
+++ b/src/gnome/Makefile.am
@@ -195,6 +195,5 @@ gw-gnc.scm gw-gnc.h gw-gnc.c gw-gnc.html: \
            (primitive-load \"./gw-gnc-spec.scm\") \
            (gw:generate-wrapset \"gw-gnc\")"
 BUILT_SOURCES = gw-gnc.scm gw-gnc.h gw-gnc.c
-CLEANFILES = gnucash.keys gnucash.desktop
-DISTCLEANFILES = gnucash g-wrapped .scm-links ${SCM_FILE_LINKS} \
-                 gw-gnc.html
+CLEANFILES = gnucash.keys gnucash.desktop gnucash g-wrapped .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS} gw-gnc.html
diff --git a/src/import-export/Makefile.am b/src/import-export/Makefile.am
index 9882c79fcf..2be30a2afa 100644
--- a/src/import-export/Makefile.am
+++ b/src/import-export/Makefile.am
@@ -77,7 +77,7 @@ if GNUCASH_SEPARATE_BUILDDIR
 #For compiling
 SCM_FILE_LINKS = 
 #For executing test cases
-SCM_FILE_LINKS += generic-import.scm
+SCM_FILE_LINKS +=
 endif
 
 noinst_DATA = .scm-links
@@ -88,6 +88,12 @@ noinst_DATA = .scm-links
 	ln -sf . gnucash
 	ln -sf . generic-import
 	ln -sf . g-wrapped
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
 	touch .scm-links
 
-DISTCLEANFILES = gnucash generic-import g-wrapped .scm-links import-export
+CLEANFILES = gnucash generic-import g-wrapped .scm-links import-export
+DISTCLEANFILES = ${SCM_FILE_LINKS}
diff --git a/src/import-export/hbci/Makefile.am b/src/import-export/hbci/Makefile.am
index dbae4434e1..9424f8b480 100644
--- a/src/import-export/hbci/Makefile.am
+++ b/src/import-export/hbci/Makefile.am
@@ -82,5 +82,3 @@ ui_DATA = \
 	gnc-plugin-hbci-ui.xml
 
 EXTRA_DIST = ${gncscm_DATA} ${libgncmod_hbci_la_empty} ${ui_DATA}
-
-CLEANFILES = gnucash g-wrapped .scm-links
diff --git a/src/import-export/qif-import/Makefile.am b/src/import-export/qif-import/Makefile.am
index 2c4142071b..82ce64c215 100644
--- a/src/import-export/qif-import/Makefile.am
+++ b/src/import-export/qif-import/Makefile.am
@@ -78,6 +78,11 @@ EXTRA_DIST = \
 
 CLEANFILES =
 
+if GNUCASH_SEPARATE_BUILDDIR
+SCM_FILE_LINKS = \
+  ${gncscm_DATA}
+endif
+
 noinst_DATA = .scm-links
 
 .scm-links: 
@@ -86,5 +91,12 @@ noinst_DATA = .scm-links
 	ln -sf . import-export
 	ln -sf . gnucash 
 	ln -sf . g-wrapped 
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
 	touch .scm-links
+
 CLEANFILES += qif-import import-export gnucash g-wrapped .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}
diff --git a/src/import-export/qif-io-core/Makefile.am b/src/import-export/qif-io-core/Makefile.am
index 5259c40f1f..d79ed6c6b2 100644
--- a/src/import-export/qif-io-core/Makefile.am
+++ b/src/import-export/qif-io-core/Makefile.am
@@ -8,15 +8,6 @@ libgncmod_qifiocore_la_SOURCES = gncmod-qifiocore.c
 
 noinst_DATA = .scm-links
 
-.scm-links:
-	rm -f gnucash import-export 
-	ln -sf . gnucash
-	ln -sf . import-export
-	touch .scm-links
-
-gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/import-export/
-gncscmmod_DATA = qif-io-core.scm
-
 gncscmdir = ${GNC_SHAREDIR}/scm
 gncscm_DATA = \
 	qif-acct-table.scm \
@@ -28,4 +19,24 @@ gncscm_DATA = \
 	qif-parse.scm \
 	qif-record-xform.scm 
 
-DISTCLEANFILES = gnucash import-export .scm-links
+if GNUCASH_SEPARATE_BUILDDIR
+SCM_FILE_LINKS = \
+  ${gncscm_DATA}
+endif
+
+.scm-links:
+	rm -f gnucash import-export 
+	ln -sf . gnucash
+	ln -sf . import-export
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
+	touch .scm-links
+
+gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/import-export/
+gncscmmod_DATA = qif-io-core.scm
+
+CLEANFILES = gnucash import-export .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}
diff --git a/src/register/register-core/Makefile.am b/src/register/register-core/Makefile.am
index 7bd0c2a8ee..36df93ab27 100644
--- a/src/register/register-core/Makefile.am
+++ b/src/register/register-core/Makefile.am
@@ -101,5 +101,5 @@ gw-register-core.scm gw-register-core.c gw-register-core.h: \
 	  (gw:generate-wrapset \"gw-register-core\")"
 
 BUILT_SOURCES = gw-register-core.scm gw-register-core.c gw-register-core.h
-DISTCLEANFILES = gnucash g-wrapped register .scm-links ${SCM_FILE_LINKS} \
-                 gw-register-core.html
+CLEANFILES = gnucash g-wrapped register .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS} gw-register-core.html
diff --git a/src/report/locale-specific/us/Makefile.am b/src/report/locale-specific/us/Makefile.am
index 1f04e83d49..414585f221 100644
--- a/src/report/locale-specific/us/Makefile.am
+++ b/src/report/locale-specific/us/Makefile.am
@@ -16,9 +16,18 @@ AM_CFLAGS = \
   -I${top_srcdir}/src/gnc-module \
   ${GUILE_INCS} ${GLIB_CFLAGS}
 
+## This is unused and therefore no longer installed and/or loaded
+gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report/locale-specific
+gncscmmod_DATA = us.scm de_DE.scm
+
+gncscmothermoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report/
+gncscmothermod_DATA = taxtxf.scm taxtxf-de_DE.scm
+
 if GNUCASH_SEPARATE_BUILDDIR
 #For executing test cases
-SCM_FILE_LINKS = taxtxf.scm
+SCM_FILE_LINKS = \
+  ${gncscmmod_DATA} \
+  ${gncscmothermod_DATA}
 endif
 
 .scm-links:
@@ -36,15 +45,9 @@ endif
 
 noinst_DATA = .scm-links
 
-## This is unused and therefore no longer installed and/or loaded
-gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report/locale-specific
-gncscmmod_DATA = us.scm de_DE.scm
-
-gncscmothermoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report/
-gncscmothermod_DATA = taxtxf.scm taxtxf-de_DE.scm
-
 EXTRA_DIST = \
   ${gncscmothermod_DATA} \
   ${gncscmmod_DATA} 
 
-CLEANFILES = ${SCM_FILE_LINKS} gnucash report locale-specific us .scm-links
+CLEANFILES = gnucash report locale-specific us .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}
diff --git a/src/report/report-gnome/Makefile.am b/src/report/report-gnome/Makefile.am
index 608b8b7903..bf592d5bae 100644
--- a/src/report/report-gnome/Makefile.am
+++ b/src/report/report-gnome/Makefile.am
@@ -80,7 +80,10 @@ EXTRA_DIST = \
 
 if GNUCASH_SEPARATE_BUILDDIR
 #Only needed when srcdir and builddir are different
+#  for compiling
 SCM_FILE_LINKS = gw-report-gnome-spec.scm
+# for running
+SCM_FILE_LINKS += ${gncmod_DATA}
 endif
 
 .scm-links: 
@@ -108,5 +111,5 @@ gw-report-gnome.scm gw-report-gnome.c gw-report-gnome.h: \
 	  (gw:generate-wrapset \"gw-report-gnome\")"
 
 BUILT_SOURCES = gw-report-gnome.scm gw-report-gnome.c gw-report-gnome.h
-DISTCLEANFILES = gnucash g-wrapped report .scm-links ${SCM_FILE_LINKS} \
-                 gw-report-gnome.html
+CLEANFILES = gnucash g-wrapped report .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS} gw-report-gnome.html
diff --git a/src/report/report-system/Makefile.am b/src/report/report-system/Makefile.am
index 656e13adc3..8b53d0c7c2 100644
--- a/src/report/report-system/Makefile.am
+++ b/src/report/report-system/Makefile.am
@@ -24,9 +24,36 @@ AM_CFLAGS = \
   ${GLIB_CFLAGS} ${GUILE_INCS} \
   ${G_WRAP_COMPILE_ARGS}
 
+gncscmdir = ${GNC_SHAREDIR}/scm
+gncscm_DATA = \
+     commodity-utilities.scm  \
+     html-acct-table.scm \
+     html-barchart.scm \
+     html-document.scm \
+     html-piechart.scm \
+     html-scatter.scm \
+     html-style-info.scm \
+     html-style-sheet.scm \
+     html-table.scm \
+     html-text.scm \
+     html-utilities.scm \
+     options-utilities.scm \
+     report-utilities.scm \
+     report.scm 
+
+gncmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report-system
+
+gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report/
+gncscmmod_DATA = report-system.scm
+
 if GNUCASH_SEPARATE_BUILDDIR
 #For executing test cases
-SCM_FILE_LINKS = report-system.scm gw-report-system-spec.scm
+# for compiling
+SCM_FILE_LINKS = gw-report-system-spec.scm
+# for running
+SCM_FILE_LINKS += \
+  ${gncscmmod_DATA} \
+  ${gncscm_DATA}
 endif
 
 .scm-links:
@@ -41,11 +68,6 @@ if GNUCASH_SEPARATE_BUILDDIR
 endif
 	touch .scm-links
 
-gncmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report-system
-
-gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report/
-gncscmmod_DATA = report-system.scm
-
 libgw_report_system_la_SOURCES = gw-report-system.c
 gwmoddir = ${GNC_GWRAP_LIBDIR}
 gwmod_DATA = gw-report-system.scm gw-report-system-spec.scm
@@ -53,23 +75,6 @@ gwmod_DATA = gw-report-system.scm gw-report-system-spec.scm
 noinst_HEADERS = gw-report-system.h
 noinst_DATA = .scm-links gw-report-system.h
 
-gncscmdir = ${GNC_SHAREDIR}/scm
-gncscm_DATA = \
-     commodity-utilities.scm  \
-     html-acct-table.scm \
-     html-barchart.scm \
-     html-document.scm \
-     html-piechart.scm \
-     html-scatter.scm \
-     html-style-info.scm \
-     html-style-sheet.scm \
-     html-table.scm \
-     html-text.scm \
-     html-utilities.scm \
-     options-utilities.scm \
-     report-utilities.scm \
-     report.scm 
-
 EXTRA_DIST = ${gncscmmod_DATA} ${gncscm_DATA} ${gwmod_DATA}
 
 CLEANFILES = ${SCM_FILE_LINKS} gnucash report .scm-links
@@ -87,5 +92,5 @@ gw-report-system.scm gw-report-system.c gw-report-system.h: \
 	  (gw:generate-wrapset \"gw-report-system\")"
 
 BUILT_SOURCES = gw-report-system.scm gw-report-system.c gw-report-system.h
-DISTCLEANFILES = gnucash g-wrapped report .scm-links ${SCM_FILE_LINKS} \
-                 gw-report-system.html
+CLEANFILES = gnucash g-wrapped report .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS} gw-report-system.html
diff --git a/src/report/standard-reports/Makefile.am b/src/report/standard-reports/Makefile.am
index 0da1402481..8c9a4b257f 100644
--- a/src/report/standard-reports/Makefile.am
+++ b/src/report/standard-reports/Makefile.am
@@ -10,14 +10,6 @@ AM_CFLAGS = \
   -I${top_srcdir}/src/gnc-module \
   ${GUILE_INCS} ${GLIB_CFLAGS}
 
-.scm-links:
-	rm -f gnucash report
-	ln -sf . gnucash
-	ln -sf ${srcdir} report 
-	touch .scm-links
-
-noinst_DATA = .scm-links
-
 gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report/
 gncscmmod_DATA = \
    account-piecharts.scm \
@@ -41,6 +33,25 @@ gncscmmod_DATA = \
    general-ledger.scm \
    transaction.scm 
 
+if GNUCASH_SEPARATE_BUILDDIR
+#For executing test cases
+SCM_FILE_LINKS = ${gncscmmod_DATA}
+endif
+
+.scm-links:
+	rm -f gnucash report
+	ln -sf . gnucash
+	ln -sf ${srcdir} report 
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
+	touch .scm-links
+
+noinst_DATA = .scm-links
+
 EXTRA_DIST = ${gncscmmod_DATA}
 
 CLEANFILES = gnucash report .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}
diff --git a/src/report/stylesheets/Makefile.am b/src/report/stylesheets/Makefile.am
index 2e789a3ed0..e1ee155c9b 100644
--- a/src/report/stylesheets/Makefile.am
+++ b/src/report/stylesheets/Makefile.am
@@ -27,21 +27,31 @@ AM_CFLAGS = \
   ${QOF_CFLAGS} \
   ${GNOME_CFLAGS}
 
+gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report/
+gncscmmod_DATA = \
+  stylesheets.scm \
+  stylesheet-plain.scm \
+  stylesheet-fancy.scm \
+  stylesheet-easy.scm
+
+if GNUCASH_SEPARATE_BUILDDIR
+#For executing test cases
+SCM_FILE_LINKS = ${gncscmmod_DATA}
+endif
+
 .scm-links:
 	rm -f gnucash report
 	ln -sf . gnucash
 	ln -sf ${srcdir} report 
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
 	touch .scm-links
 
 noinst_DATA = .scm-links
 
-gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report/
-gncscmmod_DATA = \
-  stylesheets.scm \
-  stylesheet-plain.scm \
-  stylesheet-fancy.scm \
-  stylesheet-easy.scm
-
 uidir = $(GNC_UI_DIR)
 dist_ui_DATA = \
 	gnc-plugin-stylesheets-ui.xml
@@ -49,4 +59,4 @@ dist_ui_DATA = \
 EXTRA_DIST = ${gncscmmod_DATA}
 
 CLEANFILES = gnucash report .scm-links
-
+DISTCLEANFILES = ${SCM_FILE_LINKS}
diff --git a/src/report/utility-reports/Makefile.am b/src/report/utility-reports/Makefile.am
index b085d8935d..a1a55ff507 100644
--- a/src/report/utility-reports/Makefile.am
+++ b/src/report/utility-reports/Makefile.am
@@ -12,14 +12,6 @@ AM_CFLAGS = \
   -I${top_srcdir}/src/gnc-module \
   ${GUILE_INCS} ${GLIB_CFLAGS}
 
-.scm-links:
-	rm -f gnucash report
-	ln -sf . gnucash
-	ln -sf ${srcdir} report 
-	touch .scm-links
-
-noinst_DATA = .scm-links
-
 gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/report/
 gncscmmod_DATA = \
   hello-world.scm \
@@ -29,6 +21,26 @@ gncscmmod_DATA = \
   welcome-to-gnucash.scm \
   test-graphing.scm
 
+if GNUCASH_SEPARATE_BUILDDIR
+#For separate build directory
+SCM_FILE_LINKS = \
+  ${gncscmmod_DATA}
+endif
+
+.scm-links:
+	rm -f gnucash report
+	ln -sf . gnucash
+	ln -sf ${srcdir} report 
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
+	touch .scm-links
+
+noinst_DATA = .scm-links
+
 EXTRA_DIST = ${gncscmmod_DATA}
 
 CLEANFILES = gnucash report .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}
diff --git a/src/scm/Makefile.am b/src/scm/Makefile.am
index 861caffc87..2cad2b5993 100644
--- a/src/scm/Makefile.am
+++ b/src/scm/Makefile.am
@@ -4,10 +4,9 @@ SUBDIRS = gnumeric printing
 gncscmdir = ${GNC_SCM_INSTALL_DIR}
 gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash
 
-gncscmmod_DATA = process.scm main.scm price-quotes.scm fin.scm
+gncscmmod_DATA = process.scm main.scm price-quotes.scm
 
 gnc_regular_scm_files = \
-  build-config.scm \
   command-line.scm \
   doc.scm \
   fin.scm \
@@ -16,16 +15,29 @@ gnc_regular_scm_files = \
   substring-search.scm \
   xml-generator.scm
 
-gncscm_DATA = ${gnc_regular_scm_files}
+gncscm_DATA = \
+  build-config.scm \
+  ${gnc_regular_scm_files}
 
 noinst_DATA = .scm-links
 
 configdir = ${GNC_CONFIGDIR}
 config_DATA = config
 
+if GNUCASH_SEPARATE_BUILDDIR
+SCM_FILE_LINKS = \
+  ${gncscmmod_DATA} \
+  ${gnc_regular_scm_files}
+endif
+
 .scm-links: 
 	rm -f gnucash
 	ln -sf ${srcdir} gnucash
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
 	touch .scm-links
 
 SCM_FILES = ${gncscm_DATA} ${gncscmmod_DATA}
@@ -47,5 +59,6 @@ build-config.scm: ${srcdir}/build-config.scm.in Makefile
             -e 's:@-GNC_HELPDIR-@:${GNC_HELPDIR}:'
 	mv $@.tmp $@
 
-DISTCLEANFILES = gnucash .scm-links
+CLEANFILES = gnucash .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}
 MAINTAINERCLEANFILES = build-config.scm
diff --git a/src/scm/gnumeric/Makefile.am b/src/scm/gnumeric/Makefile.am
index a551af8e76..8a1f3d14de 100644
--- a/src/scm/gnumeric/Makefile.am
+++ b/src/scm/gnumeric/Makefile.am
@@ -1,9 +1,25 @@
-
 gncscmdir = ${GNC_SCM_INSTALL_DIR}/gnumeric
-
 gncscm_DATA = \
   gnumeric-utilities.scm \
   table-utils.scm
 
+if GNUCASH_SEPARATE_BUILDDIR
+SCM_FILE_LINKS = \
+  ${gncscm_DATA}
+endif
+
+.scm-links:
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
+	touch .scm-links
+
+noinst_DATA = .scm-links
+
 EXTRA_DIST = \
   ${gncscm_DATA}
+
+CLEANFILES = .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}
diff --git a/src/scm/printing/Makefile.am b/src/scm/printing/Makefile.am
index 9a43c00742..bfd28f7fef 100644
--- a/src/scm/printing/Makefile.am
+++ b/src/scm/printing/Makefile.am
@@ -1,8 +1,25 @@
-
 gncscmdir = ${GNC_SCM_INSTALL_DIR}/printing
 gncscm_DATA = print-check.scm
 
 gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/printing
 gncscmmod_DATA = number-to-words.scm
 
+if GNUCASH_SEPARATE_BUILDDIR
+SCM_FILE_LINKS = \
+  ${gncscmmod_DATA} \
+  ${gncscm_DATA}
+endif
+
+.scm-links:
+if GNUCASH_SEPARATE_BUILDDIR
+	for X in ${SCM_FILE_LINKS} ; do \
+	  ln -sf ${srcdir}/$$X . ; \
+	done
+endif
+	touch .scm-links
+
+noinst_DATA = .scm-links
+
 EXTRA_DIST = ${gncscmmod_DATA} ${gncscm_DATA}
+CLEANFILES = .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}
diff --git a/src/tax/us/Makefile.am b/src/tax/us/Makefile.am
index 10bd08a8a2..a81fd203ab 100644
--- a/src/tax/us/Makefile.am
+++ b/src/tax/us/Makefile.am
@@ -14,9 +14,17 @@ AM_CFLAGS = \
   -I${top_srcdir}/src/gnc-module \
   ${GLIB_CFLAGS} ${GUILE_INCS}
 
+gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/tax
+gncscmmod_DATA = us.scm de_DE.scm
+
+gncscmdir = ${GNC_SHAREDIR}/scm
+gncscm_DATA = txf.scm txf-help.scm txf-de_DE.scm txf-help-de_DE.scm 
+
 if GNUCASH_SEPARATE_BUILDDIR
 #For executing test cases
-SCM_FILE_LINKS = us.scm de_DE.scm
+SCM_FILE_LINKS = \
+  ${gncscmmod_DATA} \
+  ${gncscm_DATA}
 endif
 
 .scm-links:
@@ -32,14 +40,9 @@ endif
 
 noinst_DATA = .scm-links
 
-gncscmmoddir = ${GNC_SHAREDIR}/guile-modules/gnucash/tax
-gncscmmod_DATA = us.scm de_DE.scm
-
-gncscmdir = ${GNC_SHAREDIR}/scm
-gncscm_DATA = txf.scm txf-help.scm txf-de_DE.scm txf-help-de_DE.scm 
-
 EXTRA_DIST = \
   ${gncscmmod_DATA} \
   ${gncscm_DATA}
 
-CLEANFILES = ${SCM_FILE_LINKS} gnucash tax .scm-links
+CLEANFILES = gnucash tax .scm-links
+DISTCLEANFILES = ${SCM_FILE_LINKS}