Make cp -r equivalent to cp -R. Add a new cp option --copy-contents

Make cp -r equivalent to cp -R.  Add a new cp option --copy-contents
for people who want to emulate the traditional (and rarely desirable)
cp -r behavior.

(cp invocation): Document this.
Fix some related minor bugs: --no-dereference is no longer
equivalent to -d, and --archive (-a) can override the other
symlink options.  Warn that cp -R is not portable on symbolic
links unless you also specify -P.