doc/doxygen: properly clean files

doc/doxygen/Makefile.am

@@ -175,7 +175,7 @@ $(DOX_TAG): $(dox_inputs)
 dist_pdf_DATA = $(DOX_PDF)
 
 $(DOX_PDF): $(DOX_TAG) refman.tex
-	cp $(top_srcdir)/doc/doxygen/chapters/version.sty $(DOX_DIR)
+	cp $(top_srcdir)/doc/doxygen/chapters/version.sty $(DOX_LATEX_DIR)
 	cd $(DOX_LATEX_DIR); \
 	rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
 	sed -i -e 's/__env__/\\_Environment Variables!/' -e 's/\\-\\_\\-\\-\\_\\-env\\-\\_\\-\\-\\_\\-//' ExecutionConfigurationThroughEnvironmentVariables.tex ;\
@@ -195,7 +195,7 @@ $(DOX_PDF): $(DOX_TAG) refman.tex
 	done; \
 	mv refman.pdf ../$(DOX_PDF)
 
-MAINTAINERCLEANFILES = $(DOX_TAG) \
+CLEANFILES = $(DOX_TAG) \
     -r \
     $(DOX_HTML_DIR) \
     $(DOX_LATEX_DIR) \

doc/doxygen/refman.tex

@@ -12,7 +12,7 @@
 \usepackage{textcomp}
 \usepackage{alltt}
 \usepackage{ifpdf}
-\usepackage{../version}
+\usepackage{./version}
 \ifpdf
 \usepackage[pdftex,
             pagebackref=true,