diff --git a/doc/Makefile b/doc/Makefile
index 467da6844..b11e93d55 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -1,118 +1,126 @@
 # Makefile for LAMMPS documentation
 
 SHELL 	      = /bin/bash
 SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
 BUILDDIR      = /tmp/lammps-docs-$(SHA1)
 RSTDIR        = $(BUILDDIR)/rst
 VENV          = $(BUILDDIR)/docenv
 TXT2RST       = $(VENV)/bin/txt2rst
 
 PYTHON        = $(shell which python3)
 
 ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 1)
 $(error Python3 was not found! Please check README.md for further instructions)
 endif
 
 ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 1)
 $(error virtualenv was not found! Please check README.md for further instructions)
 endif
 
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
 .PHONY: help clean-all clean html pdf old venv
 
 # ------------------------------------------
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       create HTML doc pages in html dir"
 	@echo "  pdf        create Manual.pdf and Developer.pdf in this dir"
 	@echo "  old        create old-style HTML doc pages in old dir"
 	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
 
 # ------------------------------------------
 
 clean-all:
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
 
 clean:
 	rm -rf $(RSTDIR)
 
 html: $(OBJECTS)
 	@(\
 		. $(VENV)/bin/activate ;\
 		cp -r src/* $(RSTDIR)/ ;\
 		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		deactivate ;\
 	)
 	-rm html/searchindex.js
-	-rm -rf html/_sources
+	@rm -rf html/_sources
+	@rm -rf html/PDF
+	@rm -rf html/USER
+	@cp -r src/PDF html/PDF
+	@cp -r src/USER html/USER
+	@rm -rf html/PDF/.[sg]*
+	@rm -rf html/USER/.[sg]*
+	@rm -rf html/USER/*/.[sg]*
+	@rm -rf html/USER/*/*.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
 pdf: utils/txt2html/txt2html.exe
 	@(\
 		cd src; \
 		../utils/txt2html/txt2html.exe -b *.txt; \
 		htmldoc --batch lammps.book;          \
 		for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
 			do grep -q $$s lammps.book || \
 			echo doc file $$s missing in src/lammps.book; done; \
 		rm *.html; \
 		cd Developer; \
 		pdflatex developer; \
 		pdflatex developer; \
 		mv developer.pdf ../../Developer.pdf; \
 	)
 
 old: utils/txt2html/txt2html.exe
 	@rm -rf old
 	@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
 	@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
 	  mv *.html ../old; \
 	  cp Eqs/*.jpg ../old/Eqs; \
 	  cp JPG/* ../old/JPG; \
 	  cp PDF/* ../old/PDF;
 
 fetch:
 	@rm -rf html_www Manual_www.pdf Developer_www.pdf
 	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
 	@curl -s -o Developer_www.pdf http://lammps.sandia.gov/doc/Developer.pdf
 #	@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
 #	@tar xzf lammps-doc.tar.gz
 #	@rm -f lammps-doc.tar.gz
 
 txt2html: utils/txt2html/txt2html.exe
 
 # ------------------------------------------
 
 utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
 	g++ -O -Wall -o $@ $<
 
 $(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
 	@(\
 		mkdir -p $(RSTDIR) ; \
 		. $(VENV)/bin/activate ;\
 		txt2rst $< > $@ ;\
 		deactivate ;\
 	)
 
 $(VENV):
 	@( \
 		virtualenv -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip install Sphinx; \
 		pip install sphinxcontrib-images; \
 		deactivate;\
 	)
 
 $(TXT2RST): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \
 		(cd utils/converters;\
 		python setup.py develop);\
 		deactivate;\
 	)