Learn Turkish: Zürafalar ağaç gibi uzun. - Giraffes are tall like trees.

Gibi is a postposition, which means it works like an English preposition but comes after the word it links to. So, instead of saying "like a tree", Turkish says "tree like" (ağaç gibi).

In English it says "like trees", so why is it singular ağaç instead of ağaçlar?

In Turkish, when you make a general comparison to a class or type of thing, you usually use the singular form. Ağaç gibi covers the general concept of "like a tree" or "like trees".

Where is the word for "are"? And shouldn't it be uzunlar since giraffes is plural?

In the present tense, the "to be" verb (am/is/are) is often just implied. You could say uzunlar, but because the subject Zürafalar already has the plural suffix -lar, you don't need to repeat it on the adjective. Uzun alone works perfectly.

Does the word gibi ever change to match vowel harmony?

No! Because gibi is a separate, standalone word and not a suffix, its spelling never changes to match the vowels of the noun before it. It will always be gibi.