Gemara

(Rav Yehudah): If one finds Chametz in his house on Yom Tov, he covers it with a Kli.

Beitzah 35b (Mishnah): One may lower Peros into the house through a skylight on Yom Tov, but not on Shabbos. One may cover Peros with Kelim to save them from a drip, and similarly barrels of wine or oil, and one may put a Kli under a drip on Shabbos.

36a (Ula): One may cover even bricks.

Question: The Mishnah permits only Peros!

Answer: Since the Reisha discusses lowering Peros, the Seifa discusses covering Peros.

(R. Yitzchak): One may cover only Peros Re'uyim (one may benefit from them today);

This is like R.Yitzchak taught elsewhere, that one may move a Kli only for the sake of Heter (something that one may move on Shabbos).

Shabbos 154b (Rav Huna): If an animal was carrying glass Kelim [that are Muktzeh, e.g. for bloodletting], he puts pillows and blankets underneath before untying the ropes to make the sacks fall.

Question: He is Mevatel Kli me'Heichano (makes a Kli forbidden to move)!

Answer: He discusses small loads.

Rishonim

Rif (Shabbos 66b): If an animal was carrying Muktzeh glass Kelim, one may put pillows underneath and the Kelim fall on them. This is only for a small load. One can remove the pillows [and the Kelim will not break], so he is not Mevatel Kli me'Heichano. This shows that the Halachah does not follow R. Yitzchak, who permits moving a Kli only for the sake of Heter. One may move pillows for the sake of bloodletting Kelim!

Rambam (Hilchos Shabbos 25:24): One may put a Kli under a drip [on Shabbos]. If the Kli became full, he may spill it out and return it. He need not refrain. The water must be proper for bathing. If not, one may not put a Kli. If he did, he may move it with the filthy water inside. L'Chatchilah one may not make Geraf Shel Re'i (something that repulses a person).

Rebuttal (Ra'avad): The only Heter is for proper water, if someone lives in the house, or there is concern for damage to the house. He puts his bed there so the dirt will be Geraf Shel Re'i and he may spill it.

Rosh (Beitzah 5:1): Rashi connotes that one may cover Peros on Yom Tov. I hold like the Ri, who explains that the Seifa discusses Shabbos also regarding covering Peros. Since the Reisha says "on Yom Tov, but not on Shabbos", and the Seifa says "on Shabbos", this connotes that it refers to both clauses [before it]. The Halachah does not follow R. Yitzchak.

Tosfos (6a DH Kofeh): Even though one opinion permits moving a Kli only for the sake of Heter, we can say that he needed the place of Kli. Once he was allowed to take it, he may cover the Chametz with it. Alternatively, we permit lest he come to eat it.

Question: If rain came and it will ruin merchandise, may one move it or tell a Nochri to move it? Sefer ha'Terumah permits to hide coins due to the authorities.

Answer (Rashba 1:784): Sefer ha'Terumos is wrong. Only regarding a fire, Chachamim permitted to tell a Nochri 'whoever extinguishes will not lose.' The Gemara says 'for a fire they permitted.' This excludes other Isurim of Shabbos. We learn also from Beitzah 36b. A drip was ruining Abaye's mill. Rabah told him to move his bed there, to make it [like] Geraf Shel Re'i (a Kli for excrement. One may move it if it bothers him. One may not move a mill just to avoid a loss.) If one was on the road when Shabbos came, he may give his wallet to a Nochri (153a). There Chachamim permitted, for if we do not permit, he may come to do a Torah Melachah. Here, why should we permit moving? Even telling a Nochri is permitted only to evade an Isur Torah. Normally, whatever one may not do, he may not tell a Nochri to do it.

Rashba (Avodas ha'Kodesh Beis Mo'ed 3:8:54): One may cover Peros to protect them from rain coming. The same applies to barrels of wine or oil. One may even cover bricks, lest the rain ruin them. Chachamim were concerned for monetary loss on Shabbos, and all the more so on Yom Tov!

Poskim

Shulchan Aruch (OC 338:7): If one has Peros on his roof and he sees rain coming, he may not lower them into the house through a skylight.

Magen Avraham (10): This is because it is exertion not needed for today.

Gra (DH Derech): The Shulchan Aruch teaches that it is forbidden even in a case that is permitted on Yom Tov.

Mishnah Berurah (25): We permit Peros needed for the day, even if they would not get dirty in the rain.

Shulchan Aruch (ibid.): However, he may cover them.

Beis Yosef (DH Mi): The Rif and Rosh rule unlike R. Yitzchak. The Tur did not specify. He connotes that the Ri and Rashi argue only about bricks, which are Muktzeh, but all permit covering Peros or similar things. This is wrong. Rashi forbids even Peros Re'uyim. He explains that one may cover Peros, and we do not say that he toils not for a need of Yom Tov. Chachamim permitted to avoid a loss. Rashi mentioned Yom Tov, but on Shabbos one may not cover bricks or Peros. The Ri permits covering on Shabbos bricks and Peros. The Tur says so in Siman 521 regarding Yom Tov.

Beis Yosef (DH u'Mah): I do not know why the Tur did not mention that the Rosh rules like the Ri.

Magen Avraham (11): The Yam Shel Shlomo (Beitzah 5:1) rules like Rashi, who forbids covering [even Peros. He holds that the Mishnah permits only on Yom Tov.]

Eliyahu Rabah (8): Nachalas Tzvi is lenient to avoid a loss. This is primary. Avodas ha'Kodesh is lenient. Also, the Maharshal says that the Ran forbids. I.e. in Beitzah 20a (DH Ela) he writes "we learn that even though one may not move it on Shabbos, one may move a Kli to cover it." This connotes that one may cover on Shabbos. In the Mishnah, he wrote (19b DH u'Mechasin) "we do not say that he toils not for a need of Yom Tov. Chachamim permitted to avoid a loss." This is not only for Yom Tov. Also, he discussed Yom Tov for an inference. Even on Yom Tov it is permitted only to avoid a loss. We can explain Rashi similarly. See Siman 321.

Nesiv Chayim (brought in Otzar Meforshim in Shulchan Aruch ha'Shalem): One may cover Peros and barrels of wine even on Shabbos, to avoid a loss. R. Yitzchak establishes the Mishnah to discuss Peros proper to eat. Also Ula does, for he says even bricks. Even though we establish this to refer to bricks left over from building, and they are proper to lie on them, they are no better than proper Peros and flasks of wine. A Beraisa (3b) permits covering an egg laid on Shabbos Tov to avoid a loss! The same applies to Tevel Peros. Even though R. Yitzchak establishes this to be when one needs the place of the cover, Ula does not. One should not deviate from the Shulchan Aruch's ruling.

Mishnah Berurah (26): Eliyahu Rabah and the other Acharonim prove from the Gemara that it is permitted.

Kaf ha'Chayim (55): One may cover only with Kelim that one may move. See the Magen Avraham 334:3 (brought below).

Shulchan Aruch (ibid.): One may cover even bricks to save them from a drip, even though they are Muktzeh.

Beis Yosef (DH v'Chasvu): The Rif (Shabbos 66b) and Rosh (3:18) rule unlike R. Yitzchak.

Mishnah Berurah (28): One may not move them, even if he has nothing to cover them.

Shulchan Aruch (8): One may put a Kli under a drip on Shabbos. If it became full, he may spill it out and return it. This is if the water is proper for bathing. If not, one may not, for l'Chatchilah one may not make Geraf Shel Re'i. If one did so, he may move it with the filthy water inside.

Magen Avraham (334:3): If rain fell on Muktzeh merchandise, all forbid to move it through a Yisrael. In 338:7, some forbid covering even Peros Re'uyim, and all the more so Muktzeh Peros!