Bring build process in line with CNERG

Makefile

@@ -26,7 +26,7 @@ help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  gh-preview to build HTML in directory $BUILDDIR for testing"
 	@echo "  gh-revert  to cleanup HTML build in directory $BUILDDIR after testing"
-	@echo "  gh-pages   final build and push from source branch to master branch"
+	@echo "  gh-publish final build and push from source branch to master branch"
 	@echo "  html       to make standalone HTML files"
 	@echo "  dirhtml    to make HTML files named index.html in directories"
 	@echo "  singlehtml to make a single large HTML file"
@@ -59,10 +59,12 @@ gh-publish:
 	git checkout $(GH_PUBLISH_BRANCH)
 	git checkout $(GH_SOURCE_BRANCH) -- $(GH_SOURCE_DIR)
 	git reset HEAD 
+	make clean
 	make html
 	rsync -a $(BUILDDIR)/* .
+	rsync -a $(BUILDDIR)/.* .
+	git add `(cd $(BUILDDIR); find . -type f; cd ..)`
 	rm -rf $(GH_SOURCE_DIR) $(BUILDDIR)
-	git add -A 
 	git commit -m "Generated $(GH_PUBLISH_BRANCH) for `git log $(GH_SOURCE_BRANCH) -1 --pretty=short --abbrev-commit`" && git push $(GH_UPSTREAM_REPO) $(GH_PUBLISH_BRANCH)
 	git checkout $(GH_SOURCE_BRANCH)