First 3 steps in to clearing your rifle (at least in Appleseed):
1) Mag out
2) Bolt back
3) Safety on
Why this order?
1) Removes the ammunition feeding device. If you were to pull the bolt back first without removing the ammo, you might inadvertently chamber a new round. From the anecdotal evidence I've read, a lot of (particularly new) shooters rack the bolt to clear out a round from the chamber, but sometimes they don't lock the bolt back or it drops forward accidentally. Then they forget that there was still a mag in but assume it was unloaded. Huge chance for a negligent discharge in that situation.
2) Extracts any remaining round in the firearm. As long as the magazine is out and you see the last round come out, you can be reasonably certain that the firearm is unloaded.
3) Sometimes you can't put the safety on. Like stated, usually the hammer has to be cocked before you can apply the safety. If you don't have a last round bolt hold open and you dry fired the last shot, or if you had a failure to fire you'd need to rack the bolt first. But before that you'd want to clear your ammunition feeding device.
That's why Appleseed teaches it in that order. To be absolutely certain you're clear you'd also want to inspect the chamber visually, with your finger, and insert a chamber flag. The chamber flag is probably good enough.
Then as long as you follow the other safety rules you should be set. Always keep the muzzle in a safe direction, keep your finger off the trigger until ready to fire, etc.
