diff --git a/.gitignore b/.gitignore
index f3b8cabd5..30f984f4d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,14 +1,14 @@
 *~
 *.pyc
 /Makefile
-/aclocal.m4
 /Bootstrap.*/
+/_build/
+/aclocal.m4
 /config.log
 /config.status
 /configure
 /config/build-aux/
 /autom4te*.cache/
-/sources/bootstrap1-registry/
 /sources/corba/scepter/front-end/file/parser.dylan
 /sources/corba/orb/iop-protocol/
 /sources/corba/orb/ir-protocol/
diff --git a/Makefile.in b/Makefile.in
index 74f0845f8..ad2a24f7c 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -7,7 +7,7 @@
 #   possible during cross compilation) then the workspace tool needs to be told
 #   to generate registries for that platform instead.
 # * Make sure it's still possible to build when off-network, as long as deps
-#   are already installed.
+#   are already installed. dylan-tool probably needs changes to make this work.
 
 prefix          = @prefix@
 
@@ -66,20 +66,25 @@ all: @bootstrap_target@
 # registry and submodules. (In future we can use the dylan-tool bundled with
 # the OD release instead of building it here.)
 
+# WORKSPACE_DIR is where dylan-tool generates the registry and puts the _build
+# directory. See https://opendylan.org/package/dylan-tool/index.html#workspaces
+#
 # TODO: use `$(DYLAN_TOOL) status --directory` instead, when that is fixed to
-# output only the directory name.
+# output only the workspace directory name. That will handle multi-repository
+# workspaces correctly.
+WORKSPACE_DIR = $(abs_srcdir)
 
-WORKSPACE_DIR := $(shell dirname $(abs_srcdir))
-DYLAN_TOOL_APP = $(WORKSPACE_DIR)/_build/bin/dylan-tool
+DYLAN_TOOL_APP = $(abs_srcdir)/_build/sbin/dylan-tool-app
 
 build-dylan-tool:
 	@echo Building dylan-tool...
-	@OPEN_DYLAN_USER_ROOT=$(WORKSPACE_DIR)/_build \
+	@OPEN_DYLAN_USER_ROOT=$(abs_srcdir)/_build \
+	  OPEN_DYLAN_USER_REGISTRIES=$(abs_srcdir)/sources/app/dylan-tool/registry \
 	  $(MAKE) -C sources/app/dylan-tool build
 
 # Add --verbose before "update" to debug.
 update-workspace:
-	$(DYLAN_TOOL_APP) update
+	$(DYLAN_TOOL_APP) --verbose update
 
 ########################################################################
 # Stage 1 builds a compiler that can understand new primitives used in the
@@ -90,9 +95,10 @@ update-workspace:
 
 BOOTSTRAP_1_ROOT = $(abs_builddir)/Bootstrap.1
 
-# This must be in the same directory as the main registry because files are
-# copied from one to the other and the relative pathnames won't work otherwise.
-BOOTSTRAP_1_REGISTRY = $(WORKSPACE_DIR)/bootstrap1-registry
+# Note that putting this registry anywhere but in sources/ only works because
+# dylan-tool generates files with absolute pathnames. Relative pathnames
+# wouldn't work when the registry is copied to a different directory.
+BOOTSTRAP_1_REGISTRY = $(BOOTSTRAP_1_ROOT)/registry
 
 BOOTSTRAP_1_ENV = \
         OPEN_DYLAN_TARGET_PLATFORM=$(TARGET_PLATFORM) \
@@ -117,7 +123,7 @@ bootstrap-stage-1-dirs:
 # directory.
 $(BOOTSTRAP_1_REGISTRY): update-workspace
 	mkdir -p $(BOOTSTRAP_1_REGISTRY)
-	cp -r $(WORKSPACE_DIR)/registry/$(TARGET_PLATFORM) $(BOOTSTRAP_1_REGISTRY)
+	cp -r $(WORKSPACE_DIR)/registry/* $(BOOTSTRAP_1_REGISTRY)
 	for lib in $(BOOTSTRAP_1_PRIMITIVE_LIBS); do \
 	  rm -f $(BOOTSTRAP_1_REGISTRY)/*/$$lib; \
 	done
@@ -306,7 +312,6 @@ clean:
 	-rm -rf $(abs_builddir)/Bootstrap.3
 	-rm -rf $(abs_builddir)/release
 	-rm -rf $(abs_builddir)/opendylan-*.tar.bz2
-	-rm -rf $(BOOTSTRAP_1_REGISTRY)
 	-rm -rf $(WORKSPACE_DIR)/registry
 	-rm -rf $(WORKSPACE_DIR)/_build
 	@for target_platform in $(RUNTIME_TARGET_PLATFORMS); do \
@@ -342,7 +347,7 @@ distclean: clean
 	-rm -f Makefile
 	-rm -f sources/lib/run-time/Makefile
 	-rm -f sources/jamfiles/Makefile sources/jamfiles/config.jam
-	-rm -rf build-aux
+	-rm -rf config/build-aux
 	-rm -rf autom4te.cache
 
 mostlyclean: