Quoting Commentary for Song of Songs 7:9

Kadesh U’r’chatz: Atonement for the Garden of Eden There are good reasons for the customs of Israel which are based on the Torah. The things we do are surprising for those who lack knowledge and an understanding of what makes this night different from all other nights. Flour, wine, meat for the Passover offering and festive offering and apples and nuts for charoset are understood by the sages of truth to be a way of ridding Israel of Adam’s sin in the Garden of Eden. We seek to repair through that which we sinned.
There is a controversy about whether the fruit which our Adam ate was from the vine or wheat or fig tree or an etrog tree. Since we do not know with which one he sinned, we consume all of them as part of the seder. For those who say it was from the vine, we drink four cups of wine – through this mitzvah we repair the sin of the Garden of Eden, wine for vine. Since there is a question if it was wheat that they ate, we make matzah from fine flour. Since there is still a doubt, we make charoset from apples since the etrog is sometimes also referred to in Hebrew as a tapuach, an apple⁶See Song of Songs 7:9 “and the scent of your breath like apples” The Aramaic translation of the Bible understands the word apples to be an Etrog.. Some people add figs to the charoset for this reason as well, in order to remove the sin of the tree of knowledge. In Midrash Rabbah we learn that afterwards Adam and Eve ate all types animals; therefore we use the lamb for the Passover offering and a cow for the festive offering.

Its fruit before its leaves: Rabbenu Tam posed a difficulty, that behold we see that it grows like other trees! So he explained that tapuach (which is usually translated as apple) means citron (etrog). And (in the Targum,) we translate, "your breath is like tapuchim" (Song of Songs 7:8), as "like the fragrance of citrons". And the fruit of the citron is before its leaves, since it resides on the tree from one year to the next. And after a year, the leaves of the previous year fall and new leaves come. And that is [the meaning of] its fruit [come] before - those leaves. Yet it is a wonder that he brings the verse (Song of Songs 2:3), "As a tapuach among the trees of the wood." As Israel is not compared to a tapuach [here], but it is rather the Holy One, blessed be He; as it is written [earlier in the same verse], "so is my beloved among the youths." He should have preferably brought the verse of, "your breath is like tapuchim."

Similarly, tradition imparts that the following figure the glory of the shekhinah: “like the apple among the forest’s trees” [Cant. 2:3]; “your breath is like apples’ fragrance” [Cant. 7:9]; “refresh me with apples” [Cant. 2:5]; and “under the apple tree I aroused you” [Cant. 8:5]. This figure derives from the change of the apple’s cover from green to red to white, like the appearance of the rainbow within the cloud.²³ Ezek. 1:28. The apple also figures the two cherubim, as it states in the tractate Shabbat: “‘Like the scent of a field blessed by God’ [Gen. 27:27]. R. Yehudah states in the name of Rav: ‘Like the scent of a field of apple trees.’”²⁴ b. Ta ‘anit 29b.