don't make gh-pages by default -- website should be updated only on new release

Conflicts:
	Makefile
refer to migrate() in upgrade instructions
refactor: extract function .is.dir
default.config and new.config

Conflicts:
	man/default.config.Rd
Merge branch 'master' into 85-filet
need to use new.config in tests
Merge pull request #114 from johnmyleswhite/85-filet

Extract various minor changes