They shall make an ark.
Maimonides in Hilchos Beis Habechira (1:6) states “vessels must be made for the Temple.” Maimonides includes within the mitzvos of building the Temple the fashioning of the various Temple vessels, the reason being that he maintains that both the building of the Temple and housing its vessels constitute one fulfillment, one kiyum. However, Maimonides anomalously omits the Ark from his list of Temple vessels to be contained there. Furthermore, in later chapters Maimonides details the manufacture and the form of these vessels and again omits the Ark. He later writes (4:1), there was a stone in the western part of the Holy of Holies upon which the Ark was placed and makes no further mention of the Ark, despite the fact that the Torah describes its manufacture and its dimensions in detail. Why did Maimonides make this omission?
There is another question that must be addressed. The Gemara in Yoma 52a, reflected in Hilchos Beis Habechira (4:1), informs us that there was no Ark in the Second Temple, for King Josiah had hidden it during the period of the First Temple out of concern that the the Ark would be captured during Israel’s coming exile. Why, during the construction of the Second Temple, was the Ark not rebuilt along with the other Temple vessels which were reconstructed? In fact, Nachmanides, in his Sefer Hamitzvos (mitzvas aseh 33) explicitly states that if the Ark were to break, a new Ark should be constructed.
The answer is that the status of the Ark is dependent on the Tablets that they house, which is why the Torah uses the terms “the Ark of Testimony” and “the Ark of the Covenant.” In the Second Temple, in which there were no Tablets, there was no Ark either. The placement of the Ark in the Holy of Holies was not a requirement for the Temple per se, unlike the other vessels, whose absence from any of their prescribed locations would invalidate the Temple itself. Additionally, even though Moses was commanded regarding the Ark, it appears that this command was limited to Moses alone since no other Ark would again be built. (Iggeros Hagrid, pp. 181-2)
Recognizing that the Temple he had built would ultimately be destroyed, King Solomon prepared a hiding place for the Ark, where King Josiah actually hid the Ark. While the presence of the Ark in the Holy of Holies was not a sine qua non for the Second Temple to be built, its continued presence on the Temple Mount was indeed necessary. The present holiness of the Temple Mount derives from the holiness of the ark, which still exists somewhere underneath. For this reason, the syntax of the phrase וְעָשׂ֥וּ אֲר֖וֹן is identical to the earlier phrase וְעָ֥שׂוּ לִ֖י מִקְדָּ֑שׁ, demonstrating that the sanctity of the Temple requires the presence of the Ark near the Temple, though not necessarily in the Holy of Holies. The holiness of the contemporary synagogue, called “a miniature Temple” (Ez. 11:15), similarly derives from the holiness of the Ark hidden somewhere beneath the Temple Mount. (Al Hatefilah, pp. 141-144; Shiurim Lezecher Abba Mari, pp. 172-173; Birkas Yitzchak, p. 118)