Prefer encode-time to its alias

Prefer encode-time to its alias

* lisp/calendar/icalendar.el, lisp/calendar/timeclock.el:
* lisp/emacs-lisp/timer.el, lisp/gnus/gnus-delay.el:
* lisp/gnus/gnus-sum.el, lisp/gnus/nndiary.el:
* lisp/gnus/nnrss.el, lisp/net/newst-backend.el:
* lisp/net/rcirc.el, lisp/obsolete/xesam.el:
* lisp/org/org-agenda.el, lisp/org/org-clock.el:
* lisp/org/org-element.el, lisp/org/org-timer.el:
* lisp/org/org.el, lisp/progmodes/flymake.el:
* lisp/url/url-cache.el, lisp/url/url-cookie.el:
Use encode-time instead of its alias seconds-to-time.