All the cattle are in the kraal

if all the cattle are in kraal then none of them are out.

the pronoun reference replaces a noun, but you have to make sure there's no room for confusion.

in the first sentence "her" could be referring to shely or to the sister. the answer there is "shelly called her sister and told her about the new baby."

in the second sentence "it" could be referring to the roof or the floor. the answer there is "since the roof leaks on the family room floor, we need to repair the roof."

the rigid outer part of the earth, consisting of the crust and upper mantle is the lithosphere.     answer   crust and outer part of the mantle.