update library files

Changes to be committed:

	modified:   includes/base.lib
	modified:   includes/git.lib
	modified:   includes/software.lib
edit variables

	add USER_NAME input
	change LIBS_DIR to LIB_DIR
	move UPSTREAM_PROJECT variable from setup.sh so it can be included in init.sh

Changes to be committed:

	modified:   config.sh
directory structure

	edit run instructions
	in process of getting project built with files in the right place and with the right permissions

Changes to be committed:

	modified:   init.sh
	modified:   setup.sh