Change of update procedure and location of plantuml jar file

Mege dev and update documen tation

Merge branch 'dev' into master

# Conflicts:
#	DESCRIPTION
#	NAMESPACE
#	NEWS.md
#	R/plot.plantuml.R
#	codemeta.json
#	vignettes/.gitignore
#	vignettes/graphs/diagram_png.png
#	vignettes/graphs/diagram_png_code.png
#	vignettes/graphs/diagram_svg.svg