diff --git a/.gitignore b/.gitignore
index 45ebf3129..657d13f6c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,4 @@
-doc/doxygen
 doc/_build
-doc/reference/kconfig/*.rst
-doc/misc
 build
 *.bak
 *.sav
diff --git a/doc/Makefile b/doc/Makefile
index 8df39d1f4..f2b6e8fec 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -11,8 +11,8 @@ endif
 SPHINXOPTS    ?= -q
 SPHINXBUILD   = sphinx-build
 SPHINXPROJ    = "Project ACRN"
-SOURCEDIR     = .
 BUILDDIR      ?= _build
+SOURCEDIR     = $(BUILDDIR)/rst/
 
 # document publication assumes the folder structure is setup
 # with the acrn-hypervisor and projectacrn.github.io repos as
@@ -33,40 +33,47 @@ help:
 	@echo "   specify RELEASE=name to publish as a tagged release version"
 	@echo "   and placed in a version subfolder.  Requires repo merge permission."
 
-.PHONY: help Makefile
+.PHONY: help Makefile copy-to-sourcedir doxy content kconfig html singlehtml clean publish
 
 # Generate the doxygen xml (for Sphinx) and copy the doxygen html to the
 # api folder for publishing along with the Sphinx-generated API docs.
 
-doxy:
-	$(Q)(cat acrn.doxyfile) | doxygen - > doc.log 2>&1
-	$(Q)find doxygen/xml/* | xargs sed -i 's/simplesect kind="pre"/simplesect kind="preconditions"/'
+copy-to-sourcedir:
+	$(Q)mkdir -p $(SOURCEDIR)
+	$(Q)rsync -rt --exclude=$(BUILDDIR) . $(SOURCEDIR)
 
-content:
-	$(Q)scripts/extract_content.py . misc
+doxy: copy-to-sourcedir
+	$(Q)(cat acrn.doxyfile ; echo "OUTPUT_DIRECTORY=$(SOURCEDIR)/doxygen" ) | doxygen - > $(BUILDDIR)/doc.log 2>&1
+	$(Q)find $(SOURCEDIR)/doxygen/xml/* | xargs sed -i 's/simplesect kind="pre"/simplesect kind="preconditions"/'
 
-kconfig:
+content: copy-to-sourcedir
+	$(Q)scripts/extract_content.py $(SOURCEDIR) misc
+
+kconfig: copy-to-sourcedir
 	$(Q)srctree=../hypervisor \
-	    python3 scripts/genrest.py Kconfig reference/kconfig/
+	    python3 scripts/genrest.py Kconfig $(SOURCEDIR)/reference/kconfig/
 
 pullsource:
 	$(Q)scripts/pullsource.sh
 
-html: doxy content kconfig
-	-$(Q)$(SPHINXBUILD) -t $(DOC_TAG) -b html -d $(BUILDDIR)/doctrees $(SOURCEDIR) $(BUILDDIR)/html $(SPHINXOPTS) $(OPTS) >> doc.log 2>&1
-	$(Q)./scripts/filter-doc-log.sh doc.log
+html: copy-to-sourcedir doxy content kconfig
+	-$(Q)$(SPHINXBUILD) -t $(DOC_TAG) -b html -d $(BUILDDIR)/doctrees $(SOURCEDIR) $(BUILDDIR)/html $(SPHINXOPTS) $(OPTS) >> $(BUILDDIR)/doc.log 2>&1
+	$(Q)./scripts/filter-doc-log.sh $(BUILDDIR)/doc.log
 
 singlehtml: doxy content kconfig
-	-$(Q)$(SPHINXBUILD) -t $(DOC_TAG) -b singlehtml -d $(BUILDDIR)/doctrees $(SOURCEDIR) $(BUILDDIR)/html $(SPHINXOPTS) $(OPTS) >> doc.log 2>&1
-	$(Q)./scripts/filter-doc-log.sh doc.log
+	-$(Q)$(SPHINXBUILD) -t $(DOC_TAG) -b singlehtml -d $(BUILDDIR)/doctrees $(SOURCEDIR) $(BUILDDIR)/html $(SPHINXOPTS) $(OPTS) >> $(BUILDDIR)/doc.log 2>&1
+	$(Q)./scripts/filter-doc-log.sh $(BUILDDIR)/doc.log
 
 # Remove generated content (Sphinx and doxygen)
 
 clean:
-	rm -fr $(BUILDDIR) doxygen
+	rm -fr $(BUILDDIR)
+	# Keeping these temporarily, but no longer strictly needed.
+	rm -fr doxygen
 	rm -fr misc
 	rm -fr reference/kconfig/*.rst
 
+
 # Copy material over to the GitHub pages staging repo
 # along with a README
 
diff --git a/doc/scripts/filter-doc-log.sh b/doc/scripts/filter-doc-log.sh
index 116ccf0d5..15297693a 100755
--- a/doc/scripts/filter-doc-log.sh
+++ b/doc/scripts/filter-doc-log.sh
@@ -10,6 +10,7 @@ KI_SCRIPT=scripts/filter-known-issues.py
 CONFIG_DIR=.known-issues/doc
 
 LOG_FILE=$1
+BUILDDIR=$(dirname $LOG_FILE)
 
 if [ -z "${LOG_FILE}" ]; then
         echo "Error in $0: missing input parameter <logfile>"
@@ -29,7 +30,7 @@ else
 fi
 
 if [ -s "${LOG_FILE}" ]; then
-   $KI_SCRIPT --config-dir ${CONFIG_DIR} ${LOG_FILE} > doc.warnings 2>&1
+   $KI_SCRIPT --config-dir ${CONFIG_DIR} ${LOG_FILE} > ${BUILDDIR}/doc.warnings 2>&1
    if [ -s doc.warnings ]; then
 	   echo
 	   echo -e "${red}New errors/warnings found, please fix them:"