Most of the document calls these things "atom", but the section actually defining them is "Package dependency specification" (9.2.1). Please stick to one term.
r159 replaces all atom with specification, since they're not atoms.
Remaining occurrences of "atom" replaced: https://gitweb.gentoo.org/proj/pms.git/commit/?id=3a880fe4c7769f081a6877644e916915aafe6b3a