文法について教えてください

A manifest is [an itemized list [of [[the goods] or [passengers] [a ship is carrying] ...]

"the goods or passengers a ship is carrying" is a Noun Phrase (NP)
This second "is" is internal to this phrase; it is at a lower level in the structure. It does not function as a top-level verb.


"A manifest is an itemized list of [NP]"

前のisが本動詞のisであり、後ろのisが関係代名詞の節中の動詞のisです。
後ろのisの前を見ると名詞が2つ並んでいて、これは関係代名詞が使われていることが多い形になります。